本文中所提供之抗體及抗原結合片段能夠與嚴重急性呼吸道症候群β型冠狀病毒(例如SARS-CoV-2)結合。在一些具體實施例中,抗體或抗原結合片段能夠與多種嚴重急性呼吸道症候群β型冠狀病毒(例如與如本文中所述之一或多種(例如一種、二種、三種、四種、五種、六種、或更多種)不同的嚴重急性呼吸道症候群β型冠狀病毒、視需要地包含在病毒粒子上及/或在受二或更多種嚴重急性呼吸道症候群β型冠狀病毒感染之細胞之表面上表現之表面醣蛋白)結合。在某些實施例中,多種嚴重急性呼吸道症候群β型冠狀病毒包含一或多種演化支1b嚴重急性呼吸道症候群β型冠狀病毒。在某些實施例中,目前所揭示之抗體及抗原結合片段可在感染之體外模式中及/或在動物模式中及/或人類個體中中和由一或多種嚴重急性呼吸道症候群β型冠狀病毒(例如一種、二種、三種、四種、或更多種嚴重急性呼吸道症候群β型冠狀病毒)所致之感染。亦提供編碼抗體及抗原結合片段之多核苷酸、載體、宿主細胞、及相關組成物,以及使用抗體、抗原結合片段、多核苷酸、載體、宿主細胞、及相關組成物來治療(例如減少、延遲、消除、或預防)個體之由二或更多種嚴重急性呼吸道症候群β型冠狀病毒所致之感染之方法及/或用於製造用於治療個體中由二或更多種嚴重急性呼吸道症候群β型冠狀病(例如一種、二種、三種、四種、或更多種)嚴重急性呼吸道症候群β型冠狀病所致之感染之藥物。亦提供二或更多種抗體或抗原結合片段之組合,例如用於療法及/或預防。
在更詳細闡述本揭露前,先提供本文中所使用之某些術語之定義可能有助於其理解。額外的定義闡述於整個本揭露中。
如本文中所使用,「抗嚴重急性呼吸道症候群β型冠狀病毒抗體或抗原結合片段(anti-sarbecovirus antibody or antigen-binding fragment)」特異性地結合至少一種嚴重急性呼吸道症候群β型冠狀病毒且在一些具體實施例中,可結合二或更多種、三或更多種、四或更多種、或五或更多種的嚴重急性呼吸道症候群β型冠狀病毒。
如本文中所使用,「嚴重急性呼吸道症候群β型冠狀病毒(sarbecovirus)」係指在譜系B內之任何β冠狀病毒(betacoronavirus),且包括在演化支1a、演化支1b、演化支2、及演化支3中之譜系B病毒。演化支1a嚴重急性呼吸道症候群β型冠狀病毒之實施例係SARS-CoV及蝙蝠SARS樣冠狀病毒(Bat SARS-like coronavirus)WIV1(WIV1)。演化支1b嚴重急性呼吸道症候群β型冠狀病毒之實施例係SARS-CoV-2、RatG13、穿山甲-Guanxi-2017(PANG/GX)及穿山甲-Guangdon-2019(PANG/GD)。演化支1b之實施例亦包括SARS-CoV-2變體,例如具有以下任何突變之變體:A67V、Δ69-70、T95I、G142D、137-145de、143-145de、Y145H、N211I、Δ212、V213G、ins214TDR、ins215EPE、A222V、G339D、R346K、R346S、V367F、S371L、S373P、S375F、T376A、P384L、N394S、D405N、R408S、Q414K、K417N、K417V、K417T、N439K、N440K、G446S、Y449H、Y449N、L452R、L452Q、L452X(其中X係任何胺基酸)、Y453F、S477N、T478K、V483A、E484A、E484Q、E484K、E484X(其中X係任何胺基酸)、F490R、F486V、F490S、R493Q、Q493R、S494P、G496S、Q498R、N501Y、N501T、Y505H、E516Q、T547K、Q613H、D614G、A653V、H655Y、G669S、Q677H、N679K、ins679GIAL、P681H、P681R、A701V、N764K、D796Y、N856K、Q954H、N969K、L981F、或於以下譜系中之變體:B.1.1.7及Q譜系及後代譜系(Alpha);B.1.351及後代譜系(Beta);B.1.429及B.1.427及後代譜系(Epsilon);P.1及後代譜系(Gamma);B.1.1.222;C.37;B.1.617.2;AY.1、AY.2、其他AY譜系及後代譜系(Delta);B.1.525及後代譜系(Eta);B.1.526及後代譜系(Iota);B.1.617.1及後代譜系(Kappa);1.617.3;B.1.621、及B.1.621.1及後代譜系(Mu);P.2(Zeta);及B.1.1.529.1、BA.1、BA.2、BA.2.12、BA.3、BA.4、BA.5及後代譜系(Omicron)。演化支2嚴重急性呼吸道症候群β型冠狀病毒之實施例係蝙蝠ZC45(ZC45)、蝙蝠ZXC21(ZXC21)、YN2013、RmYN02、Anlong112、SC2018、SX2011。演化支3嚴重急性呼吸道症候群β型冠狀病毒之實施例係BtkY72、及BGR2008。
圖 1中亦說明嚴重急性呼吸道症候群β型冠狀病毒演化支且
圖 2中說明嚴重急性呼吸道症候群β型冠狀病毒之間RBD之差異。
在一些具體實施例中,抗體或其抗原結合片段能夠與演化支1b之嚴重急性呼吸道症候群β型冠狀病毒結合,諸如SARS-CoV-2(包括本文中所述之所有變體)、RatG13、穿山甲-Guanxi-2017(PANG/GX)、穿山甲-Guangdon-209、或其任何組合。
在某些進一步具體實施例中,抗體或其抗原結合片段能夠與SARS-CoV-2變體結合;例如亦包括SARS-CoV-2變體之演化支1b之實施例,例如具有以下突變中任一者或多者的變體:A67V、Δ69-70、T95I、G142D、137-145de、143-145de、Y145H、N211I、Δ212、V213G、ins214TDR、ins215EPE、A222V、G339D、R346K、R346S、V367F、S371L、S373P、S375F、T376A、P384L、N394S、D405N、R408S、Q414K、K417N、K417V、K417T、N439K、N440K、G446S、Y449H、Y449N、L452R、L452Q、L452X(其中X係除L以外之任何胺基酸)、Y453F、S477N、T478K、V483A、E484A、E484Q、E484K、E484X(其中X係除E以外之任何胺基酸)、F490R、F486V、F490S、R493Q、Q493R、S494P、G496S、Q498R、N501Y、N501T、Y505H、E516Q、T547K、Q613H、D614G、A653V、H655Y、G669S、Q677H、N679K、ins679GIAL、P681H、P681R、A701V、N764K、D796Y、N856K、Q954H、N969K、L981F、或於以下譜系中之變體:B.1.1.7及Q譜系及後代譜系(Alpha);B.1.351及後代譜系(Beta);B.1.429及B.1.427及後代譜系(Epsilon);P.1及後代譜系(Gamma);B.1.1.222;C.37;B.1.617.2;AY.1、AY.2、其他AY譜系、及後代譜系(Delta);B.1.525及後代譜系(Eta);B.1.526及後代譜系(Iota);B.1.617.1及後代譜系(Kappa);1.617.3;B.1.621、及B.1.621.1及後代譜系(Mu);P.2(Zeta);及B.1.1.529.1、BA.1、BA.2、BA.2.12、BA.3、BA.4、BA.5及後代譜系(Omicron)、或其任何組合。在一些具體實施例中,SARS-Cov-2變體係Omicron變體,諸如BA.1、BA.2、BA.2.12、BA.3、BA.4、或BA.5。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3A3、或抗體或抗原結合片段包含本文中所揭示之S3A3或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3A3或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以以下之IC50抑制在人類ACE2與嚴重急性呼吸道症候群β型冠狀病毒(例如SARS-CoV-2)受體結合結構域(RBD)之間的結合交互作用:在約0.5 ng/mL至約100 ng/mL、約1 ng/mL至約100 ng/mL、約2.0 ng/mL至約100 ng/mL、約2.5 ng/mL至約100 ng/mL、約5.0 ng/mL至約100 ng/mL、約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約1 ng/mL至約50 ng/mL、約2.0 ng/mL至約50 ng/mL、約2.5 ng/mL至約50 ng/mL、約5.0 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或至少約30 ng/mL至約50 ng/mL、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3A19、或抗體或抗原結合片段包含本文中所揭示之S3A19或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3A19或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以以下之IC50抑制在人類ACE2與嚴重急性呼吸道症候群β型冠狀病毒(例如SARS-CoV-2)受體結合結構域(RBD)之間的結合交互作用:在約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或約至少約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3I2、或抗體或抗原結合片段包含本文中所揭示之S3I2或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3I2或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以以下之IC50抑制在人類ACE2與嚴重急性呼吸道症候群β型冠狀病毒(例如SARS-CoV-2)受體結合結構域(RBD)之間的結合交互作用:在約0.5 ng/mL至約100 ng/mL、約1 ng/mL至約100 ng/mL、約2.0 ng/mL至約100 ng/mL、約2.5 ng/mL至約100 ng/mL、約5.0 ng/mL至約100 ng/mL、約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約1 ng/mL至約50 ng/mL、約2.0 ng/mL至約50 ng/mL、約2.5 ng/mL至約50 ng/mL、約5.0 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或至少約30 ng/mL至約50 ng/mL、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3O13、或抗體或抗原結合片段包含本文中所揭示之S3O13或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3O13或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以以下之IC50抑制在人類ACE2與嚴重急性呼吸道症候群β型冠狀病毒(例如SARS-CoV-2)受體結合結構域(RBD)之間的結合交互作用:在約0.5 ng/mL至約100 ng/mL、約1 ng/mL至約100 ng/mL、約2.0 ng/mL至約100 ng/mL、約2.5 ng/mL至約100 ng/mL、約5.0 ng/mL至約100 ng/mL、約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約1 ng/mL至約50 ng/mL、約2.0 ng/mL至約50 ng/mL、約2.5 ng/mL至約50 ng/mL、約5.0 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或至少約30 ng/mL至約50 ng/mL、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3L17、或抗體或抗原結合片段包含本文中所揭示之S3L17或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3L17或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以以下之IC50抑制在人類ACE2與嚴重急性呼吸道症候群β型冠狀病毒(例如SARS-CoV-2)受體結合結構域(RBD)之間的結合交互作用:在約0.5 ng/mL至約100 ng/mL、約1 ng/mL至約100 ng/mL、約2.0 ng/mL至約100 ng/mL、約2.5 ng/mL至約100 ng/mL、約5.0 ng/mL至約100 ng/mL、約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約1 ng/mL至約50 ng/mL、約2.0 ng/mL至約50 ng/mL、約2.5 ng/mL至約50 ng/mL、約5.0 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或至少約30 ng/mL至約50 ng/mL、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
如本文中所使用之「S2V29」包括本文中所揭示任何VH及VL變體。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S2V29、或抗體或抗原結合片段包含本文中所揭示之S2V29或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S2V29或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以以下之IC50抑制在人類ACE2與嚴重急性呼吸道症候群β型冠狀病毒(例如SARS-CoV-2)受體結合結構域(RBD)之間的結合交互作用:在約0.5 ng/mL至約100 ng/mL、約1 ng/mL至約100 ng/mL、約2.0 ng/mL至約100 ng/mL、約2.5 ng/mL至約100 ng/mL、約5.0 ng/mL至約100 ng/mL、約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約1 ng/mL至約50 ng/mL、約2.0 ng/mL至約50 ng/mL、約2.5 ng/mL至約50 ng/mL、約5.0 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或至少約30 ng/mL至約50 ng/mL、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
如本文中所使用,「SARS-CoV-2」原本亦稱為「武漢冠狀病毒(Wuhan coronavirus)」、「武漢海產食品市場肺炎病毒(Wuhan seafood market pneumonia virus)」、或「武漢CoV(Wuhan CoV)」、「新型CoV(novel CoV)」、或「nCoV」、或「2019 nCoV」、或「武漢nCoV(Wuhan nCoV)」、或其變體,係一種譜系B之β冠狀病毒(嚴重急性呼吸道症候群β型冠狀病毒)。在2019年末,於中國湖北省武漢市首次鑑別出SARS-CoV-2,並至2020年初,在中國境內及世界之其他地區傳播。SARS CoV-2感染可導致稱為COVID-19之疾病;COVID-19之症狀包括發燒或發冷、乾咳、呼吸困難、疲勞、身體疼痛、頭痛、新出現的味覺或嗅覺喪失、喉嚨痛、鼻塞或流鼻涕、噁心或嘔吐、腹瀉、胸部持續感到受壓或疼痛、新出現的混淆誤認、不能醒來或保持清醒、及嘴唇或臉部發青。
SARS-CoV-2分離株Wuhan-Hu-1之基因組序列提供於GenBank MN908947.3(2020年1月23日),且基因組之胺基酸轉譯提供於GenBank QHD43416.1(2020年1月23日)。此等GenBank序列及所有SARS-CoV-2變體之GenBank序列係以引用方式併入本文中,作為描述根據本揭露之抗體或其抗原結合片段特異性結合的嚴重急性呼吸道症候群β型冠狀病毒或SARS-CoV-2。如同其他冠狀病毒(例如SARS-CoV),SARS-CoV-2包含含有受體結合結構域(receptor binding domain, RBD)之「棘突」或表面(「S」)I型跨膜醣蛋白。咸信RBD藉由與細胞表面受體血管收縮素轉化酶2(angiotensin-converting enzyme 2, ACE2)結合來介導譜系B SARS冠狀病毒進入呼吸上皮細胞。特定而言,咸信病毒RBD中之受體結合模體(receptor binding motif, RBM)與ACE2交互作用。
Wuhan-Hu-1表面醣蛋白之胺基酸序列提供於SEQ ID NO: 1中。Wuhan-Hu-1 RBD之胺基酸序列提供於SEQ ID NO: 2中。Wuhan-Hu-1 S蛋白質與SARS-CoV具有大約73%胺基酸序列同一性。Wuhan-Hu-1 RBM之胺基酸序列提供於SEQ ID NO: 3中。
已出現許多SARS-CoV-2變體,該等變體在基因組及胺基酸序列方面,特別是表面醣蛋白或RBD方面可有所不同。一些SARS-CoV-2變體突變增加對ACE受體之親和力及/或病毒之感染性。SARS-CoV-2之重要變體包括亦包括SARS-CoV-2變體之演化支1b之實施例,例如具有以下任何突變之變體:A67V、Δ69-70、T95I、G142D、137-145de、143-145de、Y145H、N211I、Δ212、V213G、ins214TDR、ins215EPE、A222V、G339D、R346K、R346S、V367F、S371L、S373P、S375F、T376A、P384L、N394S、D405N、R408S、Q414K、K417N、K417V、K417T、N439K、N440K、G446S、Y449H、Y449N、L452R、L452Q、L452X(其中X係除L以外之任何胺基酸)、Y453F、S477N、T478K、V483A、E484A、E484Q、E484K、E484X(其中X係除E以外之任何胺基酸)、F490R、F486V、F490S、R493Q、Q493R、S494P、G496S、Q498R、N501Y、N501T、Y505H、E516Q、T547K、Q613H、D614G、A653V、H655Y、G669S、Q677H、N679K、ins679GIAL、P681H、P681R、A701V、N764K、D796Y、N856K、Q954H、N969K、L981F、或於以下譜系中之變體:B.1.1.7及Q譜系及後代譜系(Alpha);B.1.351及後代譜系(Beta);B.1.429及B.1.427及後代譜系(Epsilon);P.1及後代譜系(Gamma);B.1.1.222;C.37;B.1.617.2;AY.1、AY.2、其他AY譜系、及後代譜系(Delta);B.1.525及後代譜系(Eta);B.1.526及後代譜系(Iota);B.1.617.1及後代譜系(Kappa);1.617.3;B.1.621及B.1.621.1及後代譜系(Mu);P.2(Zeta);及B.1.1.529.1、BA.1、BA.2、BA.2.12、BA.3、BA.4、BA.5及後代譜系(Omicron)、或其任何組合。在一些具體實施例中,SARS-Cov-2變體係Omicron變體,諸如BA.1、BA.2、BA.2.12、BA.3、BA.4、或BA.5。在美國傳播的SARS-CoV-2變體被分類為受美國疾病控制與預防中心關注之變體(參見https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html)。
在一些具體實施例中,提供用於治療嚴重急性呼吸道症候群β型冠狀病毒感染之抗體或抗原結合片段。在某些具體實施例中,嚴重急性呼吸道症候群β型冠狀病毒感染包含SARS-CoV-2感染。治療根據本揭露之SARS CoV-2感染包括治療由前述SARS-CoV-2病毒中任一者或多者所致之感染。在某些具體實施例中,治療SARS-CoV-2感染包含治療以下中任一者或多者:SARS CoV-2 Wuhan-Hu-1;亦包括SARS-CoV-2變體之演化支1b之實施例,例如具有以下任何突變之變體:A67V、Δ69-70、T95I、G142D、137-145de、143-145de、Y145H、N211I、Δ212、V213G、ins214TDR、ins215EPE、A222V、G339D、R346K、R346S、V367F、S371L、S373P、S375F、T376A、P384L、N394S、D405N、R408S、Q414K、K417N、K417V、K417T、N439K、N440K、G446S、Y449H、Y449N、L452R、L452Q、L452X(其中X係除L以外之任何胺基酸)、Y453F、S477N、T478K、V483A、E484A、E484Q、E484K、E484X(其中X係除E以外之任何胺基酸)、F490R、F486V、F490S、R493Q、Q493R、S494P、G496S、Q498R、N501Y、N501T、Y505H、E516Q、T547K、Q613H、D614G、A653V、H655Y、G669S、Q677H、N679K、ins679GIAL、P681H、P681R、A701V、N764K、D796Y、N856K、Q954H、N969K、L981F、D614、E340A、或於以下譜系中之變體:B.1.1.7及Q譜系及後代譜系(Alpha);B.1.351及後代譜系(Beta);B.1.429及B.1.427、及後代譜系(Epsilon);P.1及後代譜系(Gamma);B.1.1.222;C.37;B.1.617.2;AY.1、AY.2、其他AY譜系、及後代譜系(Delta);B.1.525及後代譜系(Eta);B.1.526及後代譜系(Iota);B.1.617.1及後代譜系(Kappa);1.617.3;B.1.621及B.1.621.1及後代譜系(Mu);P.2(Zeta);及B.1.1.529.1、BA.1、BA.2、BA.2.12、BA.3、BA.4、BA.5及後代譜系(Omicron)、BQ.1.1、XBB.1或其任何組合。在一些具體實施例中,SARS-CoV-2變體係Omicron變體,諸如BA.1、BA.2、BA.2.12、BA.3、BA.4、或BA.5。在一些具體實施例中,SARS-CoV-2變體係BQ.1.1。在一些具體實施例中,SARS-CoV-2係XBB.1。
在本說明書中,除非另有指示,否則任何濃度範圍、百分比範圍、比率範圍、或整數範圍均應理解為包括在所述範圍內之任何整數值、及(當適當時)其分數(諸如整數之十分之一及百分之一)。此外,除非另有指示,否則本文中所述之與任何物理特徵(諸如聚合物次單位、尺寸或厚度)相關之任何數值範圍應理解為包括所述範圍內之任何整數。如本文中所使用,除非另有指示,否則術語「約(about)」意指指定範圍、值或結構之±20%。應理解的是,如本文中所使用,術語「一(a/an)」係指所列舉組分中之「一或多者」。替代物(例如「或」)之使用應理解為意指替代物中之任一者、二者、或其任何組合。如本文中所使用,術語「包括(include)」、「具有(have)」、及「包含(comprise)」係同義地使用,該等術語及其變體意欲被解讀為非限制性。
術語「視需要的(optional)」或「視需要地(optionally)」意指隨後描述的要素、組分、事件、或狀況可能發生或可能不發生,且該說明書包括該要素、組分、事件、或狀況發生之情況及不發生之情況。
此外,衍生自本文中所述之結構或次單位之各種組合的個別構築體、或構築體之群組係由本申請案所揭示,其程度如同各構築體或構築體之群組個別地闡述一般。因此,特定結構或特定次單位之選擇係在本揭露之範疇內。
術語「基本上由…組成(consisting essentially of)」不等同於「包含(comprising)」,且係指申請專利範圍之指定材料或步驟,或實質上不影響所主張之標的物的基本特徵的材料或步驟。舉例而言,當結構域、區、模組、或蛋白質之胺基酸序列包括組合起來佔結構域、區、模組、或蛋白質之長度的最多20%(例如最多15%、10%、8%、6%、5%、4%、3%、2%或1%)且實質上不影響(亦即活性減少不超過50%,諸如不超過40%、30%、25%、20%、15%、10%、5%、或1%)一或多個結構域、一或多個區、一或多個模組、或一或多個蛋白質之活性(例如結合蛋白質之目標結合親和力)的延伸、刪除、突變、或其組合(例如在胺基或羧基末端處或在結構域之間的胺基酸)時,蛋白質結構域、區、或模組(例如結合結構域)或蛋白質「基本上由特定胺基酸序列組成」。
如本文中所使用,「胺基酸(amino acid)」係指天然存在的及合成的胺基酸,以及以類似於天然存在的胺基酸之方式起作用的胺基酸類似物及胺基酸擬似物。天然存在的胺基酸係由遺傳密碼子所編碼之胺基酸,以及之後經修飾之彼等胺基酸,例如羥基脯胺酸、γ-羧基麩胺酸、及O-磷酸絲胺酸。胺基酸類似物係指具有與天然存在的胺基酸相同的基本化學結構(亦即,與氫、羧基、胺基、及R基團結合的α-碳)的化合物,例如類絲胺酸、正白胺酸、甲硫胺酸亞碸、甲硫胺酸甲基鋶。此類類似物具有經修飾之R基團(例如正白胺酸)或經修飾之肽主鏈,但保有與天然存在的胺基酸相同的基本化學結構。胺基酸擬似物係指具有不同於一般胺基酸之化學結構的結構,但以類似於天然存在的胺基酸之方式起作用的化學化合物。
如本文中所使用,「突變」係指核酸分子或多肽分子之序列分別相較於參考或野生型核酸分子或多肽分子之變化。突變可導致若干不同類型的序列變化,包括一或多個核苷酸或胺基酸之取代、插入或刪除。
「保留取代」係指不會顯著影響或改變特定蛋白質之結合特性的胺基酸取代。通常而言,保留取代係其中將取代之胺基酸殘基置換為具有類似側鏈之胺基酸殘基。保留取代包括在以下群組中之一者中發現的取代:第1群組:丙胺酸(Ala或A)、甘胺酸(Gly或G)、絲胺酸(Ser或S)、蘇胺酸(Thr或T);第2群組:天冬胺酸(Asp或D)、麩胺酸(Glu或Z);第3群組:天冬醯胺(Asn或N)、麩醯胺(Gln或Q);第4群組:精胺酸(Arg或R)、離胺酸(Lys或K)、組胺酸(His或H);第5群組:異白胺酸(Ile或I)、白胺酸(Leu或L)、甲硫胺酸(Met或M)、纈胺酸(Val或V);及第6群組:苯丙胺酸(Phe或F)、酪胺酸(Tyr或Y)、色胺酸(Trp或W)。額外地或可替代地,胺基酸可藉由類似功能、化學結構、或組成(例如酸性、鹼性、脂族、芳族、或含硫)而分入保守取代群組。舉例而言,出於取代之目的,脂族群組可包括Gly、Ala、Val、Leu、及Ile。其他保留取代群組包括:含硫:Met及半胱胺酸(Cys或C);酸性:Asp、Glu、Asn、及Gln;小脂族、非極性或略微極性殘基:Ala、Ser、Thr、Pro、及Gly;極性、帶負電荷殘基及其醯胺:Asp、Asn、Glu、及Gln;極性、帶正電荷殘基:His、Arg、及Lys;大脂族、非極性殘基:Met、Leu、Ile、Val、及Cys;及大芳族殘基:Phe、Tyr、及Trp。額外資訊可見於Creighton(1984) Proteins, W.H.Freeman and Company。
如本文中所使用,「蛋白質」或「多肽」係指胺基酸殘基之聚合物。蛋白質適用於天然存在的胺基酸聚合物,以及適用於其中一或多個胺基酸殘基係對應天然存在的胺基酸之人工化學擬似物的胺基酸聚合物、及非天然存在的胺基酸聚合物。亦設想本揭露之蛋白質、肽、及多肽之變體。在某些具體實施例中,變體蛋白質、肽、及多肽包含下列者或由下列者組成:與如本文中所述之經定義之胺基酸序列或參考胺基酸序列至少70%、75%、80%、85%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或99.9%同一的胺基酸序列。
本揭露之任何多肽(例如VH、VL、Fab、Fd、抗體重鏈、抗體輕鏈)可由包含「訊息肽」(亦稱為前導序列、前導肽、或轉運肽)之多核苷酸序列所編碼。訊息肽將新合成之多肽靶向其在細胞內或外的適當位置。在定位或分泌完成期間或在定位或分泌完成之後,訊息肽可從多肽中整個移除或部分移除。具有(例如全長)訊息肽之多肽可被稱為「前蛋白質(pre-protein)」,而將其訊息肽移除-至少部分移除-之多肽可被稱為「成熟(mature)」蛋白質或多肽。在某些具體實施例中,抗體或抗原結合片段係成熟蛋白質或前蛋白質。
「核酸分子」或「多核苷酸」或「多核酸」係指包括共價連接核苷酸之聚合化合物,該等核苷酸可由天然次單位(例如嘌呤或嘧啶鹼基)或非天然次單元(例如啉環)構成。嘌呤鹼基包括腺嘌呤、鳥嘌呤、次黃嘌呤、及黃嘌呤,而嘧啶鹼基包括尿嘧啶、胸腺嘧啶、及胞嘧啶。核酸分子包括聚核糖核酸(RNA),其包括mRNA、微RNA、siRNA、病毒基因組RNA、及合成RNA;及聚去氧核糖核苷酸(DNA),其包括cDNA、基因組DNA、及合成DNA,其中之任一者可為單股或雙股。若為單股,則核酸分子可為編碼股或非編碼(反義)股。編碼胺基酸序列之核酸分子包括編碼相同胺基酸序列之所有核苷酸序列。核苷酸序列之一些型式亦可通過共轉錄或轉錄後機制移除一或多個內含子的程度來包括一或多個內含子。換言之,由於遺傳密碼之冗餘或簡併、或藉由剪接,不同核苷酸序列可編碼相同胺基酸序列。
亦設想本揭露之核酸分子之變體。變體核酸分子與如本文中所述之經定義之核酸分子或參考多核苷酸為至少70%、75%、80%、85%、90%、且較佳地95%、96%、97%、98%、99%、或99.9%同一,或在約65至68ºC下在0.015M氯化鈉、0.0015M檸檬酸鈉或在約42ºC下在0.015M氯化鈉、0.0015M檸檬酸鈉、及50%甲醯胺之嚴格雜交條件下與多核苷酸雜交。核酸分子變體保有編碼具有本文中所述之功能性,諸如結合目標分子之其結合結構域之能力。
「百分比序列同一性」係指藉由比較序列來判定二或更多個序列之間的關係。判定序列同一性之較佳方法經設計成在所比較之序列之間給出最佳匹配。舉例而言,出於最佳比較目的來比對序列(例如可將間隔引入第一及第二胺基酸或核酸序列中之一者或二者中以達最佳比對)。此外,出於比較目的,可忽略非同源序列。除非另有指示,否則本文中所提及之百分比序列同一性係根據參考序列之長度來計算。判定序列同一性及類似性之方法可見於公開可用的電腦程式中。可使用BLAST程式(例如BLAST 2.0、BLASTP、BLASTN、或BLASTX)進行序列比對及百分比同一性計算。用於BLAST程式中之數學演算法可見於Altschul
et al.,
Nucleic Acids Res.
25:3389-3402, 1997。在本揭露之上下文內,應理解,當將序列分析軟體用於分析時,分析結果係基於所提及之程式的「預設值」。「預設值」意指首次初始化時最初隨軟體加載之任何值或參數集。
其他實施例包括Clustal W, MAFFT、Clustal Omega、AlignMe、Praline、GAP、BESTFIT、Needle(EMBOSS)、Stretcher(EMBOSS)、GGEARCH2SEQ、Water(EMBOSS)、Matcher(EMBOSS)、LALIGN、及SSEARCH2SEQ。全局比對演算法(global alignment algorithm),諸如尼德曼(Needleman)及翁施(Wunsch)演算法可用於根據其整個長度比對二個序列,以使匹配數量最大化及間隔數量最小化。可使用預設值。
為了生成二個胺基酸序列之類似性評分,可使用對一些非相同之胺基酸(例如保留胺基酸取代、具有相似物理化學性質之胺基酸、及/或在異種同源物、同源物、或同種同源物中展現出頻繁取代之胺基酸)指派正分之評分矩陣。評分矩陣之非限制性實施例包括PAM30、PAM70、PAM250、BLOSUM45、BLOSUM50、BLOUM62、BLOSUM80、及BLOSUM90。
術語「單離(isolated)」意指將物質從其最初的環境(例如若其為天然存在的,則為天然環境)中移除。舉例而言,存在於活體動物中之天然存在的核酸或多肽不是經單離的,但從天然系統中之一些或所有共存材料中分離之相同核酸或多肽係經單離的。此種核酸可為載體之一部分及/或此種核酸或多肽可為組成物(例如細胞溶解物)之一部分,且仍為經單離的,在於此種載體或組成物不是該核酸或多肽之天然環境之一部分。
術語「基因(gene)」意指涉及產生多肽鏈之DNA或RNA鏈段;在某些上下文中,其包括在編碼區之前或之後的區域(例如5’非轉譯區(UTR)及3’UTR)以及在個別編碼鏈段(外顯子)之間的介入序列(內含子)。
「功能變體」係指結構上類似或結構實質上類似於本揭露之親本及參考化合物,但在組成方面略微不同(例如一個鹼基、原子或功能基團不同、經添加、或經移除),使得該多肽或編碼多肽能夠以至少50%效率、較佳地為該親本多肽之至少55%、60%、70%、75%、80%、85%、90%、95%、96%、97%、98%、99%、99.9%、或100%活性水平進行該親本多肽之至少一種功能。換言之,當相較於親本或參考多肽,功能變體在所選檢定(諸如用於測量結合親和力之檢定,例如測量締合(Ka)或解離(K
D)常數之Biacore®或四聚體染色)中展現出性能減少不超過50%時,本揭露之多肽或編碼多肽之該功能變體具有「類似結合」、「類似親和力」或「類似活性」。
如本文中所使用,「功能部分」或「功能片段」係指僅包含親本或參考化合物之結構域、部分或片段之多肽或多核苷酸,且該多肽或編碼多肽保有至少50%與親本或參考化合物之結構域、部分或片段相關的活性、較佳地至少該親本多肽之55%、60%、70%、75%、80%、85%、90%、95%、96%、97%、98%、99%、99.9%、或100%活性水平,或提供生物效益(例如效應子功能)。當相較於親本或參考多肽,該功能性部分或片段在所選檢定中展現出性能減少不超過50%(就親和力而論,如相較於親本或參考較佳地不超過20%或10%、或不超過對數差異)時,本揭露之多肽或編碼多肽之「功能部分」或「功能片段」具有「類似結合」或「類似活性」。
如本文中所使用,術語「經工程改造(engineered)」、「重組(recombinant)」、或「非天然(non-natural)」係指包括至少一個基因改變或已藉由引入外源性或異源性核酸分子來修飾之生物體、微生物、細胞、核酸分子、或載體,其中此類改變或修飾係由基因工程(亦即人為介入)來引入。基因改變包括例如引入編碼功能性RNA、蛋白質、融合蛋白質或酶之可表現的核酸分子的修飾,或其他核酸分子的添加、刪除、取代、或細胞之基因物質之其他功能性破壞。額外修飾包括例如非編碼調節區,其中該等修飾改變多核苷酸、基因、或操縱子之表現。
如本文中所使用,「異源性」或「非內源性」或「外源性」係指不是宿主細胞或個體原生之任何基因、蛋白質、化合物、核酸分子、或活性,或已被改變之宿主細胞或個體原生之任何基因、蛋白質、化合物、核酸分子、或活性。異源性、非內源性、或外源性包括已突變或以其他方式改變的基因、蛋白質、化合物、或核酸分子,使得結構、活性、或二者在原生與改變後之基因、蛋白質、化合物、或核酸分子之間係不同的。在某些具體實施例中,異源性、非內源性、或外源性基因、蛋白質、或核酸分子(例如受體、配體等)對宿主細胞或個體可能不為內源性,但編碼此類基因、蛋白質、或核酸分子之核酸可藉由接合、轉形、轉染、電穿孔等添加至宿主細胞中,其中該經添加之核酸分子可整合到宿主細胞基因組中或可作為染色體外基因物質(例如作為質體或其他自我複製載體)存在。術語「同源性(homologous」或「同源物(homolog)」係指在宿主細胞、物種、菌株找到或衍生自宿主細胞、物種、菌株之基因、蛋白質、化合物、核酸分子、或活性。舉例而言,異源性或外源性多核苷酸或編碼多肽之基因可與原生多核苷酸或基因同源,且編碼同源多肽或活性,但該多核苷酸或多肽可具有改變之結構、序列、表現水平、或其任何組合。非內源性多核苷酸或基因,以及編碼多肽或活性可來自相同物種、不同物種、或其組合。
在某些具體實施例中,若宿主細胞原生之核酸分子或其部分已被改變或突變,則該宿主細胞原生之核酸分子或其部分被視為與該宿主細胞異源,或若宿主細胞原生之核酸分子已被異源表現控制序列改變或已被與宿主細胞原生之核酸分子通常不相關的內源表現控制序列改變,則該宿主細胞原生之核酸分子被視為與該宿主細胞異源。此外,術語「異源性(heterologous)」可係指與宿主細胞不同、經改變、或不是內源之生物活性。如本文中所述,可將超過一個異源性核酸分子作為單獨核酸分子、作為複數個個別受控基因、作為多順反子核酸分子、作為編碼融合蛋白質之單一核酸分子、或其任何組合引入到宿主細胞中。
如本文中所使用,術語「內源性(endogenous)」或「原生(native)」係指正常存在於宿主細胞或個體中之多核苷酸、基因、蛋白質、化合物、分子、或活性。
如本文中所使用之術語「表現(expression)」係指基於核酸分子(諸如基因)之編碼序列產生多肽之過程。該等過程包括轉錄、轉錄後控制、轉錄後修飾、轉譯、轉譯後控制、轉譯後修飾、或其任何組合。表現之核酸分子一般可操作地連接至表現控制序列(例如啟動子)。
術語「可操作地連接(operably linked)」係指二個或更多個核酸分子締合在單一核酸片段上,使得一者之功能受另一者影響。舉例而言,當啟動子能夠影響編碼序列之表現時,該啟動子係與該編碼序列可操作地連接(亦即該編碼序列係在該啟動子之轉錄控制下)。「未連接(unlinked)」意指相關基因元件彼此不緊密締合,且一者之功能不影響另一者。
如本文中所述,可將超過一個異源性核酸分子作為單獨核酸分子、作為複數個個別受控基因、作為多順反子核酸分子、作為編碼蛋白質(例如抗體之重鏈)之單一核酸分子、或其任何組合引入到宿主細胞中。當將二或更多個異源性核酸分子引入到宿主細胞中時,應理解,可將二或更多個異源性核酸分子作為單一核酸分子(例如在單一載體上)在單獨載體上引入而整合至該宿主染色體中之單一位點或多個位點處、或其任何組合。所提及之異源性核酸分子或蛋白質活性之數目係指編碼核酸分子之數目或蛋白質活性之數目,而不是引入到宿主細胞中之單獨核酸分子之數目。
術語「構築體(construct)」係指含有重組核酸分子(或當上下文明確指示時,本揭露之融合蛋白)之任何多核苷酸。(多核苷酸)構築體可存在於載體中(例如細菌載體、病毒載體)或可整合到基因組中。「載體」是能夠運送另一個核酸分子的核酸分子。舉例而言,載體可為質體、黏質體、病毒、RNA載體或線性或環狀DNA或RNA分子,其可包括染色體、非染色體、半合成或合成核酸分子。本揭露之載體亦包括轉位子系統(例如Sleeping Beauty,參見例如
Geurts et al., Mol. Ther. 8:108, 2003: Mátés
et al., Nat. Genet.41:753, 2009)。例示性載體係能夠自主複製(附加型載體(episomal vector))、能夠將多核苷酸遞送至細胞基因組(例如病毒載體)或能夠表現其所連接之核酸分子(表現載體)者。
如本文中所使用,「表現載體」或「載體」係指含有核酸分子之DNA構築體,該核酸分子可操作地連接至能夠實現核酸分子在合適宿主中表現之合適控制序列。此類控制序列包括實現轉錄之啟動子、控制此種轉錄之視需要的操縱子序列、編碼合適mRNA核糖體結合位點之序列、及控制轉錄及轉譯終止之序列。載體可為質體、噬菌體顆粒、病毒、或僅潛在的基因組插入物。一旦轉形至合適宿主中,載體可獨立於宿主基因組複製並起作用,或可在一些情況下整合到基因組本身中或將載體中所含之多核苷酸遞送到不具有載體序列之基因組中。在本說明書中,「質體」、「表現質體」、「病毒」、及「載體」經常互換使用。
在將核酸分子插入到細胞之上下文中之術語「引入(introduced)」意指「轉染」、「轉形」、或「轉導」,並包括提及將核酸分子併入到真核細胞或原核細胞中,其中該核酸分子可併入到細胞之基因組(例如染色體、質體、色素體、或粒線體DNA)中、轉換成自主複製子、或瞬時表現(例如轉染之mRNA)。
在某些具體實施例中,本揭露之多核苷酸可以操作地連接至載體之某些元件。舉例而言,可將實現與其接合之編碼序列之表現及加工所需之多核苷酸序列可操作地連接。表現控制序列可包括適當的轉錄起始、終止、啟動子、及增強子序列;有效的RNA加工訊號,諸如剪接及多腺苷酸化訊號;穩定細胞質mRNA之序列;增強轉譯效率之序列(亦即Kozak共通序列);增強蛋白質穩定性之序列;及可能增強蛋白質分泌之序列。若表現控制序列與感興趣之基因鄰接且表現控制序列以反式或在一定距離下作用以控制感興趣之基因,則表現控制序列可為可操作地連接。
在某些具體實施例中,載體包含質體載體或病毒載體(例如慢病毒載體或γ-反轉錄病毒載體)。病毒載體包括反轉錄病毒;腺病毒;微小病毒(例如腺相關病毒);冠狀病毒;負股RNA病毒,諸如正黏液病毒(例如流感病毒)、棒狀病毒(例如狂犬病及水泡性口炎病毒)、副黏液病毒(例如麻疹及仙台(Sendai)病毒);正股RNA病毒,諸如微小RNA病毒及α病毒;及雙股DNA病毒,包括腺病毒、疱疹病毒(例如第1型及第2型單純疱疹病毒、埃-巴二氏病毒(Epstein-Barr virus)、細胞巨大病毒)、及痘病毒(例如牛痘、禽痘、及金絲雀痘)。其他病毒包括例如諾沃克病毒(Norwalk virus)、披衣病毒、黃病毒、里奧病毒(reovirus)、乳多泡病毒、嗜肝DNA病毒(hepadnavirus)及肝炎病毒。反轉錄病毒之實施例包括鳥類白血病性肉瘤、哺乳動物C型病毒、B型病毒、D型病毒、HTLV-BLV群、慢病毒、泡沫病毒(Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996)。
「反轉錄病毒」係具有RNA基因組之病毒,該RNA基因組係使用逆轉錄酶酵素逆轉錄成DNA,接著將該逆轉錄之DNA併入到宿主細胞基因組中。「γ反轉錄病毒(gammaretrovirus)」係指反轉錄病毒科家族中之一屬。γ反轉錄病毒之實施例包括小鼠幹細胞病毒、鼠類白血病病毒、貓白血病病毒、貓肉瘤病毒、及家禽網狀內皮症病毒。
「慢病毒載體」包括用於基因遞送之基於HIV之慢病毒載體,其可為整合型或未整合型,具有相對較大包裝能力,且可轉導一系列不同的細胞類型。慢病毒載體通常在三個(包裝、包膜及轉移)或更多個質體暫時轉染到生產細胞中後生成。如同HIV,慢病毒載體通過病毒表面醣蛋白與細胞表面上之受體的交互作用進入目標細胞中。在進入後,病毒RNA經歷逆轉錄,此係由病毒逆轉錄酶複合體所介導。逆轉錄之產物係雙股線性病毒DNA,其係用於將病毒整合到感染細胞之DNA中之受質。
在某些具體實施例中,病毒載體可係γ反轉錄病毒,例如莫洛尼鼠類白血病病毒(Moloney murine leukemia virus, MLV)衍生之載體。在其他具體實施例中,病毒載體可係更複雜的反轉錄病毒衍生之載體,例如慢病毒衍生之載體。HIV-1衍生之載體屬於此類別。其他實施例包括衍生自HIV-2、FIV、馬感染性貧血病毒、SIV、及馬迪-維斯納病毒(Maedi-Visna virus)(綿羊慢病毒)之慢病毒載體。使用反轉錄病毒及慢病毒病毒載體及包裝細胞供含有轉殖基因之病毒粒子轉導哺乳動物宿主細胞之方法係所屬技術領域中已知的且先前已描述於例如以下文獻中:美國專利第8,119,772號;Walchli
et al.,
PLoS One 6:327930, 2011; Zhao
et al.,
J. Immunol.174:4415, 2005;Engels
et al.,
Hum. Gene Ther. 14:1155, 2003;Frecha
et al.,
Mol.Ther.
18:1748, 2010;及Verhoeyen
et al.,
Methods Mol. Biol. 506:97, 2009。反轉錄病毒及慢病毒載體構築體及表現系統亦為可商購的。其他病毒載體亦可用於包括DNA病毒載體之多核苷酸遞送,該等DNA病毒載體包括例如基於腺病毒之載體及基於腺相關病毒(AAV)之載體;衍生自單純疱疹病毒(HSV)之載體,其包括擴增子載體、複製缺陷型HSV及減毒性HSV(Krisky
et al.,
Gene Ther.5:1517, 1998)。
可與本揭露之組成物及方法一起使用之其他載體包括衍生自桿狀病毒及α-病毒之載體。(Jolly, D J. 1999. Emerging Viral Vectors. pp 209-40 in Friedmann T. ed. The Development of Human Gene Therapy. New York: Cold Spring Harbor Lab),或質體載體(諸如睡美人載體(sleeping beauty)或其他轉位子載體)。
當病毒載體基因組包含待在宿主細胞中作為單獨轉錄物表現之複數個多核苷酸時,病毒載體亦可在二個(或更多個)轉錄物之間包含允許雙順反子或多順反子表現之額外序列。用於病毒載體之此類序列之實施例包括內部核糖體進入位點(internal ribosome entry site, IRES)、弗林蛋白酶裂解位點、病毒2A肽、或其任何組合。
本文中進一步描述質體載體,其包括用於向個體直接投予之編碼基於DNA之抗體或抗原結合片段之質體載體。
如本文中所使用,術語「宿主(host)」係指靶向用異源性核酸分子進行基因修飾以產生感興趣之多肽(例如本揭露內容之抗體)的細胞或微生物。
宿主細胞可包括可接受載體或併入核酸或表現蛋白質之任何個別的細胞或細胞培養物。該術語亦涵蓋宿主細胞之後代,不論在基因上或表型上相同或不同。合適宿主細胞可取決於載體,且可包括哺乳動物細胞、動物細胞、人類細胞、猿猴細胞、昆蟲細胞、酵母細胞、及細菌細胞。此等細胞可藉由使用病毒載體、經由磷酸鈣沉澱之轉形作用、DEAE-聚葡萄糖、電穿孔、顯微注射、或其他方法來誘導以併入載體或其他物質。參見例如Sambrook
et al.,
Molecular Cloning: A Laboratory Manual2d ed.(Cold Spring Harbor Laboratory, 1989)。
在嚴重急性呼吸道症候群β型冠狀病毒感染之上下文中,「宿主」係指感染嚴重急性呼吸道症候群β型冠狀病毒之細胞或個體。
如本文中所使用,「抗原」或「Ag」係指引起免疫反應之免疫原性分子。此免疫反應可涉及抗體產生、特異性免疫學機能健全細胞之活化、補體之活化、抗體依賴性細胞毒性、或其任何組合。抗原(免疫原性分子)可為例如肽、醣肽、多肽、醣多肽、多核苷酸、多醣、脂質等。顯而易見,抗原可為合成、以重組方式產生、或衍生自生物樣本。可含有一或多個抗原之例示性生物樣本包括組織樣品、糞便樣品、細胞、生物流體、或其組合。抗原可藉由已經修飾或經基因工程改造以表現抗原之細胞產生。抗原亦可存在於嚴重急性呼吸道症候群β型冠狀病毒(表面醣蛋白或其部分)中,諸如存在於病毒粒子中,或在受嚴重急性呼吸道症候群β型冠狀病毒感染之細胞表面上表現或呈遞。
術語「表位(epitope)」或「抗原表位(antigenic epitope)」包括由諸如免疫球蛋白之同族結合分子、或其他結合分子、結構域、或蛋白質識別且特異性結合之任何分子、結構、胺基酸序列、或蛋白質決定位。表位決定位(epitopic determinant)通常含有化學活性表面分子基團(諸如胺基酸或糖側鏈),且可具有特定三維結構特性以及特定電荷特性。當抗原係或包含肽或蛋白質時,表位可包含連續胺基酸(例如線性表位);或可包含來自蛋白質之不同部分或區域之胺基酸,該等胺基酸藉由蛋白質摺疊而變得靠近(例如,不連續或構形表位);或與蛋白質摺疊無關的緊密靠近之非鄰接胺基酸。
抗體、抗原結合片段、及組成物 在一個態樣中,本揭露提供單離之抗體、或其抗原結合片段,其能夠與嚴重急性呼吸道症候群β型冠狀病毒(例如SARS-CoV-2)之表面醣蛋白結合。在一些具體實施例中,抗體或抗原結合片段能夠與二或更多種嚴重急性呼吸道症候群β型冠狀病毒、三或更多種嚴重急性呼吸道症候群β型冠狀病毒、四或更多種嚴重急性呼吸道症候群β型冠狀病毒、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。在一些具體實施例中,抗體或抗原結合片段包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3。
在一些具體實施例中,二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒包含或一或多種、或選自演化支1b嚴重急性呼吸道症候群β型冠狀病毒或其天然存在的變體、及其任何組合。在某些具體實施例中,抗體或抗原結合片段能夠與二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合;例如能夠當嚴重急性呼吸道症候群β型冠狀病毒表面醣蛋白在宿主細胞之細胞表面及/或在嚴重急性呼吸道症候群β型冠狀病毒病毒粒子上表現時結合。在某些具體實施例中,二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒係選自SARS-CoV-2、PANG/GD、PANG/GX、RatG13、及其天然存在的變體。在一些具體實施例中,二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒包括SARS-CoV-2變體中之一或多者。在某些進一步具體實施例中,抗體或其抗原結合片段能夠與一或多種SARS-CoV-2變體結合。演化支1b之實施例亦包括SARS-CoV-2變體,例如具有以下任何突變之變體:A67V、Δ69-70、T95I、G142D、137-145de、143-145de、Y145H、N211I、Δ212、V213G、ins214TDR、ins215EPE、A222V、G339D、R346K、R346S、V367F、S371L、S373P、S375F、T376A、P384L、N394S、D405N、R408S、Q414K、K417N、K417V、K417T、N439K、N440K、G446S、Y449H、Y449N、L452R、L452Q、L452X(其中X係除L以外之任何胺基酸)、Y453F、S477N、T478K、V483A、E484A、E484Q、E484K、E484X(其中X係除E以外之任何胺基酸)、F490R、F486V、F490S、R493Q、Q493R、S494P、G496S、Q498R、N501Y、N501T、Y505H、E516Q、T547K、Q613H、D614G、A653V、H655Y、G669S、Q677H、N679K、ins679GIAL、P681H、P681R、A701V、N764K、D796Y、N856K、Q954H、N969K、L981F、D614、E340A、或於以下譜系中之變體:B.1.1.7及Q譜系及後代譜系(Alpha);B.1.351及後代譜系(Beta);B.1.429及B.1.427、及後代譜系(Epsilon);P.1及後代譜系(Gamma);B.1.1.222;C.37;B.1.617.2;AY.1、AY.2、其他AY譜系及後代譜系(Delta);B.1.525及後代譜系(Eta);B.1.526及後代譜系(Iota);B.1.617.1及後代譜系(Kappa);1.617.3;B.1.621及B.1.621.1及後代譜系(Mu);P.2(Zeta);及B.1.1.529.1、BA.1、BA.2、BA.2.12、BA.3、BA.4、BA.5及後代譜系(Omicron);BQ.1.1;XBB.1。
在一些具體實施例中,二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒包括具有以下S蛋白質突變之一或多種SARS-CoV-2變體:D614G、Q493R、G496S、Q498R、N501Y、Y453F、N439K、K417V、E484K、或其任何組合。在某些具體實施例中,二或更多種嚴重急性呼吸道症候群β型冠狀病毒包括具有以下S蛋白質突變之一或多種SARS-CoV-2變體:K417N、Q493K、G496S、或其任何組合。
在某些具體實施例中,本揭露之抗體或抗原結合片段與嚴重急性呼吸道症候群β型冠狀病毒表面醣蛋白表位或包含該表位之抗原締合或聯合,但與樣本中之任何其他分子或組分不顯著締合或聯合。在一些具體實施例中,表位係包含在S蛋白質之S1次單位中。在進一步具體實施例中,表位係包含在S蛋白質之RBD中。在一些具體實施例中,表位係構形表位或線性表位。
在某些具體實施例中,本揭露之抗體或抗原結合片段與第一嚴重急性呼吸道症候群β型冠狀病毒表面醣蛋白表位締合或聯合(例如結合),且亦可與來自樣本中存在之另一種嚴重急性呼吸道症候群β型冠狀病毒之表位締合或聯合,但與樣本中之任何其他分子或組分不顯著締合或聯合。換言之,在某些具體實施例中,本揭露之抗體或抗原結合片段針對二或更多種嚴重急性呼吸道症候群β型冠狀病毒(例如針對SARS-CoV-2 Wuhan-Hu-1及其一或多種變體)具有交叉反應性並與其特異性結合。
在某些具體實施例中,本揭露之抗體或抗原結合片段與嚴重急性呼吸道症候群β型冠狀病毒表面醣蛋白特異性結合。如本文中所使用,「特異性結合(specifically bind)」係指抗體或抗原結合片段與抗原締合或聯合的親和力或K
a(亦即特定結合交互作用之平衡常數,單位為1/M)等於或大於10
5M
-1(其等於此締合反應之締合速率(on-rate) [K
on]對解離速率(off rate) [K
off]之比率),但與樣品中之任何其他分子或組分不顯著締合或聯合。替代地,親和力可定義為特定結合交互作用之平衡解離常數(K
d),單位為M(例如10
-5M至10
-13M)。抗體可分類為「高親和力」抗體或為「低親和力」抗體。「高親和力」抗體係指具有至少10
7M
-1、至少10
8M
-1、至少10
9M
-1、至少10
10M
-1、至少10
11M
-1、至少10
12M
-1、或至少10
13M
-1之K
a的彼等抗體。「低親和力」抗體係指具有至多10
7M
-1、至多10
6M
-1、至多10
5M
-1之K
a的彼等抗體。替代地,親和力可定義為特定結合交互作用之平衡解離常數(K
d),單位為M(例如10
-5M至10
-13M)。
已知用於鑑別結合特定目標的本揭露之抗體,以及判定結合結構域或結合蛋白質親和力之多種檢定,諸如西方墨點法、ELISA(例如直接法、間接法、或三明治法)、分析型超速離心法、光譜法、及表面電漿子共振(Biacore®)分析(參見例如Scatchard
et al.,
Ann. N.Y. Acad. Sci. 51:660, 1949;Wilson,
Science 295:2103, 2002; Wolff
et al.,
Cancer Res.53:2560, 1993;及美國專利第5,283,173號、第5,468,614號、或等效物)。用於評定親和力或表觀親和力或相對親和力之檢定亦為已知。
在某些具體實施例中,本揭露之抗體或抗原結合片段以以下之EC50結合一或多種、或二或更多種演化支1b之嚴重急性呼吸道症候群β型冠狀病毒:在約0.5 ng/mL至約100 ng/mL、約1 ng/mL至約100 ng/mL、約2.0 ng/mL至約100 ng/mL、約2.5 ng/mL至約100 ng/mL、約5.0 ng/mL至約100 ng/mL、約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約1 ng/mL至約50 ng/mL、約2.0 ng/mL至約50 ng/mL、約2.5 ng/mL至約50 ng/mL、約5.0 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或至少約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL,其可藉由ELISA測定。在一些具體實施例中,抗體或抗原結合片段與來自一種、二種、三種、四種、或五種嚴重急性呼吸道症候群β型冠狀病毒之棘突(S)蛋白質RBD結合。
在一些具體實施例中,抗體或抗原結合片段能夠與各自獨立地選自演化支1b之第一及第二嚴重急性呼吸道症候群β型冠狀病毒結合,其中該抗體或抗原結合片段能夠以以下之EC50與第一嚴重急性呼吸道症候群β型冠狀病毒結合:約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL,且能夠以以下之EC50與第二嚴重急性呼吸道症候群β型冠狀病毒結合:約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3A3、或抗體或抗原結合片段包含本文中所揭示之S3A3或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3A3或變體足夠的CDR、VH、及/或VL同一性賦予類似特異性結合、或其片段,且能夠以以下之KD與SARS-CoV-2 RBD結合:在約1.0 x 10
-09M與約1.0 x 10
-08M、約1.2 x 10
-09M與約1.0 x 10
-08M、約1.5 x 10
-09M與約1.0 x 10
-08M、約2.0 x 10
-09M與約1.0 x 10
-08M、約2.25 x 10
-09M與約1.0 x 10
-08M、約2.5 x 10
-09M與約1.0 x 10
-08M、約3.0 x 10
-09M與約1.0 x 10
-08M、約3.5 x 10
-09M與約1.0 x 10
-08M、約4.0 x 10
-09M與約1.0 x 10
-08M、約4.5 x 10
-09M與約1.0 x 10
-08M、或約5.0 x 10
-09M與約1.0 x 10
-08M之間的範圍內、約1.0 x 10
-09M、或約1.2 x 10
-09M、約1.5 x 10
-09M、約2.0 x 10
-09M、約2.25 x 10
-09M、約2.5 x 10
-09M、約3.0 x 10
-09M、約4.0 x 10
-09M、約4.5 x 10
-09M、或約5.0 x 10
-09M、或不大於約1.0 x 10
-09M、或約1.2 x 10
-09M、約1.5 x 10
-09M、約2.0 x 10
-09M、約2.25 x 10
-09M、約2.5 x 10
-09M、約3.0 x 10
-09M、約4.0 x 10
-09M、約4.5 x 10
-09M、或約5.0 x 10
-09M,如可藉由生物薄層干涉法(例如使用Octet)測定。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3A19、或抗體或抗原結合片段包含本文中所揭示之S3A19或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3A19或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以以下之KD與SARS-CoV-2 RBD結合:在約1.0 x 10
-12M與約5.0 x 10
-08M、約1.5 x 10
-12M與約5.0 x 10
-08M、約2.0 x 10
-12M與約5.0 x 10
-08M、約2.25 x 10
-12M與約5.0 x 10
-08M、約2.5 x 10
-12M與約5.0 x 10
-08M、約1.0 x 10
-11M與約5.0 x 10
-08M、約1.0 x 10
-10M與約5.0 x 10
-08M、約1.0 x 10
-09M與約5.0 x 10
-08M、約1.0 x 10
-08M與約5.0 x 10
-08M之間的範圍內、約1.0 x 10
-12M、或約1.5 x 10
-12M、約2.0 x 10
-12M、約2.25 x 10
-12M、約2.5 x 10
-12M、約1.0 x 10
-11M、約1.0 x 10
-10M、約1.0 x 10
-09M、或不大於約1.0 x 10
-12M、或約1.5 x 10
-12M、約2.0 x 10
-12M、約2.25 x 10
-12M、約2.5 x 10
-12M、約1.0 x 10
-11M、約1.0 x 10
-10M、約1.0 x 10
-09M,如可藉由生物薄層干涉法(例如使用Octet)測定。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3I2、或抗體或抗原結合片段包含本文中所揭示之S3I2或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3I2或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以在約1.0 x 10
-12M與約5.0 x 10
-08M之間的範圍內之KD與SARS-CoV-2 RBD結合。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3O13、或抗體或抗原結合片段包含本文中所揭示之S3O13或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3O13或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以在約1.0 x 10
-12M與約5.0 x 10
-08M之間的範圍內之KD與SARS-CoV-2 RBD結合。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3L17、或抗體或抗原結合片段包含本文中所揭示之S3L17或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3L17或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以在約1.0 x 10
-12M與約5.0 x 10
-08M之間的範圍內之KD與SARS-CoV-2 RBD結合。
在某些實施例中,結合可藉由在宿主細胞中以重組方式表現嚴重急性呼吸道症候群β型冠狀病毒抗原(例如藉由轉染)並將宿主細胞用抗體免疫染色(例如經固定,或經固定且預滲透化),並且藉由流式細胞測量術(例如使用ZE5細胞分析儀(BioRad®)及FlowJo軟體(TreeStar))分析來測定。在一些具體實施例中,陽性結合可藉由表現嚴重急性呼吸道症候群β型冠狀病毒之細胞對比對照(例如模擬)細胞之抗體的差異染色來定義。
在一些具體實施例中,本揭露之抗體或抗原結合片段與在宿主細胞(例如Expi-CHO細胞)之表面上表現之嚴重急性呼吸道症候群β型冠狀病毒棘蛋白(亦即來自二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒)結合,如藉由流式細胞測量術所測定。
在一些具體實施例中,本揭露之抗體或抗原結合片段與嚴重急性呼吸道症候群β型冠狀病毒S蛋白結合,如使用生物薄層干涉法所測量。
在某些具體實施例中,本揭露之抗體能夠中和由一或多種、或由二或更多種嚴重急性呼吸道症候群β型冠狀病毒所致之感染。如本文中所使用,「中和抗體」係可中和,亦即預防、抑制、減少、阻礙或干擾病原體在宿主中引發及/或保持感染之能力的抗體。術語「中和抗體(neutralizing antibody)」及「中和...的抗體(an antibody that neutralizes/antibodies that neutralize)」在本文中可互換使用。在任何目前所揭示之具體實施例中,抗體或抗原結合片段能夠在感染之體外模式中及/或在感染之體內動物模式中及/或在人類中預防及/或中和由一或多種、或由二或更多種嚴重急性呼吸道症候群β型冠狀病毒所致之感染。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3A3、或抗體或抗原結合片段包含本文中所揭示之S3A3或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3A3或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以下列者中和由在假病毒系統(例如基於MLV-pp或基於VSV-pp)中之SARS-CoV-2所致之感染:約0.5 ng/mL至約100 ng/mL、約1 ng/mL至約100 ng/mL、約2.0 ng/mL至約100 ng/mL、約2.5 ng/mL至約100 ng/mL、約5.0 ng/mL至約100 ng/mL、約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約1 ng/mL至約50 ng/mL、約2.0 ng/mL至約50 ng/mL、約2.5 ng/mL至約50 ng/mL、約5.0 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或至少約30 ng/mL至約50 ng/mL、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3A19、或抗體或抗原結合片段包含本文中所揭示之S3A19或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3A19或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠以下列者中和由在假病毒系統(例如基於MLV-pp或基於VSV-pp)中之SARS-CoV-2所致之感染:在約7.5 ng/mL至約100 ng/mL、約8.0 ng/mL至約100 ng/mL、約9.0 ng/mL至約100 ng/mL、約10.0 ng/mL至約100 ng/mL、約12.5 ng/mL至約100 ng/mL、約15.0 ng/mL至約100 ng/mL、約17.5 ng/mL至約100 ng/mL、約20 ng/mL至約100 ng/mL、約25.0 ng/mL至約100 ng/mL、約27.5 ng/mL至約100 ng/mL、約30 ng/mL至約100 ng/mL、約0.5 ng/mL至約50 ng/mL、約7.5 ng/mL至約50 ng/mL、約8.0 ng/mL至約50 ng/mL、約9.0 ng/mL至約50 ng/mL、約10.0 ng/mL至約50 ng/mL、約12.5 ng/mL至約50 ng/mL、約15.0 ng/mL至約50 ng/mL、約17.5 ng/mL至約50 ng/mL、約20 ng/mL至約50 ng/mL、約25.0 ng/mL至約50 ng/mL、約27.5 ng/mL至50 ng/mL、或約30 ng/mL至約50 ng/mL之範圍內、約0.5 ng/mL、約0.9 ng/mL、約1.0 ng/mL、約1.25 ng/mL、約1.5 ng/mL、約1.75 ng/mL、約2.0 ng/mL、約2.25 ng/mL、約2.5 ng/mL、約3.0 ng/mL、約4.0 ng/mL、約5.0 ng/mL、約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL、或至少約7.5 ng/mL、約8.0 ng/mL、約9.0 ng/mL、約10.0 ng/mL、約12.5 ng/mL、約15.0 ng/mL、約17.5 ng/mL、約20.0 ng/mL、約22.5 ng/mL、約25.0 ng/mL、約27.5 ng/mL、或約30 ng/mL。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3I2、或抗體或抗原結合片段包含本文中所揭示之S3I2或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3I2或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠在約0.5 ng/mL至約100 ng/mL之間的範圍內中和由假病毒系統(例如基於MLV-pp或基於VSV-pp)中之SARS-CoV-2所致之感染。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3O13、或抗體或抗原結合片段包含本文中所揭示之S3O13或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3O13或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠在約0.5 ng/mL至約100 ng/mL之間的範圍內中和由假病毒系統(例如基於MLV-pp或基於VSV-pp)中之SARS-CoV-2所致之感染。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3L17、或抗體或抗原結合片段包含本文中所揭示之S3L17或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S3L17或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠在約0.5 ng/mL至約100 ng/mL之間的範圍內中和由假病毒系統(例如基於MLV-pp或基於VSV-pp)中之SARS-CoV-2所致之感染。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S2V29、或抗體或抗原結合片段包含本文中所揭示之S2V29或變體之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與本文中所揭示之S2V29或變體足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且能夠在約0.5 ng/mL至約100 ng/mL之間的範圍內中和由假病毒系統(例如基於MLV-pp或基於VSV-pp)中之SARS-CoV-2所致之感染。
在某些具體實施例中,抗體或抗原結合片段(i)識別二或更多種嚴重急性呼吸道症候群β型冠狀病毒之棘蛋白中之表位;(ii)能夠阻斷在一或多種嚴重急性呼吸道症候群β型冠狀病毒之棘蛋白與細胞表面受體之間的交互作用;(iii)識別在二或更多種嚴重急性呼吸道症候群β型冠狀病毒之棘蛋白中保留表位;(iv)針對二或更多種嚴重急性呼吸道症候群β型冠狀病毒具有交叉反應性;或(v)(i)至(iv)之任何組合。
除非本文中有明確不同地定義,否則抗體技術領域中具有通常知識者所理解之術語各自具有所屬技術領域中給予的含義。舉例而言,術語「抗體(antibody)」係指包含藉由雙硫鍵所交互連結之至少二個重(H)鏈及二個輕(L)鏈之完整抗體,以及具有或保有與由完整抗體所識別之抗原目標分子結合之能力的完整抗體的任何抗原結合部分或片段,諸如scFv、Fab、或Fab'2片段。因此,本文中之術語「抗體(antibody)」係在最廣泛的意義上使用且包括多株及單株抗體、包括完整抗體及其功能性(抗原結合)抗體片段、包括片段抗原結合片段(Fab)片段、F(ab')2片段、Fab'片段、Fv片段、重組IgG(rIgG)片段、單鏈抗體片段,包括單鏈可變片段(scFv),及單結構域抗體(例如sdAb、sdFv、奈米抗體)片段。該術語涵蓋免疫球蛋白之經基因工程改造及/或以其他方式修飾之形式,諸如胞內抗體(intrabody)、肽體、嵌合抗體、全人抗體、人源化抗體,及異源結合抗體(heteroconjugate antibody)、多特異性(例如雙特異性)抗體、雙功能抗體、三功能抗體、四功能抗體、串聯二scFv及串聯三scFv。除非另有說明,否則術語「抗體」應理解為涵蓋其功能性抗體片段。該術語亦涵蓋完整或全長抗體,包括任何種類或子類之抗體,包括IgG及其子類(IgG1、IgG2、IgG3、IgG4)、IgM、IgE、IgA、及IgD。
術語「V
L」或「VL」及「V
H」或「VH」分別係指來自抗體輕鏈及抗體重鏈之可變結合區。在某些具體實施例中,VL係κ類(在本文中亦為「VK」)。在某些具體實施例中,VL係λ類。可變結合區包含分散的定義明確之子區,稱為「互補決定區」(CDR)及「框架區」(FR)。術語「互補決定區(complementarity determining region)」及「CDR」與「高度變異區(hypervariable region)」或「HVR」同義,且係指抗體可變區內通常一起賦予抗原特異性及/或該抗體之結合親和力之胺基酸序列,其中在一級結構中,連續CDR(亦即,CDR1及CDR2、CDR2及CDR3)藉由框架區彼此分開。在各可變區中存在三個CDR(HCDR1、HCDR2、HCDR3;LCDR1、LCDR2、LCDR3;亦分別稱為CDRH及CDRL)。在某些具體實施例中,抗體VH包含如下四個FR及三個CDR:FR1-HCDR1-FR2-HCDR2-FR3-HCDR3-FR4,而抗體VL包含如下四個FR及三個CDR:FR1-LCDR1-FR2-LCDR2-FR3-LCDR3-FR4。通常,VH及VL通過其等個別的CDR一起形成抗原結合位點。
在任何目前所揭示之具體實施例中,抗體或抗原結合片段能夠在感染之體外模式中及/或在感染之體內動物模式中及/或在人類中預防及/或中和由一或多種、或由二或更多種嚴重急性呼吸道症候群β型冠狀病毒所致之感染。
在某些具體實施例中,提供包含VH及VL之抗體或抗原結合片段,該VH及VL分別包含如下列之胺基酸序列或由如下列之胺基酸序列組成:1) SEQ ID NO: 23及27;2) SEQ ID NO: 23及37;3) SEQ ID NO: 31及27;4) SEQ ID NO: 31及37;5) SEQ ID NO: 35及27;6) SEQ ID NO: 35及37;7) SEQ ID NO: 36及27;8) SEQ ID NO: 36及37;9) SEQ ID NO: 43及27;10) SEQ ID NO: 43及37;11) SEQ ID NO: 83及87;12) SEQ ID NO: 83及193;13) SEQ ID NO: 179及87;14) SEQ ID NO: 179及193;15) SEQ ID NO: 181及87;16) SEQ ID NO: 181及193;17) SEQ ID NO: 183及87;18) SEQ ID NO: 183及193;18) SEQ ID NO: 185及87;19) SEQ ID NO: 185及193;20) SEQ ID NO: 188及87;21) SEQ ID NO: 188及193;22) SEQ ID NO: 190及87;23) SEQ ID NO: 190及193;24) SEQ ID NO: 93及97;25) SEQ ID NO: 93及225;26) SEQ ID NO: 93及228;27) SEQ ID NO: 93及231;28) SEQ ID NO: 197及97;29) SEQ ID NO: 197及225;30) SEQ ID NO: 197及228;31) SEQ ID NO: 197及231;32) SEQ ID NO: 201及97;33) SEQ ID NO: 201及225;34) SEQ ID NO: 201及228;35) SEQ ID NO: 201及231;36) SEQ ID NO: 204及97;37) SEQ ID NO: 204及225;38) SEQ ID NO: 204及228;39) SEQ ID NO: 204及231;40) SEQ ID NO: 207及97;41) SEQ ID NO: 207及225;42) SEQ ID NO: 207及228;43) SEQ ID NO: 207及231;44) SEQ ID NO: 210及97;45) SEQ ID NO: 210及225;46) SEQ ID NO: 210及228;47) SEQ ID NO: 210及231;48) SEQ ID NO: 212及97;49) SEQ ID NO: 212及225;50) SEQ ID NO: 212及228;51) SEQ ID NO: 212及231;52) SEQ ID NO: 214及97;53) SEQ ID NO: 214及225;54) SEQ ID NO: 214及228;55) SEQ ID NO: 214及231;56) SEQ ID NO: 216及97;57) SEQ ID NO: 216及225;58) SEQ ID NO: 216及228;59) SEQ ID NO: 216及231;60) SEQ ID NO: 218及97;61) SEQ ID NO: 218及225;62) SEQ ID NO: 218及228;63) SEQ ID NO: 218及231;64) SEQ ID NO: 220及97;65) SEQ ID NO: 220及225;66) SEQ ID NO: 220及228;67) SEQ ID NO: 220及231;68) SEQ ID NO: 222及97;69) SEQ ID NO: 222及225;70) SEQ ID NO: 222及228;71) SEQ ID NO: 222及231;72) SEQ ID NO: 102及105;73) SEQ ID NO: 102及254;74) SEQ ID NO: 102及257;75) SEQ ID NO: 102及260;76) SEQ ID NO: 235及105;77) SEQ ID NO: 235及254;78) SEQ ID NO: 235及257;79) SEQ ID NO: 235及260;80) SEQ ID NO: 238及105;81) SEQ ID NO: 238及254;82) SEQ ID NO: 238及257;83) SEQ ID NO: 238及260;84) SEQ ID NO: 241及105;85) SEQ ID NO: 241及254;86) SEQ ID NO: 241及257;87) SEQ ID NO: 241及260;88) SEQ ID NO: 243及105;89) SEQ ID NO: 243及254;90) SEQ ID NO: 243及257;91) SEQ ID NO: 243及260;92) SEQ ID NO: 245及105;93) SEQ ID NO: 245及254;94) SEQ ID NO: 245及257;95) SEQ ID NO: 245及260;96) SEQ ID NO: 247及105;97) SEQ ID NO: 247及254;98) SEQ ID NO: 247及257;99) SEQ ID NO: 247及260;100) SEQ ID NO: 249及105;101) SEQ ID NO: 249及254;102) SEQ ID NO: 249及257;103) SEQ ID NO: 249及260;104) SEQ ID NO: 251及105;105) SEQ ID NO: 251及254;106) SEQ ID NO: 251及257;107) SEQ ID NO: 251及260;108) SEQ ID NO: 111及115;109) SEQ ID NO: 111及121;110) SEQ ID NO: 111及157;111) SEQ ID NO: 111及272;112) SEQ ID NO: 111及277;113) SEQ ID NO: 111及279;114) SEQ ID NO: 111及282;115) SEQ ID NO: 111及286;116) SEQ ID NO: 111及290;117) SEQ ID NO: 125及115;118) SEQ ID NO: 125及121;119) SEQ ID NO: 125及157;120) SEQ ID NO: 125及272;121) SEQ ID NO: 125及277;122) SEQ ID NO: 125及279;123) SEQ ID NO: 125及282;124) SEQ ID NO: 125及286;125) SEQ ID NO: 125及290;126) SEQ ID NO: 128及115;127) SEQ ID NO: 128及121;128) SEQ ID NO: 128及157;129) SEQ ID NO: 128及272;129) SEQ ID NO: 128及279;130) SEQ ID NO: 128及282;131) SEQ ID NO: 128及286;132) SEQ ID NO: 128及290;133) SEQ ID NO: 131及115;134) SEQ ID NO: 131及121;135) SEQ ID NO: 131及157;136) SEQ ID NO: 131及272;137) SEQ ID NO: 131及277;138) SEQ ID NO: 131及279;139) SEQ ID NO: 131及282;140) SEQ ID NO: 131及286;141) SEQ ID NO: 131及290;142) SEQ ID NO: 134及115;143) SEQ ID NO: 134及121;144) SEQ ID NO: 134及157;145) SEQ ID NO: 134及272;146) SEQ ID NO: 134及277;147) SEQ ID NO: 134及279;148) SEQ ID NO: 134及282;149) SEQ ID NO: 134及286;150) SEQ ID NO: 134及290;151) SEQ ID NO: 137及115;152) SEQ ID NO: 137及121;153) SEQ ID NO: 137及157;154) SEQ ID NO: 137及272;155) SEQ ID NO: 137及277;156) SEQ ID NO: 137及279;157) SEQ ID NO: 137及282;158) SEQ ID NO: 137及286;159) SEQ ID NO: 137及290;160) SEQ ID NO: 141及115;161) SEQ ID NO: 141及121;162) SEQ ID NO: 141及157;162) SEQ ID NO: 141及272;162) SEQ ID NO: 141及277;163) SEQ ID NO: 141及279;164) SEQ ID NO: 141及282;165) SEQ ID NO: 141及286;166) SEQ ID NO: 141 290;167) SEQ ID NO: 145及115;168) SEQ ID NO: 145及121;169) SEQ ID NO: 145及157;170) SEQ ID NO: 145及272;171) SEQ ID NO: 145及277;172) SEQ ID NO: 145及279;173) SEQ ID NO: 145及282;174) SEQ ID NO: 145及282;175) SEQ ID NO: 145及286;176) SEQ ID NO: 145及290;177) SEQ ID NO: 149及115;178) SEQ ID NO: 149及121;179) SEQ ID NO: 149及157;180) SEQ ID NO: 149及272;181) SEQ ID NO: 149及277;182) SEQ ID NO: 149及279;及183) SEQ ID NO: 149及282;184) SEQ ID NO: 149及286;185) SEQ ID NO: 149及290;186) SEQ ID NO: 153及115;187) SEQ ID NO: 153及121;188) SEQ ID NO: 153及157;189) SEQ ID NO: 153及272;190) SEQ ID NO: 153及277;191) SEQ ID NO: 153及279;192) SEQ ID NO: 153及282;193) SEQ ID NO: 153及286;194) SEQ ID NO: 153及290;195) SEQ ID NO: 264及115;196) SEQ ID NO: 264及121;197) SEQ ID NO: 264及157;198) SEQ ID NO: 264及272;199) SEQ ID NO: 264及277;200) SEQ ID NO: 264及279;201) SEQ ID NO: 264及282;202) SEQ ID NO: 264及286;203) SEQ ID NO: 264及290;204) SEQ ID NO: 266及115;205) SEQ ID NO: 266及121;206) SEQ ID NO: 266及157;207) SEQ ID NO: 266及272;208) SEQ ID NO: 266及277;209) SEQ ID NO: 266及279;210) SEQ ID NO: 266及282;211) SEQ ID NO: 266及286;212) SEQ ID NO: 266及290;213) SEQ ID NO: 269及115;214) SEQ ID NO: 269及121;215) SEQ ID NO: 269及157;216) SEQ ID NO: 269及157;217) SEQ ID NO: 269及272;218) SEQ ID NO: 269及277;219) SEQ ID NO: 269及279;219) SEQ ID NO: 269及282;220) SEQ ID NO: 269及286;或221) SEQ ID NO: 269及290。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3A3、或抗體或抗原結合片段包含S3A3之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與S3A3足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且VH及VL分別包含如SEQ ID NO: 23及27之胺基酸序列或由如SEQ ID NO: 23及27之胺基酸序列組成。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3A19、或抗體或抗原結合片段包含S3A19之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與S3A19足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且VH及VL包含下列者或由下列者組成:如SEQ ID NO: 分別為31及37;分別為35及37;分別為36及37;及分別為43及37中任一者之胺基酸序列。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3I2、或抗體或抗原結合片段包含S3I2之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與S3I2足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且VH及VL分別包含如SEQ ID NO: 83及87之胺基酸序列或由如SEQ ID NO: 83及87之胺基酸序列組成。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3O13、或抗體或抗原結合片段包含S3O13之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與S3O13足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且VH及VL分別包含如SEQ ID NO: 93及97之胺基酸序列或由如SEQ ID NO: 93及97之胺基酸序列組成。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S3L17、或抗體或抗原結合片段包含S3L17之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與S3L17足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且VH及VL分別包含如SEQ ID NO: 102及105之胺基酸序列或由如SEQ ID NO: 102及105之胺基酸序列組成。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S2V29a、或抗體或抗原結合片段包含S2V29a之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與S2V29a足夠的CDR、VH、及/或VL同一性(以賦予類似特異性結合)、或其片段,且VH及VL分別包含如SEQ ID NO: 111及115之胺基酸序列或由如SEQ ID NO: 111及115之胺基酸序列組成。
在一些具體實施例中,抗體係(或抗原結合片段係來自)S2V29b、或抗體或抗原結合片段包含S2V29b之CDR及視需要地VH及VL。在一些具體實施例中,抗體包含與S2V29b足夠的CDR、VH、及/或VL同一性以賦予類似特異性結合、或其片段,且VH及VL分別包含如SEQ ID NO: 111及121之胺基酸序列或由如SEQ ID NO: 111及121之胺基酸序列組成。
在某些具體實施例中,提供包含重鏈可變結構域(VH)之抗體或抗原結合片段,該重鏈可變結構域包含下列者或由下列者組成:如SEQ ID NO: 23、31、35、36、43、83、93、102、111、125、128、131、137、141、145、149、453、179、181、183、185、188、190、197、201、204、207、210、212、214、216、218、220、222、235、238、241、243、245、247、249、251、264、266、或269中任一者之胺基酸序列。
在某些具體實施例中,提供包含輕鏈可變結構域(VL)之抗體或抗原結合片段,該輕鏈可變結構域包含下列者或由下列者組成:如SEQ ID NO: 27、37、87、97、105、115、121、157、193、225、228、231、254、257、260、272、277、279、282、286、290中任一者之胺基酸序列。
如本文中所使用,CDR之「變體」係指具有至多1至3個胺基酸取代(例如,保留或非保留取代)、刪除、或其組合之CDR序列之功能性變體。
可根據任何已知方法或方案,諸如Kabat、Chothia、EU、IMGT、Contact、North、Martin、AbM、及AHo編號方案對CDR及框架區進行編碼(參見例如Kabat et al., "Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, Public Health Service National Institutes of Health, 1991, 5th ed.; Chothia and Lesk, J. Mol. Biol. 196:901-917(1987));Lefranc et al., Dev. Comp. Immunol. 27:55, 2003; Honegger and Plückthun, J. Mol. Bio. 309:657-670(2001); North et al. J Mol Biol.(2011) 406:228-56; doi:10.1016/j.jmb.2010.10.030; Abhinandan and Martin, Mol Immunol.(2008)45:3832-9. 10.1016/j.molimm.2008.05. 022)。此等參考文獻之抗體及CDR編號系統以引用之方式併入本文中。等效殘基位置可使用抗原受體編號及受體分類(Antigen receptor Numbering And Receptor Classification, ANARCI)軟體工具(2016,Bioinformatics 15:298-300)來標註及比較不同分子。因此,根據一個編號方案鑑別出如本文中所提供之例示性可變區(VH或VL)序列之CDR不包括包含如使用不同編號方案判定之相同可變區之CDR的抗體。在某些具體實施例中,提供抗體或抗原結合片段,其包含下列VH序列中之一或多個CDR:如SEQ ID NO: 23、31、35、36、43、83、93、102、111、125、128、131、137、141、145、149、453、179、181、183、185、188、190、197、201、204、207、210、212、214、216、218、220、222、235、238、241、243、245、247、249、251、264、266、或269中任一者;及/或下列VL序列中之一或多個CDR:如SEQ ID NO: 27、37、87、97、105、115、121、157、193、225、228、231、254、257、260、272、277、279、282、286、290中任一者,其係根據任何已知的CDR編號方法,包括Kabat、Chothia、North、EU、IMGT、Martin(增強型Chothia)、Contact、AbM、及AHo編號方法,或根據此等方法中之二或更多種之組合(例如包括屬於如由任一或所有編號方法所定義之CDR內之彼等殘基)。在某些具體實施例中,CDR係根據IMGT編號方法(視需要地使用CDR3胺基酸序列之接合定義)。在某些具體實施例中,CDR係根據由化學計算組(Chemical Computing Group, CCG)開發之抗體編號方法;例如使用分子操作環境(Molecular Operating Environment, MOE)軟體(chemcomp. com)。在一些具體實施例中,CDR係根據IMGT編號方法。
S3A3 抗體、抗原結合片段、及變體在某些具體實施例中,提供抗體或抗原結合片段,其包含如SEQ ID NO: 23之VH序列及如SEQ ID NO: 27之VL序列。
在一些具體實施例中,相對於SEQ ID NO: 23或SEQ ID NO: 27之胺基酸序列變化係分別限於相對於SEQ ID NO: 23或SEQ ID NO: 27之一或多個框架區(FR)之變化。
框架區可根據編號方案(例如IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo、或此等之二或更多者之組合)鑑別出。可根據編號方案或編號方案之組合在可變結構域內或在重鏈或輕鏈內鑑別出CDR,且較佳地,可使用相同的編號方案或編號方案之組合鑑別出FR。
在某些具體實施例中,抗體或抗原結合片段包含VH,其包含SEQ ID NO: 23中所述之VH胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體);及VL,其包含SEQ ID NO: 27中所述之VL胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體)。在一些具體實施例中,FR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列、基本上由下列組成、或由下列組成:SEQ ID NO: 23中所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列、基本上由下列組成、或由下列組成:SEQ ID NO: 27中所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含SEQ ID NO: 23中所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含SEQ ID NO: 27中所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其基本上由SEQ ID NO: 23中所述之胺基酸序列組成;及(ii)輕鏈可變結構域(VL),其基本上由SEQ ID NO: 27中所述之胺基酸序列組成。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其由SEQ ID NO: 23中所述之胺基酸序列組成;及(ii)輕鏈可變結構域(VL),其由SEQ ID NO: 27中所述之胺基酸序列組成。
在某些具體實施例中,提供抗體或抗原結合片段,其包含在如SEQ ID NO: 23之VH序列中及在如SEQ ID NO: 27之VL序列中鑑別出之CDR,其中,該等CDR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。
在某些具體實施例中,提供抗體或抗原結合片段,其包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(i) CDRH1包含下列者或由下列者組成:如SEQ ID NO: 24之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 25之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 26之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 28之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 29之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 30之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,其中該抗體或抗原結合片段能夠與在宿主細胞之細胞表面上表現之一或多種或二或更多種嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。
在某些實施例中,抗體或抗原結合片段分別包含如SEQ ID NO: 24至26及28至30之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列。
S3A19 抗體、抗原結合片段、及變體在某些具體實施例中,提供抗體或抗原結合片段,其包含下列之VH序列:如SEQ ID NO: 31、35、36、及43中任一者及如SEQ ID NO: 37之VL序列。
在一些具體實施例中,相對於SEQ ID NO: 31、35、36、及43中任一者或SEQ ID NO: 37之胺基酸序列變化係分別限於相對於SEQ ID NO: 31、35、36、及43中任一者或SEQ ID NO: 37之一或多個框架區(FR)之變化。
框架區可根據編號方案(例如IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo、或此等之二或更多者之組合)鑑別出。可根據編號方案或編號方案之組合在可變結構域內或在重鏈或輕鏈內鑑別出CDR,且較佳地,可使用相同的編號方案或編號方案之組合鑑別出FR。
在某些具體實施例中,抗體或抗原結合片段包含VH,其包含下列者:SEQ ID NO: 31、35、36、及43中任一者所述之VH胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體);及VL,其包含SEQ ID NO: 37中所述之VL胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體)。在一些具體實施例中,FR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 31、35、36、及43中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列、基本上由下列組成、或由下列組成:SEQ ID NO: 37中所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者:SEQ ID NO: 31、35、36、及43中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含SEQ ID NO: 37中所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其基本上由下列者組成:SEQ ID NO: 31、35、36、及43中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其基本上由SEQ ID NO: 37中所述之胺基酸序列組成。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其由下列者組成:SEQ ID NO: 31、35、36、及43中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其基本上由SEQ ID NO: 37中所述之胺基酸序列組成。
S3A19抗體可如表3中所述。
在某些具體實施例中,提供抗體或抗原結合片段,其包含在下列者中鑑別出之CDR:如SEQ ID NO: 31、35、36、及43中任一者之VH序列及如SEQ ID NO: 37之VL序列,其中,該等CDR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。
在某些具體實施例中,提供抗體或抗原結合片段,其包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(i) CDRH1包含下列者或由下列者組成:如SEQ ID NO: 32之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 33之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 34之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 38之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 39之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 40之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,其中該抗體或抗原結合片段能夠與在宿主細胞之細胞表面上表現之一或多種或二或更多種嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。
在任何目前所揭示之具體實施例中,抗體或抗原結合片段分別包含如SEQ ID NO: 32至34及38至40之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列。
S3I2 抗體、抗原結合片段、及變體在某些具體實施例中,提供抗體或抗原結合片段,其包含下列之VH序列:如SEQ ID NO: 83、179、181、183、185、188、190中任一者及如SEQ ID NO: 87或193中任一者之VL序列。
在一些具體實施例中,相對於SEQ ID NO: 83、179、181、183、185、188、190中任一者或SEQ ID NO: 87或193中任一者之胺基酸序列變化係分別限於相對於SEQ ID NO: 83、179、181、183、185、188、190中任一者或SEQ ID NO: 87或193中任一者之一或多個框架區(FR)之變化。
框架區可根據編號方案(例如IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo、或此等之二或更多者之組合)鑑別出。可根據編號方案或編號方案之組合在可變結構域內或在重鏈或輕鏈內鑑別出CDR,且較佳地,可使用相同的編號方案或編號方案之組合鑑別出FR。
在某些具體實施例中,抗體或抗原結合片段包含VH,其包含下列者:SEQ ID NO: 83、179、181、183、185、188、190中任一者所述之VH胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體);及VL,其包含SEQ ID NO: 87或193中任一者所述之VL胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體)。在一些具體實施例中,FR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 83、179、181、183、185、188、190中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 87或193中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者:SEQ ID NO: 83、179、181、183、185、188、190中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含SEQ ID NO: 87或193中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其基本上由下列者組成:SEQ ID NO: 83、179、181、183、185、188、190中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其基本上由SEQ ID NO: 87或193中任一者所述之胺基酸序列組成。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其由下列者組成:SEQ ID NO: 83、179、181、183、185、188、190中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其由SEQ ID NO: 87或193中任一者所述之胺基酸序列組成。
在某些具體實施例中,提供抗體或抗原結合片段,其包含在下列者中鑑別出之CDR:如SEQ ID NO: 83、179、181、183、185、190中任一者之VH序列及如SEQ ID NO: 87或193之中任一者之VL序列,其中,該等CDR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。
在某些具體實施例中,提供抗體或抗原結合片段,其包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(i) CDRH1包含下列者或由下列者組成:如SEQ ID NO: 84之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 85之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 86或186中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 88或194中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 89之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 90之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,其中該抗體或抗原結合片段能夠與在宿主細胞之細胞表面上表現之一或多種或二或更多種嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。
在某些實施例中,抗體或抗原結合片段分別包含如SEQ ID NO: 84至86或84、85及186及88至90或194、89、及90之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列。
S3O13 抗體、抗原結合片段、及變體在某些具體實施例中,提供抗體或抗原結合片段,其包含下列之VH序列:如SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者及下列之VL序列:如SEQ ID NO: 97、225、228、或231中任一者。
在一些具體實施例中,相對於SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者或SEQ ID NO: 97、225、228、或231中任一者之胺基酸序列變化係分別限於相對於SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者或SEQ ID NO: 97、225、228、或231中任一者之一或多個框架區(FR)之變化。
框架區可根據編號方案(例如IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo、或此等之二或更多者之組合)鑑別出。可根據編號方案或編號方案之組合在可變結構域內或在重鏈或輕鏈內鑑別出CDR,且較佳地,可使用相同的編號方案或編號方案之組合鑑別出FR。
在某些具體實施例中,抗體或抗原結合片段包含VH,其包含下列者:SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者所述之VH胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體);及VL,其包含下列者:SEQ ID NO: 97、225、228、或231中任一者所述之VL胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體)。在一些具體實施例中,FR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 97、225、228、或231中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者:SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列者:SEQ ID NO: 97、225、228、或231中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其基本上由下列者組成:SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其基本上由下列者組成:SEQ ID NO: 97、225、228、或231中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其由下列者組成:SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其由下列者組成:SEQ ID NO: 97、225、228、或231中任一者所述之胺基酸序列。
在某些具體實施例中,提供抗體或抗原結合片段,其包含在下列者中鑑別出之CDR:如SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者之VH序列及如SEQ ID NO: 97、225、228、或231中任一者之VL序列,其中,該等CDR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。
在某些具體實施例中,提供抗體或抗原結合片段,其包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(i) CDRH1包含下列者或由下列者組成:如SEQ ID NO: 94、198、或208中任一者之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 95之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 96、199、202、或205中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 98、226、229、232中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 39之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 99之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,其中該抗體或抗原結合片段能夠與在宿主細胞之細胞表面上表現之一或多種或二或更多種嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。
在某些實施例中,抗體或抗原結合片段分別包含下列之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列:如SEQ ID NO: 94至96;198、95及96;208、95及96;94、95、及199;198、95及199;208、95、及199;94、95、及202;198、95、及205;208、95、及199;205、95、及202;或208、95、及205、及98、39、及99;226、39、及99;或229、39、及232。
S3L17 抗體、抗原結合片段、及變體在某些具體實施例中,提供抗體或抗原結合片段,其包含下列之VH序列:如SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者及下列之VL序列:如SEQ ID NO: 105、254、257,或260中任一者。
在一些具體實施例中,相對於SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者或SEQ ID NO: 105、254、257、或260中任一者之胺基酸序列變化係分別限於相對於SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者或SEQ ID NO: 105、254、257、或260中任一者之一或多個框架區(FR)之變化。
框架區可根據編號方案(例如IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo、或此等之二或更多者之組合)鑑別出。可根據編號方案或編號方案之組合在可變結構域內或在重鏈或輕鏈內鑑別出CDR,且較佳地,可使用相同的編號方案或編號方案之組合鑑別出FR。
在某些具體實施例中,抗體或抗原結合片段包含VH,其包含下列者:SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者所述之VH胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體);及VL,其包含下列者:SEQ ID NO: 105、254、257、或260中任一者所述之VL胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體)。在一些具體實施例中,FR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 105、254、257、或260中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者:SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列者:SEQ ID NO: 105、254、257、或260中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其基本上由下列者組成:SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其基本上由下列者組成:SEQ ID NO: 105、254、257、或260中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其由下列者組成:SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其由下列者組成:SEQ ID NO: 105、254、257、或260中任一者所述之胺基酸序列。
在某些具體實施例中,提供抗體或抗原結合片段,其包含在下列者中鑑別出之CDR:如SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者之VH序列及如SEQ ID NO: 105、254、257、或260中任一者之VL序列,其中,該等CDR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。
在某些具體實施例中,提供抗體或抗原結合片段,其包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(i) CDRH1包含下列者或由下列者組成:如SEQ ID NO: 103之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 85之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 104、236、或239中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 106或255中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 107之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 108或258中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,其中該抗體或抗原結合片段能夠與在宿主細胞之細胞表面上表現之一或多種或二或更多種嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。
在某些實施例中,抗體或抗原結合片段分別包含下列之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列:如SEQ ID NO: 103、85、及104;103、85、及236;或103、85、及239、及106至108;106、107、及258;255、107、及108;或255、107、或258。
在一些具體實施例中,抗體或抗原結合片段包含如表3中所述之S3A3、S3A19 VH.1、S3A19 VH.2、S3A19 VH.3、S3A19 VH.1-VH.3共通抗體(consensus antibody)、S3I2、S3O13、或S3L17之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列。在某些具體實施例中,抗體或抗原結合片段包含與如表3中所述之S3A3、S3A19 VH.1、S3A19 VH.2、S3A19 VH.3、o3A19 VH.1-VH.3共通抗體、S3I2、S3O13、或S3L17之(各自)VH及VL胺基酸序列具有至少85%、至少86%、至少87%、至少88%、至少89%、至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、或至少99%同一性之VH及VL胺基酸序列,或包含如表3中所述之S3A3、S3A19 VH.1、S3A19 VH.2、S3A19 VH.3、o3A19 VH.1-VH.3共通抗體、S3I2、S3O13、或S3L17之(各自)VH及VL胺基酸序列。在某些具體實施例中,抗體或抗原結合片段包含如表3中所述之S3A3、S3A19 VH.1、S3A19 VH.2、S3A19 VH.3、S3A19 VH.1-VH.3共通抗體、S3I2、S3O13、或S3L17之(各自)VH及VL胺基酸序列。
S2V29 抗體、抗原結合片段、及變體在某些具體實施例中,提供抗體或抗原結合片段,其包含下列之VH序列:如SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及下列之VL序列:如SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者。
在一些具體實施例中,相對於SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者或SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者之胺基酸序列變化係分別限於相對於SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者或SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者之一或多個框架區(FR)之變化。
框架區可根據編號方案(例如IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo、或此等之二或更多者之組合)鑑別出。可根據編號方案或編號方案之組合在可變結構域內或在重鏈或輕鏈內鑑別出CDR,且較佳地,可使用相同的編號方案或編號方案之組合鑑別出FR。
在某些具體實施例中,抗體或抗原結合片段包含VH,其包含下列者:SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者所述之VH胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體);及VL,其包含下列者:SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者所述之VL胺基酸序列之FR1、FR2、FR3、及/或FR4(或包含一個、二個、三個、四個、或五個胺基酸取代、插入、及/或刪除之FR1、FR2、FR3、及/或FR4之變體)。在一些具體實施例中,FR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列者、基本上由下列者組成、或由下列者組成:SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其包含下列者:SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其包含下列者:SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其基本上由下列者組成:SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其基本上由下列者組成:SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者所述之胺基酸序列。
在一些具體實施例中,抗體或抗原結合片段包含:(i)重鏈可變結構域(VH),其由下列者組成:SEQ ID NO: 1 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者所述之胺基酸序列;及(ii)輕鏈可變結構域(VL),其由下列者組成:SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者所述之胺基酸序列。
在某些具體實施例中,提供抗體或抗原結合片段,其包含在下列者中鑑別出之CDR:如SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者之VH序列及如SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者之VL序列,其中,該等CDR係根據IMGT、Kabat、Chothia、North、EU、Martin(增強型Chothia)、Contact、AbM、CCG、或AHo編號系統、或根據其任何組合定義。
在某些具體實施例中,提供抗體或抗原結合片段,其包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(i) CDRH1包含下列者或由下列者組成:如SEQ ID NO: 112之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 113、126、129、132、135、138、142、146、150、154、267、或270中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 114、139、143、147、151、或155中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 116、273、或283中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 117、274、或287中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 118、122、158、275、280、284、288、或291中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,其中該抗體或抗原結合片段能夠與在宿主細胞之細胞表面上表現之一或多種或二或更多種嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。
在某些實施例中,抗體或抗原結合片段分別包含下列之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列:如SEQ ID NO: 112至114;112、126、及114;112、129及114;112、132、及114;112、135、及114;112、138、及114;112、142、及114;112、146、及114;112、150、及114;112、154、及114;112、267、及114;112、270、及114;112、113、及139;112、126、及139;112、129及139;112、132、及139;112、135、及139;112、138、及139;112、142、及139;112、146、及139;112、150、及139;112、154、及139;112、267、及139;112、270、及139;112、113、及143;112、126、及143;112、129及143;112、132、及143;112、135、及143;112、138、及143;112、142、及143;112、146、及143;112、150、及143;112、154、及143;112、267、及143;112、270、及143;112、113、及147;112、126、及147;112、129及147;112、132、及147;112、135、及147;112、138、及147;112、142、及147;112、146、及147;112、150、及147;112、154、及147;112、267、及147;112、270、及147;112、113、及151;112、126、及151;112、129 及151;112、132、及151;112、135、及151;112、138、及151;112、142、及151;112、146、及151;112、150、及151;112、154、及151;112、267、及151;112、270、及151;112、113、及155;112、126、及155;112、129及155;112、132、及155;112、135、及155;112、138、及155;112、142、及155;112、146、及1551;112、150、及155;112、154、及155;112、267、及155;或112、270、及155;及116至118;116、274、及118;116、287、及118;116、117、及122;116、274、及122;116、287、及122;116、117、及158;116、274、及275;116、287、及275;116、117、及280;116、274、及280;116、287、及280;116、117、及284;116、274、及284;116、287、及284;116、117、及288;116、274、及288;116、287、及288;116、117、及291;116、274、及291;116、287、及291;273、117、及118;273、274、及118;273、287、及118;273、117、及122;273、274、及122;273、287、及122;273、117、及158;273、274、及275;273、287、及275;273、117、及280;273、274、及280;1273、287、及280;273、117、及284;273、274、及284;273、287、及284;273、117、及288;273、274、及288;273、287、及288;273、117、及291;273、274、及291;273、287、及291;283、117、118;283、274、及118;283、287、及118;283、117、及122;283、274、及122;283、287、及122;283、117、及158;283、274、及275;283、287、及275;283、117、及280;283、274、及280;283、287、及280;283、117、及284;283、274、及284;283、287、及284;283、117、及288;283、274、及288;283、287、及288;283、117、及291;283、274、及291;或283、287、及291。
在某些實施例中,抗體或抗原結合片段分別包含下列之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列:如SEQ ID NO: 分別為112至114及116至118(S2V29a);分別為112至114及116、117、及122(S2V29b)。
在某些具體實施例中,抗體或抗原結合片包含VH或VL,其分別包含下列者或由下列者組成:SEQ ID NO: 111及157、或與此等序列具有至少85%、90%、或95%同一性,特別是具有如本文中所揭示之框架區突變。在仍進一步具體實施例中,抗體或抗原結合片段包含如SEQ ID NO: 111及157之VH及VL中所述之CDR,其係根據如本文中所述之任何編號方案。在一些具體實施例中,抗體或抗原結合片段分別包含如SEQ ID NO: 112至114及116至117、及158之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列。任何此等抗體可包括如本文中所述之Fc修飾,或可具有未經修飾之人類IgG1恆定區。具體而言,抗體可具有如SEQ ID NO: 111之VH、如SEQ ID NO: 44至80之CH、如SEQ ID NO: 157之VL及如SEQ ID NO: 292之CL。
在特定具體實施例中,抗體或抗原結合片段的重鏈包含下列者或由下列者組成:與SEQ ID NO: 293具有至少85%、90%、95%、或99%同一性之序列,且輕鏈包含下列者或由下列者組成:與SEQ ID NO: 294具有至少85%、90%、95%、或99%同一性之序列。在一些具體實施例中,抗體或抗原結合片段的重鏈包含SEQ ID NO: 293之胺基酸序列或由SEQ ID NO: 293之胺基酸序列組成且輕鏈包含SEQ ID NO: 294之胺基酸序列或由SEQ ID NO: 294之胺基酸序列組成。
在特定具體實施例中,抗體或抗原結合片段的重鏈包含下列者或由下列者組成:與SEQ ID NO: 295具有至少85%、90%、95%、或99%同一性之序列,且輕鏈包含下列者或由下列者組成:與SEQ ID NO: 296具有至少85%、90%、95%、或99%同一性之序列。在一些具體實施例中,抗體或抗原結合片段的重鏈包含SEQ ID NO: 295之胺基酸序列或由SEQ ID NO: 295之胺基酸序列組成且輕鏈包含SEQ ID NO: 296之胺基酸序列或由SEQ ID NO: 296之胺基酸序列組成。
術語「CL」係指「免疫球蛋白輕鏈恆定區」或「輕鏈恆定區」,亦即來自抗體輕鏈之恆定區。術語「CH」係指「免疫球蛋白重鏈恆定區」或「重鏈恆定區」,其可根據抗體同型進一步分成CH1、CH2、及CH3(IgA, IgD, IgG);或CH1、CH2、CH3、及CH4結構域(IgE, IgM)。在本文中進一步描述抗體重鏈之Fc區。在任何目前所揭示之具體實施例中,本揭露之抗體或抗原結合片段包含CL、CH1、CH2、及CH3中任一者或多者。在任何目前所揭示之具體實施例中,本揭露之抗體或抗原結合片段可包含CL、CH1、CH2、及CH3中任一者或多者。在某些實施例中,CL包含與SEQ ID NO: 292之胺基酸序列具有至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、至少99%、或100%同一性之胺基酸序列。在某些實施例中,CL包含與人類λ輕鏈恆定結構域具有至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、至少99%、或100%同一性之胺基酸序列。
術語「CH」係指「免疫球蛋白重鏈恆定區」或「重鏈恆定區」,其可根據抗體同型進一步分成CH1、CH2、及CH3(IgA, IgD, IgG);或CH1、CH2、CH3、及CH4結構域(IgE, IgM)。在本文中進一步描述抗體重鏈之Fc區。在任何目前所揭示之具體實施例中,本揭露之抗體或抗原結合片段包含CL、CH1、CH2、及CH3中任一者或多者。
在一些具體實施例中,抗體或抗原結合片段包含(例如人類)IgG(例如IgG1、IgG2、IgG3、或IgG4)、IgA、IgD、IgE、或IgM同型,或包含來自此等同型中之二或更多者之胺基酸序列。在一些具體實施例中,抗體或抗原結合片段包含IgG1同型;應理解,此種抗體或抗原結合片段可包含在重鏈恆定結構域中之一或多個胺基酸取代且仍被視為「IgG1」同型。在一些具體實施例中,IgG1包含下列者或由下列者組成:與SEQ ID NO: 44至80中所述胺基酸序列具有至少85%、至少86%、至少87%、至少88%、至少89%、至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、或至少99%同一性之胺基酸序列,或包含SEQ ID NO: 44至80中所述之胺基酸序列或由SEQ ID NO: 44至80中所述之胺基酸組成。
應理解,例如在哺乳動物細胞株中之生產可移除抗體重鏈之一或多個C端離胺酸(參見例如Liu et al. mAbs 6(5):1145-1154(2014))。因此,本揭露之抗體或抗原結合片段可包含其中C端離胺酸殘基或C端甘胺酸-離胺酸存在或不存在之重鏈、CH1-CH3、CH3、或Fc多肽;換言之,涵蓋其中重鏈、CH1-CH3、或Fc多肽之C端殘基不是離胺酸之具體實施例、及其中離胺酸係C端殘基之具體實施例。在某些具體實施例中,組成物包含本揭露之複數個抗體及/或抗原結合片段,其中一或多個抗體或抗原結合片段不包含在重鏈、CH1-CH3、或Fc多肽處之C端末端處之離胺酸殘基或C端甘胺酸-離胺酸,且其中一或多個抗體或抗原結合片段包含在重鏈、CH1-CH3、或Fc多肽之C端末端處之離胺酸殘基。
「Fab」(片段抗原結合)係抗體與抗原結合之部分,且包括經由鏈間雙硫鍵連接至輕鏈的重鏈之可變區及CH1。各Fab片段就抗原結合而言為單價,亦即其具有單一抗原結合位點。抗體之胃蛋白酶處理產出單一大型F(ab')2片段,其大致對應於二個雙硫鍵連接之Fab片段,具有二價抗原結合活性並仍能夠交聯抗體。Fab及F(ab')2兩者均為「抗原結合片段」之實施例。Fab'片段與Fab片段不同之處在於在CH1結構域之羧基端處具有額外少量殘基,該結構域包括來自抗體鉸鏈區之一或多個半胱胺酸。Fab'-SH係本文對其中恆定結構域之(一或多個)半胱胺酸殘基帶有游離硫醇基之Fab'的命名。F(ab')2抗體片段最初係作為具有絞鏈半胱胺酸在其間之成對的Fab'片段產生。亦已知抗體片段之其他化學偶合。
Fab片段可例如藉由肽連接子接合以形成單鏈Fab,本文中亦稱為「scFab」。在此等具體實施例中,存在於原生Fab中之鏈間雙硫鍵可能不存在,且連接子完全或部分用於連接或連結單一多肽鏈中之Fab片段。重鏈衍生之Fab片段(例如包含VH+CH1、由VH+CH1組成、或基本上由VH+CH1組成、或「Fd」)及輕鏈衍生之Fab片段(例如包含VL+CL、由VL+CL組成、或基本上由VL+CL組成)可以任何排列連接以形成scFab。舉例而言,scFab可以N端至C端之方向,根據(重鏈Fab片段-連接子-輕鏈Fab片段)或(輕鏈Fab片段-連接子-重鏈Fab片段)排列。本文中進一步詳細討論用於scFab之肽連接子及例示性連接子序列。
「Fv」係含有完整抗原辨識及抗原結合位點之小抗體片段。此片段通常由緊密、非共價締合之一個重鏈可變區及一個輕鏈可變區之二聚物組成。然而,即使單一可變結構域(或僅包含對抗原具有特異性之三個CDR之Fv之一半)亦具有辨識及結合抗原之能力,儘管一般親和力比整個結合位點低。
「單鏈Fv」亦縮寫為「sFv」或「scFv」,係包含連結成單一多肽鏈之V
H及V
L抗體結構域之抗體片段。在一些具體實施例中,scFv多肽包含設置在V
H與V
L結構域之間並連接該等結構域之多肽連接子,該多肽連接子使scFv能夠保有或形成抗原結合之所欲結構。此種肽連接子可使用所屬技術領域眾所周知之標準方法併入到融合多肽中。關於scFv之綜述,參見Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315(1994); Borrebaeck 1995, 見下文。在某些具體實施例中,抗體或抗原結合片段包含scFv,其包含VH結構域、VL結構域、及將VH結構域連接至VL結構域之肽連接子。在特定具體實施例中,scFv包含藉由肽連接子將VH結構域連接至VL結構域,該scFv可呈VH-連接子-VL位向或呈VL-連接子-VH位向。本揭露之任何scFv可經工程改造,使得VL結構域之C端末端藉由短的肽序列連接至VH結構域之N端末端,或反之亦然(亦即(N)VL(C)-連接子-(N)VH(C)或(N)VH(C)-連接子-(N)VL(C))。替代地,在一些具體實施例中,連接子可連接至VH結構域、VL結構域、或兩者之N端部分或末端。
肽連接子序列可例如基於以下進行選擇:(1)其呈現可撓性延伸構形(flexible extended conformation)之能力;(2)其不能或缺乏呈現可與第一及第二多肽上及/或目標分子上之功能性表位交互作用的二級結構的能力;及/或(3)缺乏或相對缺乏可能與多肽及/或目標分子反應之疏水性或帶電荷殘基。有關連接子設計(例如長度)之其他考量因素可包括其中VH及VL可能形成功能性抗原結合位點之構形或構形範圍。在某些具體實施例中,肽連接子序列含有例如Gly、Asn及Ser殘基。其他近乎中性之胺基酸(諸如Thr及Ala)亦可包括在連接子序列中。可有利地用作連接子之其他胺基酸序列包括揭示於以下者:Maratea et al., Gene 40:39 46(1985);Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258 8262(1986);美國專利第4,935,233號、及美國專利第4,751,180號。連接子之其他說明性及非限制性實施例可包括當以單次疊代或重複1至5次或更多次、或更多存在時,例如Glu-Gly-Lys-Ser-Ser-Gly-Ser-Gly-Ser-Glu-Ser-Lys-Val-Asp(SEQ ID NO: 19)(Chaudhary et al., Proc. Natl. Acad. Sci.USA 87:1066-1070(1990))及Lys-Glu-Ser-Gly-Ser-Val-Ser-Ser-Glu-Gln-Leu-Ala-Gln-Phe-Arg-Ser-Leu-Asp(SEQ ID NO: 20)(Bird et al., Science 242:423-426 (1988))及五聚物Gly-Gly-Gly-Gly-Ser(SEQ ID NO: 21)。可使用任何合適的連接子,且通常可為約3、4、5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、20、21、22、23、24、25、26、27、28、29、30、40、50、60、70、80、90、100個胺基酸長、或小於約200個胺基酸長,且較佳地將包含可撓性結構(對藉由連接子連結之二個區域、結構域、模體、片段、或模組之間的構形運動可提供可撓性及空間),且較佳地將為具生物惰性及/或具有低的人類免疫原性風險。例示性連接子包括包含下列者或由下列者組成:SEQ ID NO: 4至13及連接子SEQ A及B中任一者或多者所述之胺基酸序列。在某些具體實施例中,連接子包含下列者或由下列者組成:與SEQ ID NO: 4至13及連接子SEQ A及B中任一者所述之胺基酸序列具有至少75%(亦即至少約75%、80%、85%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或更多)同一性之胺基酸序列。
scFv可使用本文中所揭示之VH及VL序列之任何組合或CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3序列之任何組合來構建。
在一些具體實施例中,不需要連接子序列;例如,當第一及第二多肽具有可用於分開功能性結構域並預防立體干擾之非必需N端(或C端)胺基酸區域時。
在抗體開發期間,在生殖系可變(V)、接合(J)、及多樣性(D)基因基因座中之DNA可能會重新排列,且在編碼序列中可能發生核苷酸之插入及/或刪除。體細胞突變可由所得序列編碼,且可由參考對應已知生殖系序列來鑑別。在一些情況下,對抗體之所欲性質(例如與SARS-CoV-2抗原結合)非至關重要、或會對抗體賦予非所欲性質(例如增加投予抗體之個體之免疫原性風險)、或兩者之體細胞突變可被對應生殖系編碼之胺基酸、或被不同的胺基酸置換,使得抗體之所欲性質得以改善或維持且抗體之非所欲性質減少或消除。因此,在一些具體實施例中,如相較於親代抗體或抗原結合片段,本揭露之抗體或抗原結合片段在可變區中包含至少一個另外的生殖系編碼之胺基酸,前提是該親代抗體或抗原結合片段包含一或多個體細胞突變。本揭露之例示性抗嚴重急性呼吸道症候群β型冠狀病毒抗體之可變區及CDR胺基酸序列提供於本文之表1、及表3中。
在某些具體實施例中,抗體或抗原結合片段包含胺基酸修飾(例如取代突變),以移除非所欲之氧化、去胺、及/或異構化之風險。
本文提供在可變區(例如VH、VL、框架或CDR)中包含一或多個胺基酸改變的變體,其係相較於目前揭示之S3A3、S3A19、S3I2、S3O13、S3L17、或S2V29(「親代」)抗體,其中該變體抗體能夠與SARS-CoV-2抗原結合。
在某些具體實施例中,VH包含下列者或由下列者組成:與如SEQ ID NO: 23之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代;及/或(ii)VL包含下列者或由下列者組成:與如SEQ ID NO: 27之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中變化視需要地限於一或多框架區及/或變化包含對生殖系編碼之胺基酸的一或多個取代。
在某些具體實施例中,VH包含下列者或由下列者組成:與如SEQ ID NO: 31、35、36、及43中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代;及/或(ii)VL包含下列者或由下列者組成:與如SEQ ID NO: 37之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代。
在某些具體實施例中,VH包含下列者或由下列者組成:與如SEQ ID NO: 83、179、181、183、185、188、及190中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代;及/或(ii)VL包含下列者或由下列者組成:與如SEQ ID NO: 87及193中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代。
在某些具體實施例中,VH包含下列者或由下列者組成:與如SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、及222中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代;及/或(ii)VL包含下列者或由下列者組成:與如SEQ ID NO: 97、225、228、及231中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代。
在某些具體實施例中,VH包含下列者或由下列者組成:與如SEQ ID NO: 102、235、238、241、243、245、247、249、及251中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代;及/或(ii)VL包含下列者或由下列者組成:與如SEQ ID NO: 105、254、257、及260中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代。
在某些具體實施例中,VH包含下列者或由下列者組成:與如SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、及269中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代;及/或(ii)VL包含下列者或由下列者組成:與如SEQ ID NO: 115、121、157、272、277、279、282、286、及290中之一或多者之胺基酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之胺基酸序列,其中該變化視需要地限於一或多框架區及/或該變化包含對生殖系編碼之胺基酸的一或多個取代。
在一些具體實施例中,抗體或抗原結合片段係IgG(例如IgG1、IgG2、IgG3、或IgG4)、IgA、IgM、IgE、或IgD同型,或包含來自此等中之二或更多者之胺基酸序列。在一些具體實施例中,抗體或其抗原結合片段係人類的、人源化的、或嵌合的。
抗體或抗原結合片段可為任何同種異型或同種異型之組合。「同種異型」係指在IgG子類別之中發現的等位基因變異。舉例而言,同種異型可包含G1m1(或G1m(a))、G1m2(或G1m(x))、G1m3(或G1m(f))、G1m17(或Gm(z))m)、G1m27、及/或G1m28(G1m27及G1m28已被描述為「異構同種異型(alloallotype)」)。
G1m3及G1m17同種異型在CH1結構域中位在相同位置(根據EU編號,位置214)。G1m3包含R214(EU),而G1m17包含K214(EU)。G1m1同種異型位在CH3結構域(在位置356及358(EU))中且係指E356D及M358L之置換。G1m2同種異型係指在位置431(EU)之丙胺酸被甘胺酸置換。G1m同種異型、異構同種異型、及其特性係所屬技術領域已知的且描述於例如下列中:www.imgt.org/IMGTrepertoire/ Proteins/allotypes/human/IGH/IGHC/G1m_allotypes.html及Lefranc, M.-P. and Lefranc, G. Human Gm, Km and Am allotypes and their molecular characterization: a remarkable demonstration of polymorphism In: B. Tait, F. Christiansen (Eds.), Immunogenetics, chap. 34, Humana Press, Springer, New York, USA. Methods Mol. Biol. 2012; 882, 635-680. PMID: 22665258, LIGM: 406中,其內容及同種異型及同種異型之資訊係以引用方式併入本文中。
G1m1同種異型可例如與G1m3、G1m17、G1m27、G1m2、及/或G1m28同種異型組合。在一些具體實施例中,同種異型係G1m3,且無G1m1(G1m3,-1)。在一些具體實施例中,同種異型係G1m17,1同種異型。在一些具體實施例中,同種異型係G1m3,1。在一些具體實施例中,同種異型係G1m17,且無G1m1(G1m17,-1)。視需要地,此等同種異型可與G1m2、G1m27或G1m28同種異型組合(或不組合)。舉例而言,同種異型可為G1m17,1,2。
在一些具體實施例中,本揭露之抗體或抗原結合片段包含G1m3同種異型或G1m3,1同種異型。在一些具體實施例中,本揭露之抗體或抗原結合片段包含G1m3同種異型且包含M428L及N434S或M428L及N434A突變或增強與人類FcRn結合的任何其他一或多種突變,諸如本文中所述者。在一些具體實施例中,本揭露之抗體或抗原結合片段包含G1m3,1同種異型且包含M428L及N434S或M428L及N434A突變或增強與人類FcRn結合的任何其他一或多種突變,諸如本文中所述者。在一些具體實施例中,本揭露之抗體或抗原結合片段包含G1m17,1同種異型。在一些具體實施例中,本揭露之抗體或抗原結合片段包含G1m17,1同種異型且包含M428L及N434S或M428L及N434A突變或增強與人類FcRn結合的任何其他一或多種突變,如本文進一步所述。
在一些具體實施例中,抗體或抗原結合片段包含人類抗體、單株抗體、純化抗體、單鏈抗體、Fab、Fab'、F(ab')2、Fv、scFv、或scFab。
在某些具體實施例中,本揭露之抗體或抗原結合片段係單特異性(例如與單個表位結合)或多特異性(例如與多個表位及/或目標分子結合)。抗體及抗原結合片段可以各種型式構建。例示性抗體型式揭示於Spiess et al., Mol. Immunol. 67(2):95(2015),及於Brinkmann and Kontermann, mAbs 9(2):182-212(2017)中,其型式及製造其之方法以引用方式併入本文中,且包括例如雙特異性T細胞銜接器(bispecific T cell engager, BiTEs)、DART、杵入臼(knobs-into-holes, KIH)組裝體、scFv-CH3-KIH組裝體、KIH共同輕鏈抗體、TandAb、三重體、TriBi微型體、Fab-scFv、scFv-CH-CL-scFv、F(ab')2-scFv2、四價HCab、內抗體、CrossMab、雙重作用Fab(dual action Fab, DAF)(二合一或四合一)、DutaMab、DT-IgG、電荷配對、Fab臂交換(Fab-arm exchange)、股交換工程改造體(SEEDbody)、三功能抗體(Triomab)、LUZ-Y組裝體、Fcab、κλ體、正交Fab、DVD-Igs(例如美國專利第8,258,268號,其型式以全文引用方式併入本文中)、IgG(H)-scFv、scFv-(H)IgG、IgG(L)-scFv、scFv-(L)IgG、IgG(L,H)-Fv、IgG(H)-V、V(H)-IgG、IgG(L)-V、V(L)-IgG、KIH IgG-scFab、2scFv-IgG、IgG-2scFv、scFv4-Ig、Zybody、及DVI-IgG(四合一)、以及所謂FIT-Ig(例如PCT公開案第WO 2015/103072號,其型式以全文引用方式併入本文中)、所謂WuxiBody形式(例如PCT公開案第WO 2019/057122號,其型式以全文引用方式併入本文中)、及所謂肘內插入(In-Elbow-Insert)Ig形式(IEI-Ig;例如PCT公開案號WO 2019/024979及WO 2019/ 025391,其型式以全文引用方式併入本文中)。
在某些具體實施例中,抗體或抗原結合片段包含二或更多個的VH結構域、二或更多個VL結構域、或兩者(亦即二或更多個VH結構域及二或更多個VL結構域)。在特定具體實施例中,抗原結合片段包含形式(N端至C端方向)VH-連接子-VL-連接子-VH-連接子-VL,其中二個VH序列可為相同或不同的且二個VL序列可為相同或不同的。此類連接之scFv可包括排列成結合至給定目標之VH及VL結構域之任何組合,且以包含二或更多個VH及/或二或更多個VL之形式,可結合一個、二個、或更多個不同的表位或抗原。應瞭解,併入多個抗原結合結構域之形式可包括任何組合或取向的VH及/或VL序列。舉例而言,抗原結合片段可包含形式VL-連接子-VH-連接子-VL-連接子-VH、VH-連接子-VL-連接子-VL-連接子-VH、或VL-連接子-VH-連接子-VH-連接子-VL。
所構建之本揭露之單特異性或多特異性抗體或抗原結合片段包含本文中所揭示之VH及VL序列之任何組合及/或CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3序列之任何組合。在一些具體實施例中,雙特異性或多特異性抗體或抗原結合片段可包含本揭露之一個、二個、或更多個抗原結合結構域(例如VH及VL)。可存在與相同或不同的SARS-CoV-2表位結合的二或更多個結合結構域,且在一些具體實施例中,如本文中所提供之雙特異性或多特異性抗體或抗原結合片段可包含另外的SARS-CoV-2結合結構域,及/或可包含與不同抗原或病原體共同結合的結合結構域。
在任何目前揭示之具體實施例中,抗體或抗原結合片段可為多特異性;例如雙特異性、三特異性等。
在某些具體實施例中,抗體或抗原結合片段包含:(i)第一VH及第一VL;及(ii)第二VH及第二VL,其中該第一VH及該第二VH係不同的。
在一些具體實施例中,第一VH及VL包含i)分別與SEQ ID NO: 23及27中所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列;ii)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為31、35、36、或43中任一者及37;分別為14及15;分別為16及17;分別為18及19;分別為20及21;分別為20及22;iii)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為83、179、181、183、185、188、或190中任一者及87或193中任一者;iv)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為93、197、201、204、207、210、212、214、216、218、220、或222中任一者及97、225、228、或231中任一者;v)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為102、235、238、241、243、245、247、249、或251中任一者及105、254、257、或260中任一者;或vi)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及115、121、157、272、277、279、282、286、或290中任一者;且其中該第二VH及VL包含i)分別與SEQ ID NO: 23及27中所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列;ii)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為31、35、36、或43中任一者及37;分別為14及15;分別為16及17;分別為18及19;分別為20及21;分別為20及22;iii)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為83、179、181、183、185、188、或190中任一者及87或193中任一者;iv)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為93、197、201、204、207、210、212、214、216、218、220、或222中任一者及97、225、228、或231中任一者;v)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為102、235、238、241、243、245、247、249、或251中任一者及105、254、257、或260中任一者;或vi)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及115、121、157、272、277、279、282、286、或290中任一者;其中該第一VH及第二VL不同於該第二VH及VL,且其中該第一VH及該第一VL一起形成第一抗原結合位點,且其中該第二VH及該第二VL一起形成第二抗原結合位點。在一些具體實施例中,抗體或抗原結合片段可進一步包含Fc多肽或其片段,該Fc多肽或其片段包含下列者或由下列者組成:與SEQ ID NO: 44至80中所述胺基酸序列具有至少85%、至少86%、至少87%、至少88%、至少89%、至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、或至少99%同一性之胺基酸序列,或包含SEQ ID NO: 44至80中所述之胺基酸序列或由SEQ ID NO: 44至80中所述之胺基酸組成。
在某些具體實施例中,抗體或抗原結合片段包含Fc多肽、或其片段。「Fc」片段或Fc多肽包含由雙硫鍵固持在一起之兩個抗體H鏈之羧基端部分(亦即IgG之CH2及CH3結構域)。Fc可包含由二個Fc多肽(亦即二個CH2-CH3多肽)構成之二聚物。抗體「效應子功能」係指可歸因於抗體之Fc區(原生序列Fc區或胺基酸序列變體Fc區)的彼等生物活性,且隨著抗體同型而變化。抗體效應子功能之實施例包括:C1q結合及補體依賴性細胞毒性;Fc受體結合;抗體依賴性細胞介導之細胞毒性(ADCC);吞噬作用;細胞表面受體(例如B細胞受體)之下調;及B細胞活化。如本文中所討論,可對Fc結構域進行修飾(例如胺基酸取代),以便修飾(例如改善、減少、或切除)含Fc多肽(例如本揭露之抗體)之一或多種官能性。此類功能包括例如,Fc受體(FcR)結合、抗體半衰期調節(例如藉由與FcRn結合)、ADCC功能、蛋白質A結合、蛋白質G結合、及補體結合。修飾(例如改善、減少、或切除)Fc官能性之胺基酸修飾包括例如T250Q/M428L、M252Y/S254T/T256E、H433K/N434F、M428L/N434S、M428L/N434A、E233P/L234V/L235A/ G236+A327G/A330S/P331S、E333A、S239D/A330L/I332E、P257I/Q311、K326W/E333S、S239D/I332E/G236A、N297Q、K322A、S228P、L235E+E318A/K320A/K322A、L234A/L235A(本文亦稱為「LALA」)、及L234A/L235A/ P329G突變,該等突變係總結及註釋在由InvivoGen(2011)出版之"Engineered Fc Regions"中且可在網上獲得:invivogen.com/PDF/review/review-Engineered-Fc-Regions-invivogen.pdf?utm_source=review&utm_medium=pdf&utm_campaign=review&utm_content=Engineered-Fc-Regions,並以引用方式併入本文中。
舉例而言,為了活化補體級聯,當一或多個免疫球蛋白分子與抗原目標附接時,C1q蛋白質複合物可與至少二個IgG1分子或一個IgM分子結合(Ward, E. S., and Ghetie, V., Ther.Immunol.2(1995)77-94)。Burton, D. R.描述(Mol. Immunol. 22(1985)161-206)包含胺基酸殘基318至337之重鏈區涉及補體固定作用。Duncan, A. R.及Winter, G.(Nature 332(1988)738-740)使用定點誘變,報導Glu318、Lys320及Lys322形成與C1q之結合位點。Glu318、Lys320、及Lys322殘基在C1q之結合中的作用係藉由含有此等殘基之短合成肽抑制補體介導之裂解的能力來確認。
舉例而言,FcR結合可藉由(抗體之)Fc部分與Fc受體(FcR)的交互作用來介導,該Fc受體係在包括造血細胞之細胞上之特化細胞表面受體。Fc受體屬於免疫球蛋白超家族,並顯示出藉由免疫複合物之吞噬作用來介導移除經抗體包覆之病源體、及經由抗體依賴性細胞介導之細胞毒性裂解包覆有對應抗體之紅血球及各種其他細胞目標(例如腫瘤細胞)(ADCC; Van de Winkel, J. G., and Anderson, C. L., J. Leukoc.Biol.49(1991) 511-524)。FcR係藉由其對免疫球蛋白類之特異性來定義;IgG抗體之Fc受體稱為FcγR、IgE之Fc受體稱為FcεR、IgA之Fc受體稱為FcαR,依此類推,而新生兒Fc受體稱為FcRn。Fc受體結合係描述例如於Ravetch, J. V., and Kinet, J. P., Annu. Rev. Immunol. 9(1991)457-492;Capel, P. J., et al., Immunomethods 4(1994)25-34; de Haas, M., et al., J Lab. Clin. Med.126 (1995)330-341;及 Gessner, J. E., et al., Ann. Hematol. 76(1998)231-248中。
受體藉由原生IgG抗體(FcγR)之Fc結構域之交聯觸發各種效應子功能,包括吞噬作用、抗體依賴性細胞毒性、及發炎介質之釋放、以及免疫複合物清除及抗體產生之調節。本文設想提供受體(例如FcγR)之交聯的Fc部分。在人類中,迄今為止已定性三類的FcγR,該等為:(i) FcγRI (CD64),其以高親和力結合單體IgG,並在巨噬細胞、單核球、嗜中性球、及嗜酸性球上表現;(ii) FcγRII (CD32),其以中至低親和力結合複合型IgG,特別是在白血球上且廣泛地表現,據信為抗體介導之免疫力之中心參予者,且其可被分成FcγRIIA、FcγRIIB、及FcγRIIC,彼等在免疫系統中發揮不同功能,但以類似之低親和力與IgG-Fc結合,且此等受體之胞外結構域(ectodomain)係高度同源;及(iii) FcγRIII(CD16),其以中至低親和力結合IgG且已發現呈兩種形式:FcγRIIIA,其已在NK細胞、巨噬細胞、嗜酸性球、及一些單核球及T細胞上發現,且據信介導ADCC;及FcγRIIIB,其在嗜中性球上高度表現。
FcγRIIA在參予殺滅之許多細胞(例如巨噬細胞、單核球、嗜中性球)上發現且似乎能夠活化殺滅過程。FcγRIIB似乎在抑制過程中發揮作用並在B細胞、巨噬細胞上及在肥大細胞及嗜酸性球上發現。重要的是,已顯示在肝中發現所有FcγRIIB之75%(Ganesan, L. P. et al., 2012: "FcγRIIb on liver sinusoidal endothelium clears small immune complexes," Journal of Immunology 189: 4981-4988)。FcγRIIB在稱為LSEC之肝竇狀內皮細胞(liver sinusoidal endothelium)上及在肝中之庫弗氏細胞(Kupffer cell)中大量表現,且LSEC係小型免疫複合物清除之主要部位(Ganesan, L. P. et al., 2012: FcγRIIb on liver sinusoidal endothelium clears small immune complexes. Journal of Immunology 189: 4981-4988)。
在一些具體實施例中,本文中所揭示之抗體及其抗原結合片段包含與特別是Fc區之FcγRIIb結合之Fc多肽或其片段,諸如例如IgG類型抗體。再者,可以藉由引入突變S267E及L328F來工程改造Fc部分以增強FcγRIIB結合,如由 Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies. Molecular Immunology 45, 3926-3933所述。藉此,可增強免疫複合物之清除(Chu, S., et al., 2014: Accelerated Clearance of IgE In Chimpanzees Is Mediated By Xmab7195, An Fc-Engineered Antibody With Enhanced Affinity For Inhibitory Receptor FcγRIIb. Am J Respir Crit, American Thoracic Society International Conference Abstracts)。在一些具體實施例中,本揭露之抗體、或其抗原結合片段包含具有突變S267E及L328F之經工程改造之Fc部分,特別是如由Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies. Molecular Immunology 45, 3926-3933所述。
在B細胞上,FcγRIIB可作用為壓制進一步免疫球蛋白產生並將同型轉換成例如IgE類。在巨噬細胞上,FcγRIIB被認為抑制通過FcγRIIA所介導之吞噬作用。在嗜酸性球及肥大細胞上,該B形式是可有助於通過IgE與其獨立受體結合來壓制此等細胞之活化。
關於FcγRI結合,在E233至G236、P238、D265、N297、A327、及P329中之至少一者之原生IgG中之修飾減少與FcγRI的結合。將在位置233至236處之IgG2殘基取代到對應位置IgG1及IgG4中,使IgG1及IgG4與FcγRI的接合降低103倍並消除人類單核球對抗體敏化之紅血球細胞之反應(Armour, K. L., et al. Eur. J.Immunol.29(1999) 2613-2624)。
關於FcγRII結合,發現例如E233至G236、P238、D265、N297、A327、P329、D270、Q295、A327、R292及K414中之至少一者之IgG突變減少與FcγRIIA的結合。
人類FcγRIIA之兩個等位基因形式係「H131」變體及「R131」變體,該H131以較高親和力與IgG1 Fc結合,且該R131以較低親和力與IgG1 Fc結合。參見例如Bruhns et al., Blood 113:3716-3725(2009)。
關於FcγRIII結合,發現例如E233至G236、P238、D265、N297、A327、P329、D270、Q295、A327、S239、E269、E293、Y296、V303、A327、K338、及D376中之至少一者之突變減少與FcγRIIIA的結合。在人類IgG1上定位用於Fc受體之結合位點、上文提及之突變位點、及用於測量與FcγRI及FcγRIIA結合之方法描述於Shields, R. L., et al., J. Biol.Chem.276(2001) 6591-6604中。
人類FcγRIIA之兩個等位基因形式係「F158」變體及「V158」變體,該F158以較低親和力與IgG1 Fc結合及,該V158以較高親和力與IgG1 Fc結合。參見例如Bruhns et al., Blood 113:3716-3725(2009)。
關於與FcγRII結合,原生IgG Fc之二個區域似乎參予在FcγRII與IgG之間的交互作用,即(i) IgG Fc之下鉸鏈位點,特別是胺基酸殘基L、L、G、G(234至237,EU標號),及(ii) IgG Fc之CH2結構域之相鄰區域,特別是在鄰近於下鉸鏈區域之上CH2結構域,例如在P331之區域中之環圈及股(Wines, B.D., et al., J. Immunol. 2000; 164: 5313 - 5318)。再者,FcγRI似乎與在IgG Fc上之相同位點結合,而FcRn及蛋白質A與IgG Fc上之不同位點結合,該等位點似乎位在CH2至CH3界面處(Wines, B.D., et al., J. Immunol. 2000; 164: 5313-5318)。
亦設想增加本揭露之Fc多肽或其片段與(亦即一或多個)Fcγ受體之結合親和力的突變(例如,如相較於參考Fc多肽或其片段或含有不包含一或多個突變之參考Fc多肽或其片段)。參見例如Delillo and Ravetch, Cell 161(5):1035-1045(2015)and Ahmed et al., J. Struc. Biol. 194(1):78 (2016),Fc突變及其技術以引用方式併入本文中。
在任何本文中所揭示之具體實施例中,抗體或抗原結合片段可包含Fc多肽或其片段,其包含選自以下之突變:G236A;S239D;A330L;及I332E;或該等突變中之任二或更多者之組合;例如S239D/I332E;S239D/A330L/ I332E;G236A/S239D/I332E;G236A/A330L/I332E(本文亦稱為「GAALIE」);或G236A/S239D/A330L/I332E。在一些具體實施例中,Fc多肽或其片段不包含S239D。在一些具體實施例中,Fc多肽或其片段在位置239處(EU編號)包含S。在一些具體實施例中,Fc多肽或其片段包含SEQ ID NO: 52至58中所述之胺基酸序列。
在某些具體實施例中,Fc多肽或其片段可包含參予FcRn結合之Fc多肽或其片段之至少一部分或由參予FcRn結合之Fc多肽或其片段之至少一部分組成。在某些具體實施例中,Fc多肽或其片段包含一或多個胺基酸修飾,其改善對(例如增強結合至)FcRn之結合親和力(例如在約6.0之pH下)且,在一些具體實施例中,藉此延長包含該Fc多肽或其片段之分子之體內半衰期(例如相較於在其他方面相同但不包含該(等)修飾之參考Fc多肽或其片段或抗體)。在某些具體實施例中,Fc多肽或其片段包含或衍生自IgG Fc且延長半衰期之突變包含下列中任一者或多者:M428L;N434S;N434H;N434A;N434S;M252Y;S254T;T256E;T250Q;P257I;Q311I;D376V;T307A;E380A(EU編號)。在某些具體實施例中,延長半衰期之突變包含M428L/N434S(本文亦稱為「MLNS」、「LS」、「_LS」、及「-LS」)。在某些具體實施例中,延長半衰期之突變係在包含SEQ ID NO: 59至64中所述之胺基酸序列或由SEQ ID NO: 59至64中所述之胺基酸序列組成之Fc多肽或其片段中。在某些具體實施例中,半衰期延長之突變包含M252Y/S254T/T256E。在某些具體實施例中,半衰期延長之突變包含T250Q/M428L。在某些具體實施例中,半衰期延長之突變包含P257I/Q311I。在某些具體實施例中,半衰期延長之突變包含P257I/N434H。在某些具體實施例中,半衰期延長之突變包含D376V/N434H。在某些具體實施例中,半衰期延長之突變包含T307A/E380A/ N434A。在某些具體實施例中,延長半衰期之突變包含M428L/N434A(本文亦稱為「MLNA」、「LA」、「_LA」、及「-LA」)。在某些具體實施例中,延長半衰期之突變係在包含SEQ ID NO: 65至70中所述之胺基酸序列或由SEQ ID NO: 65至70中所述之胺基酸序列組成之Fc多肽或其片段中。
在一些具體實施例中,抗體或抗原結合片段包括包含取代突變M428L/N434S或M428L/N434A之Fc部分。在一些具體實施例中,抗體或抗原結合片段包括包含取代突變G236A/A330L/I332E之Fc多肽或其片段。在某些具體實施例中,抗體或抗原結合片段包括(例如IgG)Fc部分,其包含G236A突變、A330L突變、及I332E突變(GAALIE),且不包含S239D突變(例如在位置239處包含原生S)。在特定具體實施例中,抗體或抗原結合片段包括包含下列取代突變的Fc多肽或其片段:M428L/N434S及G236A/A330L/ I332E,(且可包含SEQ ID NO: 71至75中所述之胺基酸序列或由SEQ ID NO: 71至75中所述之胺基酸序列組成),且視需要地不包含S239D(例如在239處包含S)。在特定具體實施例中,抗體或抗原結合片段包括包含下列取代突變的Fc多肽或其片段:M428L/N434A及G236A/A330L/I332E,(且可包含SEQ ID NO: 76至80中所述之胺基酸序列或由SEQ ID NO: 76至80中所述之胺基酸序列組成),且視需要地不包含S239D(例如在239處包含S)。在某些具體實施例中,抗體或抗原結合片段包括包含下列取代突變的Fc多肽或其片段:M428L/N434S(或M428L/N434A)及G236A/S239D/ A330L/I332E。
在一些具體實施例中,提供抗體或抗原結合片段(本文進一步描述),其在(例如人類)IgG1重鏈中包含(i)至(xviii)中任一者中所述之一或多個胺基酸突變:(i) G236A、L328V、及Q295E;(ii) G236A、P230A、及Q295E;(iii) G236A、R292P、及I377N;(iv) G236A、K334A、及Q295E;(v) G236S、R292P、及Y300L;(vi) G236A及Y300L;(vii) G236A、R292P、及Y300L;(viii) G236S、G420V、G446E、及L309T;(ix) G236A及R292P;(x) R292P及Y300L;(xi) G236A及R292P;(xii) Y300L;(xiii) E345K、G236S、L235Y、及S267E;(xiv) E272R、L309T、S219Y、及S267E;(xv) G236Y;(xvi) G236W;(xvii) F243L、G446E、P396L、及S267E;(xviii) G236A、S239D、及H268E,其中胺基酸殘基之編號係根據如Kabat中所述之EU索引。在某些具體實施例中,抗體或抗原結合片段經去岩藻醣基化(afucosylated)。在一些具體實施例中,抗體或抗原結合片段進一步包含增強與人類FcRn結合的一或多個突變,諸如M428L及N434S突變或M428L及N434A突變(EU編號)或增強與人類FcRn結合的任何其他(一或多個)突變,諸如本文中所述者。在某些具體實施例中,抗體或抗原結合片段經去岩藻醣基化。
在特定具體實施例中,抗體或抗原結合片段包含I) VH及VL,其具有下列SEQ ID NO中任一者所述之胺基酸序列:分別為23及27;分別為31及37;分別為35及37;及分別為36及37;II) 在如具有下列中任一者所述之胺基酸序列的VH及VL中所述之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3:分別為1) SEQ ID NO: 23及27;2) SEQ ID NO: 23及37;3) SEQ ID NO: 31及27;4) SEQ ID NO: 31及37;5) SEQ ID NO: 35及27;6) SEQ ID NO: 35及37;7) SEQ ID NO: 36及27;8) SEQ ID NO: 36及37;9) SEQ ID NO: 43及27;10) SEQ ID NO: 43及37;11) SEQ ID NO: 83及87;12) SEQ ID NO: 83及193;13) SEQ ID NO: 179及87;14) SEQ ID NO: 179及193;15) SEQ ID NO: 181及87;16) SEQ ID NO: 181及193;17) SEQ ID NO: 183及87;18) SEQ ID NO: 183及193;18) SEQ ID NO: 185及87;19) SEQ ID NO: 185及193;20) SEQ ID NO: 188及87;21) SEQ ID NO: 188及193;22) SEQ ID NO: 190及87;23) SEQ ID NO: 190及193;24) SEQ ID NO: 93及97;25) SEQ ID NO: 93及225;26) SEQ ID NO: 93及228;27) SEQ ID NO: 93及231;28) SEQ ID NO: 197及97;29) SEQ ID NO: 197及225;30) SEQ ID NO: 197及228;31) SEQ ID NO: 197及231;32) SEQ ID NO: 201及97;33) SEQ ID NO: 201及225;34) SEQ ID NO: 201及228;35) SEQ ID NO: 201及231;36) SEQ ID NO: 204及97;37) SEQ ID NO: 204及225;38) SEQ ID NO: 204及228;39) SEQ ID NO: 204及231;40) SEQ ID NO: 207及97;41) SEQ ID NO: 207及225;42) SEQ ID NO: 207及228;43) SEQ ID NO: 207及231;44) SEQ ID NO: 210及97;45) SEQ ID NO: 210及225;46) SEQ ID NO: 210及228;47) SEQ ID NO: 210及231;48) SEQ ID NO: 212及97;49) SEQ ID NO: 212及225;50) SEQ ID NO: 212及228;51) SEQ ID NO: 212及231;52) SEQ ID NO: 214及97;53) SEQ ID NO: 214及225;54) SEQ ID NO: 214及228;55) SEQ ID NO: 214及231;56) SEQ ID NO: 216及97;57) SEQ ID NO: 216及225;58) SEQ ID NO: 216及228;59) SEQ ID NO: 216及231;60) SEQ ID NO: 218及97;61) SEQ ID NO: 218及225;62) SEQ ID NO: 218及228;63) SEQ ID NO: 218及231;64) SEQ ID NO: 220及97;65) SEQ ID NO: 220及225;66) SEQ ID NO: 220及228;67) SEQ ID NO: 220及231;68) SEQ ID NO: 222及97;69) SEQ ID NO: 222及225;70) SEQ ID NO: 222及228;71) SEQ ID NO: 222及231;72) SEQ ID NO: 102及105;73) SEQ ID NO: 102及254;74) SEQ ID NO: 102及257;75) SEQ ID NO: 102及260;76) SEQ ID NO: 235及105;77) SEQ ID NO: 235及254;78) SEQ ID NO: 235及257;79) SEQ ID NO: 235及260;80) SEQ ID NO: 238及105;81) SEQ ID NO: 238及254;82) SEQ ID NO: 238及257;83) SEQ ID NO: 238及260;84) SEQ ID NO: 241及105;85) SEQ ID NO: 241及254;86) SEQ ID NO: 241及257;87) SEQ ID NO: 241及260;88) SEQ ID NO: 243及105;89) SEQ ID NO: 243及254;90) SEQ ID NO: 243及257;91) SEQ ID NO: 243及260;92) SEQ ID NO: 245及105;93) SEQ ID NO: 245及254;94) SEQ ID NO: 245及257;95) SEQ ID NO: 245及260;96) SEQ ID NO: 247及105;97) SEQ ID NO: 247及254;98) SEQ ID NO: 247及257;99) SEQ ID NO: 247及260;100) SEQ ID NO: 249及105;101) SEQ ID NO: 249及254;102) SEQ ID NO: 249及257;103) SEQ ID NO: 249及260;104) SEQ ID NO: 251及105;105) SEQ ID NO: 251及254;106) SEQ ID NO: 251及257;107) SEQ ID NO: 251及260;108) SEQ ID NO: 111及115;109) SEQ ID NO: 111及121;110) SEQ ID NO: 111及157;111) SEQ ID NO: 111及272;112) SEQ ID NO: 111及277;113) SEQ ID NO: 111及279;114) SEQ ID NO: 111及282;115) SEQ ID NO: 111及286;116) SEQ ID NO: 111及290;117) SEQ ID NO: 125及115;118) SEQ ID NO: 125及121;119) SEQ ID NO: 125及157;120) SEQ ID NO: 125及272;121) SEQ ID NO: 125及277;122) SEQ ID NO: 125及279;123) SEQ ID NO: 125及282;124) SEQ ID NO: 125及286;125) SEQ ID NO: 125及290;126) SEQ ID NO: 128及115;127) SEQ ID NO: 128及121;128) SEQ ID NO: 128及157;129) SEQ ID NO: 128及272;129) SEQ ID NO: 128及279;130) SEQ ID NO: 128及282;131) SEQ ID NO: 128及286;132) SEQ ID NO: 128及290;133) SEQ ID NO: 131及115;134) SEQ ID NO: 131及121;135) SEQ ID NO: 131及157;136) SEQ ID NO: 131及272;137) SEQ ID NO: 131及277;138) SEQ ID NO: 131及279;139) SEQ ID NO: 131及282;140) SEQ ID NO: 131及286;141) SEQ ID NO: 131及290;142) SEQ ID NO: 134及115;143) SEQ ID NO: 134及121;144) SEQ ID NO: 134及157;145) SEQ ID NO: 134及272;146) SEQ ID NO: 134及277;147) SEQ ID NO: 134及279;148) SEQ ID NO: 134及282;149) SEQ ID NO: 134及286;150) SEQ ID NO: 134及290;151) SEQ ID NO: 137及115;152) SEQ ID NO: 137及121;153) SEQ ID NO: 137及157;154) SEQ ID NO: 137及272;155) SEQ ID NO: 137及277;156) SEQ ID NO: 137及279;157) SEQ ID NO: 137及282;158) SEQ ID NO: 137及286;159) SEQ ID NO: 137及290;160) SEQ ID NO: 141及115;161) SEQ ID NO: 141及121;162) SEQ ID NO: 141及157;162) SEQ ID NO: 141及272;162) SEQ ID NO: 141及277;163) SEQ ID NO: 141及279;164) SEQ ID NO: 141及282;165) SEQ ID NO: 141及286;166) SEQ ID NO: 141 290;167) SEQ ID NO: 145及115;168) SEQ ID NO: 145及121;169) SEQ ID NO: 145及157;170) SEQ ID NO: 145及272;171) SEQ ID NO: 145及277;172) SEQ ID NO: 145及279;173) SEQ ID NO: 145及282;174) SEQ ID NO: 145及282;175) SEQ ID NO: 145及286;176) SEQ ID NO: 145及290;177) SEQ ID NO: 149及115;178) SEQ ID NO: 149及121;179) SEQ ID NO: 149及157;180) SEQ ID NO: 149及272;181) SEQ ID NO: 149及277;182) SEQ ID NO: 149及279;及183) SEQ ID NO: 149及282;184) SEQ ID NO: 149及286;185) SEQ ID NO: 149及290;186) SEQ ID NO: 153及115;187) SEQ ID NO: 153及121;188) SEQ ID NO: 153及157;189) SEQ ID NO: 153及272;190) SEQ ID NO: 153及277;191) SEQ ID NO: 153及279;192) SEQ ID NO: 153及282;193) SEQ ID NO: 153及286;194) SEQ ID NO: 153及290;195) SEQ ID NO: 264及115;196) SEQ ID NO: 264及121;197) SEQ ID NO: 264及157;198) SEQ ID NO: 264及272;199) SEQ ID NO: 264及277;200) SEQ ID NO: 264及279;201) SEQ ID NO: 264及282;202) SEQ ID NO: 264及286;203) SEQ ID NO: 264及290;204) SEQ ID NO: 266及115;205) SEQ ID NO: 266及121;206) SEQ ID NO: 266及157;207) SEQ ID NO: 266及272;208) SEQ ID NO: 266及277;209) SEQ ID NO: 266及279;210) SEQ ID NO: 266及282;211) SEQ ID NO: 266及286;212) SEQ ID NO: 266及290;213) SEQ ID NO: 269及115;214) SEQ ID NO: 269及121;215) SEQ ID NO: 269及157;216) SEQ ID NO: 269及157;217) SEQ ID NO: 269及272;218) SEQ ID NO: 269及277;219) SEQ ID NO: 269及279;219) SEQ ID NO: 269及282;220) SEQ ID NO: 269及286;或221) SEQ ID NO: 269及290,其係如有本文中所揭示之任何CDL判定方案所判定;或(III)具有如其中下列之胺基酸序列之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3(i)分別為SEQ ID NO: 24至26或32至34及28至30或38至40;(ii)分別為SEQ ID NO: 32至34及38至40;(iii)分別為SEQ ID NO: 84至86或84、85及186及88至90或194、89、及90;(iv)分別為SEQ ID NO: 94至96;198、95及96;208、95及96;94、95、及199;198、95及199;208、95、及199;94、95、及202;198、95、及205;208、95、及199;205、95、及202;或208、95、及205、及98、39、及99;226、39、及99;或229、39、及232;(v)分別為*SEQ ID NO: 112至114;112、126、及114;112、129及114;112、132、及114;112、135、及114;112、138、及114;112、142、及114;112、146、及114;112、150、及114;112、154、及114;112、267、及114;112、270、及114;112、113、及139;112、126、及139;112、129及139;112、132、及139;112、135、及139;112、138、及139;112、142、及139;112、146、及139;112、150、及139;112、154、及139;112、267、及139;112、270、及139;112、113、及143;112、126、及143;112、129及143;112、132、及143;112、135、及143;112、138、及143;112、142、及143;112、146、及143;112、150、及143;112、154、及143;112、267、及143;112、270、及143;112、113、及147;112、126、及147;112、129及147;112、132、及147;112、135、及147;112、138、及147;112、142、及147;112、146、及147;112、150、及147;112、154、及147;112、267、及147;112、270、及147;112、113、及151;112、126、及151;112、129 及151;112、132、及151;112、135、及151;112、138、及151;112、142、及151;112、146、及151;112、150、及151;112、154、及151;112、267、及151;112、270、及151;112、113、及155;112、126、及155;112、129及155;112、132、及155;112、135、及155;112、138、及155;112、142、及155;112、146、及1551;112、150、及155;112、154、及155;112、267、及155;或112、270、及155;及116至118;116、274、及118;116、287、及118;116、117、及122;116、274、及122;116、287、及122;116、117、及158;116、274、及275;116、287、及275;116、117、及280;116、274、及280;116、287、及280;116、117、及284;116、274、及284;116、287、及284;116、117、及288;116、274、及288;116、287、及288;116、117、及291;116、274、及291;116、287、及291;273、117、及118;273、274、及118;273、287、及118;273、117、及122;273、274、及122;273、287、及122;273、117、及158;273、274、及275;273、287、及275;273、117、及280;273、274、及280;1273、287、及280;273、117、及284;273、274、及284;273、287、及284;273、117、及288;273、274、及288;273、287、及288;273、117、及291;273、274、及291;273、287、及291;283、117、118;283、274、及118;283、287、及118;283、117、及122;283、274、及122;283、287、及122;283、117、及158;283、274、及275;283、287、及275;283、117、及280;283、274、及280;283、287、及280;283、117、及284;283、274、及284;283、287、及284;283、117、及288;283、274、及288;283、287、及288;283、117、及291;283、274、及291;或283、287、及291;及(A) Fc部分,其包含下列之取代突變:(i) G236A、L328V、及Q295E;(ii) G236A、P230A、及Q295E;(iii) G236A、R292P、及I377N;(iv) G236A、K334A、及Q295E;(v) G236S、R292P、及Y300L;(vi) G236A 及Y300L;(vii) G236A、R292P、及Y300L;(viii) G236S、G420V、G446E、及L309T;(ix) G236A 及R292P;(x) R292P 及Y300L;(xi) G236A 及R292P;(xii) Y300L;(xiii) E345K、G236S、L235Y、及S267E;(xiv) E272R、L309T、S219Y、及S267E;(xv) G236Y;(xvi) G236W;(xvii) F243L、G446E、P396L、及S267E;(xviii) G236A、S239D、及H268E;(xix) M428L/ N434S;(xx) M428L/N434A;(xxi) G236A/A330L/I332E/ M428L/N434S;(xxii) G236A/A330L/I332E/M428L/N434A;或(xxiii)(i)至(xxii)中任二者或多者;或(B) Fc部分,其包含Fc多肽或其片段或由Fc多肽或其片段組成,該Fc多肽或其片段包含下列者或由下列者組成:與SEQ ID NO: 44至80具有至少85%、至少86%、至少87%、至少88%、至少89%、至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、或至少99%同一性之胺基酸序列,視需要地不是其天然存在的變體,或包含SEQ ID NO: 52至80中所述之胺基酸序列或由SEQ ID NO: 52至80中所述之胺基酸序列組成。
在某些具體實施例中,抗體或抗原結合片段包含改變醣基化的突變,其中改變醣基化的該突變包含N297A、N297Q、或N297G,及/或該抗體或抗原結合片段係部分或完全去醣基化(aglycosylated)及/或部分或完全去岩藻醣基化。宿主細胞細胞系及製造部分或完全去醣基化或部分或完全去岩藻醣基化抗體及抗原結合片段之方法係已知的(參見例如PCT公開案號WO 2016/181357;Suzuki et al. Clin. Cancer Res.13(6):1875-82(2007);Huang et al.MAbs 6:1-12(2018))。
本揭露之抗體或抗原結合片段可為岩藻醣基化的(例如包含一或多個岩藻醣基部分,且一般包含原生(野生型)岩藻醣基化模式(fucosylation pattern)或相較於原生包括一或多個額外,或較少岩藻醣基部分的岩藻醣基化模式)、或可為去岩藻醣基化的。特別是,原生IgG1抗體在N297處攜帶聚醣位點,且此一般係在抗體中可找到核心岩藻醣部分之唯一位點,儘管一些聚醣位點可在抗體發展期間通過突變(例如在可變結構域中)而產生。Fc多肽或其片段、或抗體之岩藻醣基化可藉由引入胺基酸突變以引入或中斷岩藻醣基化位點(例如在N297處之突變,諸如N297Q或N297A,以中斷可包括核心岩藻醣部分的聚醣之形成)來實現,然而一般較佳的是維持N297及其聚醣,諸如藉由在已經基因工程改造而缺乏岩藻醣基化多肽之能力(或具有抑制能力或能力受損)的宿主細胞中表現多肽;藉由在其中宿主細胞岩藻醣基化多肽之能力受損之條件下(例如在2-氟-L-岩藻醣(2FF)存在下)、或類似條件下表現多肽。去岩藻醣基化多肽可包含無岩藻醣部分、或實質上無岩藻醣部分,及/或可藉由經基因工程改造而缺乏岩藻醣基化多肽之能力(或具有抑制能力或能力受損)的宿主細胞來表現及/或可在其中宿主細胞岩藻醣基化多肽之能力受損之條件下(例如在2-氟-L-岩藻醣(2FF)存在下)表現。在一些具體實施例中,多肽在Asn297處不包含核心岩藻醣部分。在一些具體實施例中,去岩藻醣基化多肽具有增加與FcγRIIIA的結合。在一些情況下,將2FF添加至包含表現抗體之宿主細胞之培養基中,產生約85%或更多的未攜帶岩藻醣部分之抗體。因此,當在2FF或類似試劑存在下產生複數個抗體時,該複數個抗體可被描述為「去岩藻醣基化」。在一些情況下,複數個多肽或抗體可被描述為例如去岩藻醣基化,意指該複數個多肽或抗體之約85%或更多的單一多肽或抗體分子不含岩藻醣部分。在某些較佳具體實施例中,去岩藻醣基化抗體或多肽或其群體或複數個抗體或多肽在EU位置297處包含天冬醯胺酸(N)。岩藻醣基化或缺乏岩藻醣基化可使用例如質譜法(例如電灑質譜法(ESI-MS))評定。在一些具體實施例中,提供包含複數個目前所揭示之多肽中任一者或多者的組成物,其中該組成物包含去岩藻醣基化多肽。
在某些具體實施例中,即使一旦在個體中沒有發現可偵測到的抗體或抗原結合片段(亦即當在投予後抗體或抗原結合片段已自個體中清除時)水平,該抗體或抗原結合片段亦能夠在個體中引發持續的保護。本文將此種保護稱為疫苗效應(vaccinal effect)。不希望受理論束縛,據信樹狀細胞可使抗體及抗原之複合物內化,然後誘導或促進針對抗原之內源性免疫反應。在某些具體實施例中,抗體或抗原結合片段包含一或多個修飾,諸如例如Fc中之突變,其包含G236A、A330L、及I332E,該等突變能夠活化可誘導例如T細胞對抗原之免疫力的樹狀細胞。
在某些具體實施例中,本揭露之抗體或抗原結合片段包含Fc變體,其選自表1中總結之Fc變體(亦參見PCT公開案號WO 2022/251119)。在某些具體實施例中,Fc變體、或抗體或抗原結合片段經岩藻醣基化。在其他具體實施例中,Fc變體、或抗體或抗原結合片段經去岩藻醣基化。
表1. Fc變體(岩藻醣基化,除非另有指示)及其性質
變體 (
一或多個取代突變 vs. 野生型人類 IgG1 Fc) 所示之一或多個變體之某些性質,如相較於岩藻醣基化野生型人類 IgG1
G236A_L328V_Q295E
與人類FcγRIIa(H131等位基因及R131等位基因)的結合增加;與人類FcγRIIb的結合可相比或減少(例如由MSD檢定及/或表面電漿共振);與人類FcγRIIa(H131等位基因或R131等位基因)的結合對比與人類FcγRIIb的結合之比率增加;與人類FcRn的結合可相比;可相比的生產效價;在宿主細胞中經由FcγRIIa之訊號傳導增加及/或在宿主細胞中經由FcγRIIb之訊號傳導降低;Tm與野生型相差12
⸰C或更低;G236S_R292P_Y300L具有改善與C1q的結合
G236A_P230A_Q295E
G236A_R292P_I377N
G236A_K334A_Q295E
G236S_R292P_Y300L
G236A_Y300L
與人類FcγRIIa的結合增加(H131(超過18倍)及R131(超過4倍));與人類FcγRIIb的結合類似或與人類FcγRIIb的結合減少(例如由表面電漿共振所測量);與人類FcγRIIa(H131或R131)的結合對比與人類FcγRIIb的結合之比率增加;與人類FcRn的結合可相比;可相比的生產效價;在宿主細胞中經由FcγRIIa之訊號傳導增加及/或在宿主細胞中經由FcγRIIb之訊號傳導降低;Tm與野生型相差4.5
⸰C
G236A_R292P_Y300L
與人類FcγRIIa的結合增加(H131(超過14倍)及R131(超過2.7倍));與人類FcγRIIb的結合類似;與人類FcγRIIa(H131或R131)的結合對比與人類FcγRIIb的結合之比率增加;與人類FcγRIIIa (V158等位基因及F158等位基因)的結合增加;與人類FcRn的結合可相比;可相比的生產效價;在宿主細胞中經由FcγRIIa及/或FcγRIIIa之訊號傳導增加及/或在宿主細胞中經由FcγRIIb之訊號傳導降低;在宿主細胞中經由FcγRIIa之訊號傳導增加及/或在宿主細胞中經由FcγRIIb之訊號傳導降低;Tm與野生型相差4
⸰C;與人類C1q的結合可相比
G236S_G420V_G446E_L309T
與人類FcγRIIa的結合增加;與人類FcγRIIb的結合降低(小於0.5倍);與人類FcγRIIa(H131或R131)的結合對比與人類FcγRIIb的結合之比率增加;與人類FcRn的結合可相比;可相比的生產效價;在宿主細胞中經由FcγRIIa及/或FcγRIIIa之訊號傳導增加、及/或在宿主細胞中經由FcγRIIb之訊號傳導降低;Tm與野生型相差4
⸰C或更低
G236A_R292P
R292P_Y300L
與人類FcγRIIIa(V158及F158)的結合增加;與人類C1q的結合增加;Tm與野生型相差4
⸰C
Y300L
與人類C1q的結合增加
E345K_G236S_L235Y_S267E
E272R_L309T_S219Y_S267E
G236Y
G236W
F243L_G446E_P396L_S267E
G236A(去岩藻醣基化)
與人類FcγRIIa (H131)及小鼠FcγRIIa (R131)的結合增加,結合人類FcγRIIb降低,與人類FcγRIIIa (V158)及小鼠FcγRIIIa (F158)的結合增加,與人類FcγRIIIb的結合增加,與人類FcRn的結合有所降低,Tm與野生型相差0.15
⸰C或與野生型相差0.9
⸰C或野生型相差0.8
⸰C或野生型相差0.7
⸰C
S239D_H268E_G236A
與下列所有測試之人類FcγR的結合及經由所有測試之人類FcγR的訊號傳導增加:FcγRIIA (H131); FcγRIIA (R131);FcγRIIB;FcγRIIIA (V158);FcγRIIIA (F158);FcγRIIIB;此外,當帶有S239D_H268E_G236A_M428L_N434S之抗HBV抗體與hBsAg結合時,將由此形成之免疫複合物與MoDC一起培育;隨後將MoDC與供體CD4+ T細胞一起培育,如相較於僅帶有M428L_N434S之抗體,導致NFAT+CD69+ CD3+CD4+ T細胞之百分比增加。
在一些具體實施例中,提供抗微小病毒抗體或抗原結合片段,其在(例如人類)IgG1重鏈中包含下列(i)至(xviii)中任一者中所述之一或多個胺基酸突變:(i) G236A、L328V、及Q295E;(ii) G236A、P230A、及Q295E;(iii) G236A、R292P、及I377N;(iv) G236A、K334A、及Q295E;(v) G236S、R292P、及Y300L;(vi) G236A及Y300L;(vii) G236A、R292P、及Y300L;(viii) G236S、G420V、G446E、及L309T;(ix) G236A及R292P;(x) R292P及Y300L;(xi) G236A及R292P;(xii) Y300L;(xiii) E345K、G236S、L235Y、及S267E;(xiv) E272R、L309T、S219Y、及S267E;(xv) G236Y;(xvi) G236W;(xvii) F243L、G446E、P396L、及S267E;(xviii) G236A、S239D、及H268E,其中胺基酸殘基之編號係根據如Kabat中所述之EU索引。在某些具體實施例中,抗體或抗原結合片段經去岩藻醣基化。在一些具體實施例中,抗體或抗原結合片段進一步包含增強與人類FcRn結合的一或多個突變,諸如M428L及N434S突變或M428L及N434A突變(EU編號)或增強與人類FcRn結合的任何其他一或多個突變,諸如本文中所述者。在某些具體實施例中,抗體或抗原結合片段經去岩藻醣基化。
在任何目前所揭示之具體實施例中,抗體或抗原結合片段包含Fc多肽或其片段,其包括CH2(或其片段)、CH3(或其片段)、或CH2及CH3,其中如分別相較於對應野生型CH2或CH3,該CH2、該CH3、或兩者可為任何同型且可含有胺基酸取代或其他修飾。在某些具體實施例中,本揭露之Fc包含締合形成二聚物的兩個CH2-CH3多肽。
在任何目前所揭示之具體實施例中,抗體或抗原結合片段包含Fc多肽或其片段,其包括CH2(或其片段)、CH3(或其片段)、或CH2及CH3,其中如分別相較於對應野生型CH2或CH3,該CH2、該CH3、或兩者可為任何同型且可含有胺基酸取代或其他修飾。在某些具體實施例中,本揭露之Fc包含締合形成二聚物的兩個CH2-CH3多肽。
在任何目前揭示之具體實施例中,抗體或抗原結合片段可為單株的。如本文中所使用之術語「單株抗體(monoclonal antibody)」(mAb)係指自實質上均質的抗體之群體中獲得之抗體,亦即包含該群體之個別抗體係相同的,除了可能存在之可能天然發生之突變(在一些情況下為少量)以外。單株抗體對導向單一抗原位點具有高度特異性。此外,與包括導向不同表位之不同抗體的多株抗體製劑相反,各單株抗體係導向抗原之單一表位。除了其特異性以外,單株抗體有利之處在於其可被合成而不被其他抗體所污染。術語「單株(monoclonal)」不應解讀為要求藉由任何特定方法來產生抗體。舉例而言,可用於本發明之單株抗體可藉由首先由Kohler
et al.,
Nature256:495 (1975)描述之融合瘤方法製備,或可使用重組DNA方法在細菌、真核動物、或植物細胞中製得(參見例如美國專利第4,816,567號)。單株抗體亦可使用描述於例如Clackson
et al.,
Nature,
352:624-628(1991)及Marks
et al.,
J. Mol. Biol.,
222:581-597(1991)中之技術自噬菌體抗體庫中單離。單株抗體亦可使用PCT公開案號WO 2004/076677A2中所揭示之方法獲得。
本揭露之抗體及抗原結合片段包含「嵌合抗體」,其中該重鏈及/或輕鏈之一部分與衍生自特定物種或屬於特定抗體類別或子類別之抗體中之對應序列同一或同源,而該(等)鏈之其餘部分與衍生自另一物種或屬於另一抗體類別或子類別之抗體中之對應序列同一或同源,以及此等抗體之片段,只要其展現所欲生物活性(參見美國專利第4,816,567號;第5,530,101號及第7,498,415號;及Morrison
et al., Proc.Natl.Acad.Sci.USA,
81:6851-6855(1984))。舉例而言,嵌合抗體可包含人類及非人類殘基。此外,嵌合抗體可包含在受體抗體中或在供體抗體中未發現的殘基。進行此等修飾進一步改良抗體性能。進一步細節,請參見Jones
et al.,
Nature321:522-525(1986); Riechmann
et al.,
Natur e332:323-329(1988); and Presta,
Curr. Op. Struct.Biol. 2:593-596(1992)。嵌合抗體亦包括靈長類化及人源化抗體。
「人源化抗體」通常被認為係具有自非人類來源引入一或多個胺基酸殘基到其中的人類抗體。此等非人類胺基酸殘基一般取自可變結構域。人源化可依照Winter及同事之方法(Jones
et al.,
Nature, 321:522-525(1986); Reichmann
et al.,
Nature, 332:323-327(1988); Verhoeyen
et al.,
Science, 239:1534-1536(1988)),藉由以非人類可變序列取代人類抗體之對應序列來進行。因此,此類「人源化」抗體係嵌合抗體(美國專利第4,816,567號;第5,530,101號及第7,498,415號),其中實質上少於完整的人類可變結構域已由來自非人類物種之對應序列所取代。在一些情況下,「人源化」抗體係由非人類細胞或動物所產生之抗體且包含人類序列,例如H
C結構域。
「人類抗體」係僅含有由人類所產生之抗體中存在的序列的抗體。然而,如本文中所使用,人類抗體可包含未在天然存在的人類抗體(譬如自人類單離之抗體)中發現的殘基或修飾,包括本文中所述之彼等修飾及變體序列。此等一般進一步改良或增強抗體性能。在一些情況下,人類抗體係由基因轉殖動物所產生。舉例而言,參見美國專利第5,770,429號;第6,596,541號及第7,049,426號。
在某些具體實施例中,本揭露之抗體或抗原結合片段係嵌合的、人源化的、或人類的。
多核苷酸、載體、及宿主細胞 在另一態樣中,本揭露提供單離之多核苷酸,其編碼任何目前所揭示之抗體或其抗原結合片段、或其部分(例如CDR、VH、VL、重鏈、或輕鏈)。在某些具體實施例中,多核苷酸序列經密碼子最佳化以在宿主細胞中表現。一旦知道或鑑別編碼序列,可使用已知技術及工具執行密碼子最佳化,例如使用GenScript®OptimiumGene
TM工具;亦參見Scholten
et al.,
Clin.Immunol.119:135, 2006)。密碼子最佳化之序列包括部分經密碼子最佳化的序列(亦即一或多個密碼子經最佳化以在宿主細胞中表現)及完全經密碼子最佳化的序列。
應瞭解,由於例如遺傳密碼之簡併性、剪接等,所以編碼本揭露之抗體及抗原結合片段之多核苷酸可擁有不同的核苷酸序列,同時仍編碼相同的抗體及抗原結合片段。
在一些具體實施例中,多核苷酸包含下列者或由下列者組成:與如SEQ ID NO: 81、82、91、92、100、101、109、110、119、120、123、127、130、133、136、140、144、148、152、156、159、180、182、184、187、189、191、192、195、196、200、203、206、209、211、213、215、217、219、221、223、224、227、230、233、234、237、240、242、244、246、248、250、252、253、256、259、261、262、263、265、268、271、276、278、281、285、及289中之一或多者,特別是SEQ ID NO: 123及159之核酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之核酸序列。在更特定具體實施例中,單一多核苷酸包含下列者或由下列者組成:與如SEQ ID NO: 81、91、100、109、119、123、127、130、133、136、140、144、152、180、182、184、187、189、191、196、200、203、206、209、211、213、215、217、219、221、223、262、263、265、及268中之一或多者及SEQ ID NO: 82、92、101、110、120、159、192、195、224、227、230、233、234、237、240、242、244、246、248、250、252、253、256、259、261、271、276、278、281、285、及289中之一或多者,特別是SEQ ID NO: 123及159之核酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之核酸序列。在其他更特定具體實施例中,提供至少二個多核苷酸,其中第一多核苷酸包含下列者或由下列者組成:與如SEQ ID NO: 81、91、100、109、119、123、127、130、133、136、140、144、152、180、182、184、187、189、191、196、200、203、206、209、211、213、215、217、219、221、223、262、263、265、及268中之一或多者,特別是SEQ ID NO: 123之核酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之核酸序列及第二多核苷酸包含下列者或由下列者組成:與SEQ ID NO: 82、92、101、110、120、159、192、195、224、227、230、233、234、237、240、242、244、246、248、250、252、253、256、259、261、271、276、278、281、285、及289中之一或多者,特別是SEQ ID NO: 159之核酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之核酸序列。
在一些具體實施例中,單一多核苷酸或多核苷酸之組合包含二個核酸序列之組合或由二個核酸序列之組合組成,該等二個核酸序列與如SEQ ID NO: i) 81及82;ii) 91、180、182、184、187、189、或191中任一者及92、192、或195中任一者;iii) 100、196、200、203、206、209、211、213、215、217、219、221、或223中任一者及101、224、227、230、或233中任一者;iv) 109及110、234、237、240、242、244、246、248、250、252、253、256、259、或261中任一者;或v) 119、123、127、130、133、136、140、144、148、152、156、262、263、265、或268中任一者及120、159、271、276、178、281、285、或289中任一者,特別是123及159之核酸序列均具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性。
在任何目前所揭示之具體實施例中,多核苷酸可包含去氧核糖核酸(DNA)及核糖核酸(RNA)。在一些具體實施例中,RNA包含傳訊RNA(mRNA)。
亦提供載體,其中載體包含或含有如本文中所揭示之多核苷酸(例如編碼與二或更多種嚴重急性呼吸道症候群β型冠狀病毒結合的抗體或抗原結合片段的多核苷酸)。載體可包含本文中所揭示之任何一個或多個載體。在特定具體實施例中,提供包含編碼抗體或抗原結合片段、或其部分之DNA質體構築體的載體(例如所謂的「DMAb」,參見例如Muthumani
et al.,
J Infect Dis.214(3):369-378(2016);Muthumani
et al.,
Hum Vaccin Immunother 9:2253-2262 (2013)); Flingai
et al.,
Sci Rep.5:12616(2015); 及Elliott
et al.,
NPJ Vaccines18(2017),其編碼抗體之DNA構築體及相關使用之方法,包括其之投予係以引用方式併入本文中)。在某些具體實施例中,DNA質體構築體包含編碼抗體或抗原結合片段之重鏈及輕鏈(或VH及VL)之單一開放閱讀框,其中編碼重鏈之序列及編碼輕鏈之序列係視需要地被編碼蛋白酶切割位點之多核苷酸及/或被編碼自我剪切肽之多核苷酸隔開。在一些具體實施例中,抗體或抗原結合片段之取代基組分係由包含在單一質體中之多核苷酸所編碼。在其他具體實施例中,抗體或抗原結合片段之取代基組分係由包含在二或多個質體(譬如第一質體包含編碼重鏈、VH、或VH+CH之多核苷酸,第二質體包含編碼同族輕鏈、VL、或VL+CL之多核苷酸)中之多核苷酸所編碼。在某些具體實施例中,單一質體包含編碼來自本揭露之二或更多個抗體或抗原結合片段之重鏈及/或輕鏈之多核苷酸。例示性表現載體係pVax1,可得自Invitrogen®。本揭露之DNA質體可藉由例如電穿孔(例如肌內電穿孔)、或用適當的配方(例如玻尿酸酶)遞送至個體。
在另一個態樣中,本揭露亦提供表現根據本揭露之抗體或抗原結合片段之宿主細胞;或包含或含有根據本揭露之載體或多核苷酸。
此類細胞之實施例包括但不限於真核細胞,例如酵母細胞、動物細胞、昆蟲細胞、植物細胞;及原核細胞,包括大腸桿菌。在一些具體實施例中,細胞係哺乳動物細胞。在某些此類具體實施例中,細胞係哺乳動物細胞系,諸如CHO細胞(例如DHFR-CHO細胞(Urlaub
et al., PNAS 77:4216(1980))、人類胚胎腎細胞(例如HEK293T細胞)、PER.C6細胞、Y0細胞、Sp2/0細胞。NS0細胞、人類肝細胞,例如Hepa RG細胞、骨髓瘤細胞或融合瘤細胞。哺乳動物宿主細胞系之其他實施例包括小鼠塞特利氏細胞(sertoli cell)(例如TM4細胞);藉由SV40(COS-7)轉化之猴腎CV1系;幼齡倉鼠腎細胞(BHK);非洲綠猴腎細胞(VERO-76);猴腎細胞(CV1);人類子宮頸癌細胞(HELA);人類肺細胞(W138);人類肝細胞(Hep G2);犬腎細胞(MDCK;水牛鼠肝細胞(BRL 3A);小鼠乳腺腫瘤(MMT 060562);TRI細胞;
MRC5細胞;及FS4細胞。適用於抗體生產之哺乳動物宿主細胞系亦包括於例如Yazaki and Wu,
Methods in Molecular Biology, Vol. 248(B. K. C. Lo, ed., Humana Press, Totowa, N.J.), pp. 255-268(2003)中所述者。
在某些具體實施例中,宿主細胞係原核細胞,諸如大腸桿菌。肽在諸如大腸桿菌之原核細胞中之表現係十分成熟的(參見例如Pluckthun, A.
Bio/Technology 9:545-551 (1991))。舉例而言,可在細菌中生產抗體,特別是當不需要醣基化及Fc效應子功能時。對於在細菌中表現抗體片段及多肽,參見例如美國專利第5,648,237號;第5,789,199號;及第5,840,523號。
在特定具體實施例中,細胞可用表現載體根據本說明以載體進行轉染。術語「轉染(transfection)」係是指將核酸分子(諸如DNA或RNA(例如mRNA)分子)引入細胞中,例如引入到真核細胞中。在本說明之上下文中,術語「轉染」涵蓋熟習此技藝者已知用於將核酸分子引入到細胞中,諸如引入到真核細胞中,包括引入到哺乳動物細胞中之任何方法。此類方法涵蓋,例如電穿孔、脂質轉染(例如基於陽離子脂質及/或脂質體)、磷酸鈣沉澱、基於奈米粒子之轉染、基於病毒之轉染、或基於陽離子聚合物(諸如DEAE-葡聚糖或聚乙烯亞胺)之轉染等。在某些具體實施例中,引入係非病毒的。
再者,本揭露之宿主細胞可用根據本揭露之載體穩定或暫時轉染,例如以用於根據本揭露表現抗體、或其抗原結合片段。在此類具體實施例中,細胞可用如本文中所述之載體穩定轉染。替代地,如本文中所揭示,細胞可用編碼抗體或抗原結合片段的根據本揭露之載體暫時轉染。在任何目前所揭示之具體實施例中,多核苷酸對於宿主細胞可為異源的。
因此,本揭露亦提供異源表現本揭露之抗體或抗原結合片段的重組宿主細胞。舉例而言,細胞可為與自其獲得完全或部分抗體之物種不同的物種(例如表現人類抗體或經工程改造之人類抗體的CHO細胞)。在一些具體實施例中,宿主細胞之細胞類型本質上不表現抗體或抗原結合片段。再者,宿主細胞可對抗體或抗原結合片段賦予不存在於抗體或抗原結合片段之原生狀態中(或於抗體或抗原結合片段工程改造自或衍生自之親代抗體之原生狀態中)之轉譯後修飾(PTM;例如醣基化或岩藻醣基化)。此種PTM可能導致功能上的差異(例如減少免疫原性)。因此,藉由如本文中所揭示之宿主細胞所生產之本揭露之抗體或抗原結合片段可包括一個或多個與其原生狀態之抗體(或親代抗體)不同的轉譯後修飾(例如由CHO細胞生產之人類抗體可包含更多的與當自人類中單離及/或由原生人類B細胞或血漿細胞所生產時的抗體不同的轉譯後修飾)。
可用於表現本揭露之結合蛋白質之昆蟲細胞為所屬技術領域已知的,且包括例如,草地貪夜蛾(
Spodoptera frugipera)Sf9細胞、BTI-TN5B1-4細胞中之粉紋夜蛾(Trichoplusia)、及草地貪夜蛾SfSWT01「Mimic
TM」細胞。參見例如Palmberger
et al.,
J. Biotechnol.152(3-4):160-166(2011)。已經鑑別出許多桿狀病毒株,該等可與昆蟲細胞搭配使用,特別是用於草地貪夜蛾細胞之轉染。
真核微生物(諸如絲狀真菌或酵母)亦是用於選殖或表現編碼蛋白質之載體的合適宿主,且包括具有「人源化」醣基化途徑之真菌及酵母菌株,導致生產具有部分或完全人類醣基化模式之抗體。參見Gerngross,
Nat. Biotech.22: 1409-1414(2004); Li
et al.,
Nat. Biotech.24:210-215 (2006)。
植物細胞亦可利用作為表現本揭露之結合蛋白之宿主。舉例而言,PLANTIBODIES™技術(描述於例如美國專利第5,959,177號;第6,040,498號;第6,420,548號;第7,125,978號;及第6,417,429號)採用基因轉殖植物來生產抗體。
在某些實施例中,宿主細胞包含哺乳動物細胞。在特定具體實施例中,宿主細胞係CHO細胞、HEK293細胞、PER.C6細胞、Y0細胞、Sp2/0細胞、NS0細胞、人類肝細胞、骨髓瘤細胞、或融合瘤細胞。
在相關態樣中,本揭露提供產生抗體或抗原結合片段之方法,其中該方法包含在足以產生抗體、或抗原結合片段之條件及時間下培養本揭露之宿主細胞。舉實例而言,可用於單離及純化重組產生的抗體之方法可包括自合適的宿主細胞/載體系統獲得上清液,該宿主細胞/載體系統將重組抗體分泌到培養基中,然後使用可商購的過濾器濃縮培養基。濃縮後,可將濃縮物施用於單一合適的純化基質或一系列合適的基質,例如親和力基質或離子交換樹脂。可採用一或多個逆相HPLC步驟來進一步純化重組多肽。當自其天然環境中單離免疫原時,亦可採用此等純化方法。大規模生產本文中所述之一或多個單離/重組抗體之方法包括批次細胞培養,其經監測及控制以維持適當的培養條件。可溶性抗體之純化可根據本文中所述及所屬技術領域中已知之方法執行,且與國內及國外監管機構之法律及準則相符。
組成物 本文亦提供組成物,其單獨或以任何組合包含目前所揭示之抗體、抗原結合片段、多核苷酸、載體、或宿主細胞中任一者或多者,且可進一步包含醫藥上可接受之載體、賦形劑或稀釋劑。載體、賦形劑、及稀釋劑在本文中進一步詳細討論。
在某些具體實施例中,組成物包含根據本揭露之二或更多個不同的抗體或抗原結合片段。在某些具體實施例中,組合中使用之抗體或抗原結合片段各自獨立地具有下列特性中之一或多者:中和一種、二種、三種、四種、五種、或更多種天然存在的嚴重急性呼吸道症候群β型冠狀病毒變體;不與彼此競爭棘蛋白結合;結合不同的嚴重急性呼吸道症候群β型冠狀病毒棘蛋白表位;減少對嚴重急性呼吸道症候群β型冠狀病毒之抗性的形成;當組合時,減少對嚴重急性呼吸道症候群β型冠狀病毒之抗性的形成;有效地中和一種、二種、三種、四種、五種或更多種活的嚴重急性呼吸道症候群β型冠狀病毒;當組合使用時,對中和一種、二種、三種、四種、五種或更多種或更多種活的嚴重急性呼吸道症候群β型冠狀病毒展現加成效應或協同效應;展現效應子功能;在感染之一或多種相關動物模式中具有保護性;能夠足量產生以供大規模生產。
在某些具體實施例中,組成物包含根據本揭露之二或更多個不同的抗體或抗原結合片段。在某些具體實施例中,第一抗體或抗原結合片段及第二抗體或抗原結合片段可A)均為S3A3的抗體或抗原結合片段、與S3A3具有足夠的CDR、VH、及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 23之VH序列及如SEQ ID NO: 27之VL序列,ii)如於SEQ ID NO: 23及27中所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 24至26(H1至H3)及28至30(L1至L3)中所述之CDR;B)均為S3A19的抗體或抗原結合片段、與S3A19具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 31、35、36或43中任一者之VH序列及如SEQ ID NO: 37之VL序列,iii)如於SEQ ID NO: 31、35、36、或43中任一者及SEQ ID NO: 37所述之CDR,其係根據本文中所揭示之任何編號系統,或如於SEQ ID NO: 32至34(H1至H3)及37至40(L1至L3)中所述之CDR;C)均為S3I2的抗體或抗原結合片段、與S3I2具有足夠的CDR、VH、及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 83、179、181、183、185、188、或190中任一者之VH序列及如SEQ ID NO: 87或194中任一者之VL序列,ii)如於SEQ ID NO: 83、179、181、183、185、188、或190中任一者,及SEQ ID NO: 87或193中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 84(H1)、85(H2)、及86或186(H3),及88或194(L1)、89(L2)、及90(L3)中所述之CDR;D)均為S3O13的抗體或抗原結合片段、與S3O13具有足夠的CDR、VH、及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者之VH序列及如SEQ ID NO: 97、225、228、或231中任一者之VL序列,ii)如於SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者及SEQ ID NO: 97、225、228、或231中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 94、198、或208(H1)、95(H2)、及96、199、202、或205(H3),及98、226、229、或232(L1)、39(L2)、及99(L3)中所述之CDR;E)均為S3L17的抗體或抗原結合片段、與S3L17具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者之VH序列及如SEQ ID NO: 105、254、257、或260中任一者之VL序列,ii)如於SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者及SEQ ID NO: 105、254、257、或260中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 103(H1)、85(H2)、及104、236、或239(H3),及106或255(L1)、107(L2)、及108或258(H3)中所述之CDR;F)均為S2V29(或S2V29a或S2V29b兩者)的抗體或抗原結合片段、與S2V29具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者之VH序列及如SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者之VL序列,ii)如於SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 112(H1)、113 126、129、132、135、138、142、146、150、154、267、或270(H2)、及114、139、143、147、151、或155(H3)及116、273、或283(L1)、117、274、或287(L2)、及118、122、158、275、280、284、288、或192(L3)中所述之CDR;G)為根據A)、B), C)、D)、E)、或F)之抗體或抗原結合片段及根據A)、B)、C)、D)、E)、或F)之不同的抗體或抗原結合片段。
在某些具體實施例中,組成物包含根據本揭露之二或更多個不同的抗體或抗原結合片段。在某些具體實施例中,第一抗體或抗原結合片可為A) S3A3的抗體或抗原結合片段、與S3A3具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 23之VH序列及如SEQ ID NO: 27之VL序列,ii)如於SEQ ID NO: 23及27中所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 24至26(H1至H3)及28至30(L1至L3)中所述之CDR;B) S3A19的抗體或抗原結合片段、與S3A19具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 31、35、36或43中任一者之VH序列及如SEQ ID NO: 37之VL序列,iii)如於SEQ ID NO: 31、35、36、或43中任一者及SEQ ID NO: 37所述之CDR,其係根據本文中所揭示之任何編號系統,或如於SEQ ID NO: 32至34(H1至H3)及37至40(L1至L3)中所述之CDR;C) S3I2的抗體或抗原結合片段、與S3I2具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 83、179、181、183、185、188、或190中任一者之VH序列及如SEQ ID NO: 87或194中任一者之VL序列,ii)如於SEQ ID NO: 83、179、181、183、185、188、或190中任一者,及SEQ ID NO: 87或193中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 84(H1)、85(H2)、及86或186(H3)及88或194(L1)、89(L2)、及90(L3)中所述之CDR;D) S3O13的抗體或抗原結合片段、與S3O13具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者之VH序列及如SEQ ID NO: 97、225、228、或231中任一者之VL序列,ii)如於SEQ ID NO: 93、197、201、204、207、210、212、214、216、218、220、或222中任一者及SEQ ID NO: 97、225、228、或231中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 94、198、或208(H1)、95(H2)、及96、199、202、或205(H3),及98、226、229、或232(L1)、39(L2)、及99(L3)中所述之CDR;E) S3L17的抗體或抗原結合片段、與S3L17具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者之VH序列及如SEQ ID NO: 105、254、257、或260中任一者之VL序列,ii)如於SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者及SEQ ID NO: 105、254、257、或260中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 103(H1)、85(H2)、及104、236、或239(H3),及106或255(L1)、107(L2)、及108或258(H3)中所述之CDR;F) S2V29(或S2V29a或S2V29b兩者)的抗體或抗原結合片段、與S2V29具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者之VH序列及如SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者之VL序列,ii)如於SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 112(H1)、113 126、129、132、135、138、142、146、150、154、267、或270(H2)、及114、139、143、147、151、或155(H3)及116、273、或283(L1)、117、274、或287(L2)、及118、122、158、275、280、284、288、或192(L3)中所述之CDR;且第二抗體或抗原結合片段可為索托韋單抗(sotrovimab)、S2K146、S2X259、S2X324、S2X324-v3.1、或S309或其抗原結合片段,特別是具有:具有SEQ ID NO: 14之胺基酸序列之VH及具有:具有SEQ ID NO: 15之胺基酸序列之VL的抗體或抗原結合片段、具有:具有SEQ ID NO: 16之胺基酸序列之VH及具有:具有SEQ ID NO: 17之胺基酸序列之VL的抗體或抗原結合片段、具有:具有SEQ ID NO: 18之胺基酸序列之VH及具有:具有SEQ ID NO: 19之胺基酸序列之VL的抗體或抗原結合片段、具有:具有SEQ ID NO: 20之胺基酸序列之VH及具有:具有SEQ ID NO: 22之胺基酸序列之VL的抗體或抗原結合片段、具有:具有SEQ ID NO: 21之胺基酸序列之VH及具有:具有SEQ ID NO: 22之胺基酸序列之VL的抗體或抗原結合片段、或具有:具有SEQ ID NO: 41之胺基酸序列之VH及具有:具有SEQ ID NO: 42之胺基酸序列之VL的抗體或抗原結合片段、或具有如根據本文中所揭示之任何編號系統之任何前述VH及VL組合中發現的CDR的抗體或抗原結合片段。在特定具體實施例中,第二抗體或其抗原結合片段可為索托韋單抗或S2K146。
在一些具體實施例中,組成物可包含或可包含:包含下列者或由下列者組成之抗體或抗原結合片段:A)第一抗體或抗原結合片段,其可為S3L17的抗體或抗原結合片段、與S3L17具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者之VH序列及如SEQ ID NO: 105、254、257、或260中任一者之VL序列,ii)如於SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者及SEQ ID NO: 105、254、257、或260中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 103(H1)、85(H2)、及104、236、或239(H3),及106或255(L1)、107(L2)、及108或258(H3)中所述之CDR;及B)第二抗體或抗原結合片段,其可為S2V29(或S2V29a或S2V29b兩者)的抗體或抗原結合片段、與S2V29具有足夠的CDR、VH,及/或VH同一性以賦予類似特異性結合的抗體、或其片段,諸如包含下列者:i)如SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者之VH序列及如SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者之VL序列,ii)如於SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者所述之CDR,其係根據本文中所揭示之任何編號系統,或iii)如於SEQ ID NO: 112(H1)、113 126、129、132、135、138、142、146、150、154、267、或270(H2)、及114、139、143、147、151、或155(H3)及116、273、或283(L1)、117、274、或287(L2)、及118、122、158、275、280、284、288、或192(L3)中所述之CDR。
在一些具體實施例中,提供之組成物包含第一抗體或抗原結合片段及第二抗體或抗原結合片段(多特異性(例如雙特異性)抗體或抗原結合片段)或提供之組合療法包含第一抗體或抗原結合片段及第二抗體或抗原結合片段,其中該第一抗體或抗原結合片段及第二抗體或抗原結合片段分別包含、或該多特異性抗體或抗原結合片段包含CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3、及視需要地VH及VL,其係根據:(i)任何S3A3抗體及任何S3A19抗體;(ii)任何S3A3抗體及索托韋單抗;(iii)任何S3A3抗體及S2K146;(iv)任何S3A3抗體及S2X259;(v)任何S3A3抗體及任何S2X324抗體;(vi)任何S3A3抗體及S309;(vi)任何S3A19抗體及索托韋單抗;(vii)任何S3A19抗體及S2K146;(viii)任何S3A19抗體及S2X259;(ix)任何S3A19抗體及任何S2X324抗體;(x)任何S3A19抗體及S309;(xi)任何S3I2抗體及任何S3A3抗體;(xii)任何S3I2抗體及任何S3A19抗體;(xiii)任何S3I2抗體及索托韋單抗;(xiv)任何S3I2抗體及S2K146;(xv)任何S3I2抗體及S2X259;(xvi)任何S3I2抗體及任何S2X324抗體;(xvii)任何S3I2抗體及S309;(xviii)任何S3I2抗體及任何S3O13抗體;(xix)任何S3I2抗體及任何S3L17抗體;(xx)任何S3O13抗體及任何S3A3抗體;(xxi)任何S3O13抗體及任何S3A19抗體;(xxii)任何S3O13抗體及索托韋單抗;(xxiii)任何S3O13抗體及S2K146;(xxiv)任何S3O13抗體及S2X259;(xxv)任何S3O13抗體及任何S2X324抗體;(xxvi)任何S3O13抗體及S309;(xxvii)任何S3O13抗體及任何S3L17抗體;(xxviii)任何S3L17抗體及任何S3A3抗體;(xxix)任何S3L17抗體及任何S3A19抗體;(xxx)任何S3L17抗體及索托韋單抗;(xxxi)任何S3L17抗體及S2K146;(xxxii)任何S3L17抗體及S2X259;(xxxiii)任何S3L17抗體及任何S2X324抗體;(xxxiv)任何S3L17抗體及S309;(xxxv)任何S2V29抗體及任何S3A3抗體;(xxxvi)任何S2V29抗體及任何S3A19抗體;(xxxvii)任何S2V29抗體及索托韋單抗;(xxxviii)任何S2V29抗體及S2K146;(xxxix)任何S2V29抗體及S2X259;(xl)任何S2V29抗體及任何S2X324抗體;(xli)任何S2V29抗體及S309;(lxlii)任何S2V29抗體及任何S3L17抗體;及(xliii)任何S2V29抗體及任何S3O13抗體。
在某些具體實施例中,組成物包含第一載體、及第二載體,該第一載體包含第一質體及該第二載體包含第二質體,其中該第一質體包含編碼抗體或其抗原結合片段之重鏈、VH、或VH+CH之多核苷酸,且第二質體包含編碼抗體或其抗原結合片段之同源輕鏈、VL、或VL+CL之多核苷酸。在某些具體實施例中,組成物包含與合適的遞送媒劑或載劑偶合之多核苷酸(例如mRNA)。用於向人類個體投予之例示性媒劑或載劑包括脂質或脂質衍生之遞送媒劑,諸如脂質體、固體脂質奈米粒子、油性懸浮液、次微米脂質乳劑、脂質微氣泡(lipid microbubble)、逆相脂質微胞(inverse lipid micelle)、耳蝸脂質體(cochlear liposome)、脂質微管、脂質微柱(lipid microcylinder)、或脂質奈米粒子(LNP)或奈米級平台(參見例如Li
et al. Wilery Interdiscip Rev. Nanomed Nanobiotechnol. 11(2):e1530 (2019))。用於設計適當的mRNA及調配mRNA-LNP並遞送該mRNA-LNP之原理、試劑及技術係描述於例如Pardi
et al.(
J Control Release 217345-351(2015));Thess
et al.(
Mol Ther 23: 1456-1464(2015));Thran
et al.(
EMBO Mol Med 9(10):1434-1448(2017);Kose
et al.(
Sci. Immunol.4eaaw6647 (2019);及Sabnis
et al.(
Mol. Ther. 26:1509-1519(2018))中,該等技術包括加帽、密碼子最佳化、核苷修飾、mRNA之純化、將mRNA併入到穩定的脂質奈米粒子(例如可離子化陽離子脂質/磷脂醯膽鹼/膽固醇/PEG-脂質;可離子化脂質:二硬脂醯基PC:膽固醇:聚乙二醇脂質)中、及該mRNA-LNP之皮下、肌內、皮內、靜脈內、腹膜內、及氣管內投予,並以引用方式併入本文中。
方法及用途 本文亦提供將本揭露之抗體或抗原結合片段、核酸、載體、細胞、或組成物用於診斷嚴重急性呼吸道症候群β型冠狀病毒感染(例如在人類個體中、或自人類個體獲得之樣本中)之方法。
診斷方法(例如體外、離體)可包括使抗體、抗體片段(例如抗原結合片段)與樣本接觸。此類樣本可自個體中單離,例如取自下列之單離之組織樣本,例如:鼻道、鼻竇腔、唾液腺、肺、肝、胰、腎、耳朵、眼睛、胎盤、消化道、心、卵巢、腦下垂體、腎上腺、甲狀腺、腦、皮膚或血液。診斷之方法亦可包括偵測抗原/抗體複合物,特別是在抗體或抗體片段與樣品接觸後。此種偵測步驟可在工作台上執行,亦即不會與人體或動物身體有任何接觸。偵測方法之實施例係所屬技術領域中具有通常知識者眾所周知的且包括例如ELISA(酶聯免疫吸附檢定法),包括直接式、間接式及三明治式ELISA。
本文亦提供使用本揭露之抗體或抗原結合片段、或包含其之組成物治療個體之方法,其中該個體患有、據信患有由嚴重急性呼吸道症候群β型冠狀病毒所致之感染、或處於患有由嚴重急性呼吸道症候群β型冠狀病毒所致之感染之風險中。「治療(treat/treatment)」或「改善(ameliorate)」係指對個體(例如人類或非人類哺乳動物,諸如靈長類、馬、貓、狗、山羊、小鼠、或大鼠)之疾病、病症或病況之醫療管理。一般而言,包含本揭露之抗體或組成物之適當劑量或治療方案係以足以引發治療或預防效益之量投予。治療或預防(prophylactic/preventive)效益包含改善臨床預後;減少或減輕與疾病相關之症狀;降低症狀發生;改善生活品質;更長的無病狀態;減低疾病程度、穩定疾病狀態;延遲或預防疾病進展;緩解;存活;延長存活期;或其任何組合。在某些實施方式中,治療或預防效益包括減少或預防嚴重急性呼吸道症候群β型冠狀病毒感染之住院治療(亦即以統計學上顯著之方式)。在某些具體實施例中,治療或預防效益包括減少嚴重急性呼吸道症候群β型冠狀病毒感染之住院治療時間(亦即以統計學上顯著之方式)。在某些具體實施例中,治療或預防效益包括對呼吸干預,諸如插管及/或使用呼吸器裝置之需求減少或消除。在某些具體實施例中,治療或預防效益包括逆轉晚期疾病病理及/或減少死亡率。
本揭露之抗體、抗原結合片段、多核苷酸、載體、宿主細胞、或組成物之「治療有效量」或「有效量」係指足以產生治療效果之組成物或分子之量,該治療效果包括以統計學上顯著之方式改善臨床預後;減少或減輕與疾病相關之症狀;降低症狀發生;改善生活質量;更長的無病狀態;減低疾病程度、穩定疾病狀態;延遲疾病進展;緩解;生存;或延長生存期。當提及單獨投予個別活性成分時,治療有效量係指該成分或單獨表現該成分之細胞之效應。當提及組合時,無論是連續、依序或同時投予,治療有效量係指產生治療效應之活性成分、或組合輔助活性成分與表現活性成分之細胞的組合量。組合可包含,例如特異性結合嚴重急性呼吸道症候群β型冠狀病毒抗原的兩種不同抗體,該等抗原在某些具體實施例中可為相同或不同的嚴重急性呼吸道症候群β型冠狀病毒抗原,及/或可包含相同或不同的表位。
因此,在某些具體實施例中,提供用於治療個體之嚴重急性呼吸道症候群β型冠狀病毒感染之方法,其中該等方法包含向個體投予有效量的本文中所揭示之抗體、抗原結合片段、多核苷酸、載體、宿主細胞、或組成物。
可藉由本揭露所治療之個體通常係人類及其他靈長類個體,例如用於獸醫醫學目的之猴子及猿類。根據本揭露亦可治療其他模式生物,諸如小鼠及大鼠。在任何前述具體實例中,個體可為人類個體。個體可為男性或女性,且可為任何合適的年齡,包括嬰兒、少年、青少年、成人、及老年個體。
據信許多準則會造成與嚴重急性呼吸道症候群β型冠狀病毒感染相關之嚴重症狀或死亡之高風險。此等包括但不限於年齡、職業、一般健康狀況、既往健康狀況、及生活方式。在一些具體實施例中,根據本揭露治療之個體包含一或多個風險因子。
在某些具體實施例中,根據本揭露治療之人類個體係嬰兒、兒童、年輕人、中年人、或老年人。在某些具體實施例中,根據本揭露治療之人類個體係小於1歲、或係1至5歲、或在5至125歲之間(例如5、10、15、20、25、30、35、40、45、50、55、60、65、70、75、80、85、90、95、100、105、110、115、或125歲,包括其中或其間之任何及所有年齡)。在某些具體實施例中,根據本揭露治療之人類個體係0至19歲、20至44歲、45至54歲、55至64歲、65至74歲、75至84歲、或85歲、或更老。中年人,且尤其是高齡者據信特別危險。在特定具體實施例中,人類個體係45至54歲、55至64歲、65至74歲、75至84歲、或85歲、或更老。在一些具體實施例中,人類個體係男性。在一些具體實施例中,人類個體係女性。
在某些具體實施例中,根據本揭露治療之人類個體係療養院或長期照護機構之住民、係安寧照護工作者、係醫療照護提供者或醫療照護工作者、係第一現場應急人員(first responder)、係經診斷有或疑似患有嚴重急性呼吸道症候群β型冠狀病毒感染之個體的家庭成員或有其他密切接觸者、係超重或臨床上肥胖者、係吸煙者或曾經係吸煙者、患有或曾經患有慢性阻塞性肺疾病(COPD)者、係氣喘(例如患有中度至重度氣喘)者、患有自體免疫疾病或病況(例如糖尿病)者、及/或患有免疫系統受損或耗竭(例如由於AIDS/HIV感染、癌症(諸如血症)、淋巴細胞耗竭(lymphodepleting)療法(例如化學療法)、骨髓或器官移植、或遺傳免疫病況)者、患有慢性肝病者、患有心血管疾病者、患有肺部或心臟缺陷者、工作或長時間與其他人緊密接觸(諸如在工廠、運輸中心、醫院環境等)者。
在某些實施方式中,根據本揭露治療之個體已接受嚴重急性呼吸道症候群β型冠狀病毒疫苗且該疫苗例如藉由個體之疫苗接種後感染或症狀、藉由臨床診斷或科學或監管準則被判定為無效的。
在某些具體實施例中,治療係作為暴露前後(peri-exposure)預防投予。在某些具體實施例中,治療係向患有輕度至中度疾病,可在門診環境中之個體投予。在某些具體實施例中,治療係向患有中度至重度疾病,諸如需要住院之個體投予。
投予目前所揭示之組成物之典型途徑因此包括但不限於口服、局部、經皮、吸入、腸胃外、舌下、口頰、直腸、陰道、及鼻內。如本文中所使用之術語「腸胃外(parenteral)」包括皮下注射、靜脈內、肌內、胸骨內注射或輸注技術。在某些具體實施例中,投予包含藉由選自下列的途徑投予:口服、靜脈內、腸胃外、胃內、胸膜內、肺內、直腸內、皮內、腹膜內、腫瘤內、皮下、局部、經皮、腦池內、鞘內、鼻內、及肌內。在特定具體實施例中,方法包含向個體口服投予抗體、抗原結合片段、多核苷酸、載體、宿主細胞、或組成物。
調配根據本發明之某些具體實施例之醫藥組成物,以使含於其中之活性成分在向患者投予該組成物後為生物可用的。將向個體或患者投予之組成物可呈一或多個劑量單位之形式,其中例如錠劑可為單一劑量單位,且本文中所述之呈氣霧劑形式之抗體或抗原結合之容器可容納複數個劑量單位。製備此類劑型之實際方法對所屬技術領域中具有通常知識者為已知的或將顯而易見的;例如參見Remington: The Science and Practice of Pharmacy, 20th Edition(Philadelphia College of Pharmacy and Science, 2000)。待投予之組成物將在任何情況下含有有效量的本揭露之抗體或抗原結合片段、多核苷酸、載體、宿主細胞、或組成物,以用於根據本文中之教示治療感興趣之疾病或病況。
組成物可呈固體或液體之形式。在一些具體實施例中,一或多種載劑係微粒,使得組成物例如呈錠劑或粉劑形式。一或多種載劑可為液體,且組成物為例如口服油、可注射液體或可用於例如吸入投予之氣霧劑。當意欲口服投予時,醫藥組成物較佳地呈固體或液體形式,其中半固體、半液體、懸浮液及凝膠形式係包括在本文中視為固體或液體之形式內。
作為用於口服投予之固體組成物,醫藥組成物可經調配成粉劑、顆粒劑、壓縮錠劑、丸劑、膠囊、口嚼錠、粉片等。此種固體組成物將一般含有一或多種惰性稀釋劑或可食用載劑。此外,可存在下列中之一或多者:黏合劑,諸如羧甲基纖維素、乙基纖維素、微晶纖維素、黃蓍膠或明膠;賦形劑,諸如澱粉、乳糖或糊精;崩解劑,諸如海藻酸、海藻酸鈉、澱粉羥基乙酸鈉(Primogel)、玉米澱粉等;潤滑劑,諸如硬脂酸鎂或氫化植物油(Sterotex);助滑劑,諸如膠態二氧化矽;甜味劑,諸如蔗糖或糖精;調味劑,諸如薄荷、水楊酸甲酯或柑橘調味劑;及著色劑。當組成物呈膠囊之形式,例如明膠膠囊時,除以上類型之材料之外,其亦可含有諸如聚乙二醇或油之液體載劑。
組成物可呈液體之形式,例如酏劑、糖漿、溶液、乳劑或懸浮液。作為二個實施例,液體可用於口服投予或用於藉由注射遞送。當意欲用於口服投予時,除本發明化合物之外,較佳的組成物亦含有甜味劑、防腐劑、染料/著色劑及增味劑中之一或多者。在意欲藉由注射投予之組成物中,可包括界面活性劑、防腐劑、濕潤劑、分散劑、懸浮劑、緩衝劑、穩定劑及等張劑中之一或多者。
液體醫藥組成物,無論其為溶液、懸浮液或其他類似形式,均可包括以下佐劑中之一或多者:無菌稀釋劑,諸如注射用水、鹽水溶液(較佳地為生理鹽水)、林格氏溶液(Ringer's solution)、等張氯化鈉、非揮發性油(諸如可充當溶劑或懸浮介質之合成單甘油酯或二甘油酯)、聚乙二醇、甘油、丙二醇或其他溶劑;抗菌劑,諸如苯甲醇或對羥基苯甲酸甲酯;抗氧化劑,諸如抗壞血酸或亞硫酸氫鈉;螯合劑,諸如乙二胺四乙酸;緩衝劑,諸如乙酸鹽、檸檬酸鹽或磷酸鹽;及用於張力調節之劑,諸如氯化鈉或右旋糖。腸胃外製劑可封裝於由玻璃或塑膠製成之安瓿、拋棄式注射器或多劑量小瓶中。生理鹽水係較佳的佐劑。可注射醫藥組成物較佳地係無菌的。
意欲用於腸胃外或口服投予之液體組成物應含有一定量之如本文中所揭示之抗體或抗原結合片段以使得獲得合適的劑量。一般而言,此量係組成物中之至少0.01%的抗體或抗原結合片段。當意欲用於口服投予時,此量可在組成物之重量之0.1%與約70%之間變化。某些口服醫藥組成物含有在約4%與約75%之間的抗體或抗原結合片段。在某些具體實施例中,製備根據本發明之醫藥組成物及製劑以使腸胃外劑量單位在稀釋前含有在0.01至10重量%之間的抗體或抗原結合片段。
組成物可意欲用於局部投予,在該情況下,載劑可合適地包含溶液、乳劑、軟膏或凝膠基質。舉例而言,基質可包含以下中之一或多者:石蠟脂、羊毛脂、聚乙二醇、蜂蠟、礦物油、稀釋劑(諸如水及醇)、及乳化劑及穩定劑。增稠劑可存在於組成物中以用於局部投予。若意欲用於經皮投予,則組成物可包括經皮貼片或離子導入(iontophoresis)裝置。醫藥組成物可意欲用於呈例如栓劑之形式的直腸投予,該栓劑將在直腸中融化並釋放出藥物。用於直腸投予之組成物可含有油性基質作為合適的非刺激性賦形劑。合適的基質包括但不限於羊毛脂、可可豆脂及聚乙二醇。
組成物可包括改變固體或液體劑量單位之物理形式的各種材料。舉例而言,組成物可包括圍繞活性成分形成包覆殼體之材料。形成包覆殼體的材料一般為惰性,且可選自例如糖、蟲膠、及其他腸溶包覆劑。替代地,活性成分可包裝在明膠膠囊中。呈固體或液體形式之組成物可包括與本揭露之抗體或抗原結合片段結合且藉此幫助遞送化合物之劑。可起此能力作用的合適的劑包括單株或多株抗體、一或多種蛋白質或脂質體。組成物可基本上由可作為氣霧劑投予之劑量單位組成。術語氣霧劑(aerosol)用於表示範圍為膠體本質之彼等系統至由加壓封裝組成之系統的多種系統。可藉由液化或壓縮氣體或藉由施配活性成分的合適的泵系統來遞送。氣霧劑可以單相、雙相、或三相系統形式遞送,以便遞送一或多種活性成分。氣霧劑之遞送包括必需容器、活化劑、閥門、子容器等,其在一起可形成套組。所屬技術領域中具有通常知識者在無需過度實驗之情況下即可判定較佳的氣霧劑。
應理解,本揭露內容之組成物亦涵蓋用於如本文中所述之多核苷酸的載劑分子(例如脂質奈米粒子、奈米級遞送平台等)。
醫藥組成物可藉由所屬醫藥技術領域中眾所周知之方法製備。舉例而言,意欲藉由注射投予之組成物可藉由將包含如本文中所述之抗體、其抗原結合片段、或抗體結合物及視需要地,鹽、緩衝液及/或穩定劑中之一或多者的組成物與無菌蒸餾水組合以形成溶液來製備。可添加界面活性劑以促進形成均質溶液或懸浮液。界面活性劑係與肽組成物非共價交互作用以促進抗體或其抗原結合片段在水性遞送系統中之溶解或均質懸浮的化合物。
一般而言,適當劑量及治療方案以足以提供治療及/或預防效益(諸如本文中所述,包括改善臨床預後(例如,腹瀉或相關脫水、或發炎之頻率、持續時間、或嚴重程度降低,或更長的無疾病及/或總存活期,或減少症狀嚴重程度)之量提供一或多個組成物。對於預防用途,劑量應足以預防與疾病或病症相關之疾病、延遲其發作、或減低其嚴重程度。根據本文中所述之方法所投予之組成物之預防效益可藉由執行臨床前(包括體外及體內動物研究)及臨床研究,並藉由適當的統計、生物學、及臨床方法及技術對自其獲得之數據進行分析來判定,其等全部均可由所屬技術領域中具有通常知識者容易地實踐。
組成物係以有效量投予(例如以治療嚴重急性呼吸道症候群β型冠狀病毒感染),該有效量將視多種因素而變化,包括所採用之特定化合物之活性;化合物之代謝穩定性及作用時間長度;個體之年齡、體重、一般健康狀況、性別、及飲食;投予模式及時間;排泄速率;藥物組合;特定病症或病況之嚴重程度;及個體正經受的療法。在某些具體實施例中,在根據本揭露之配方及方法投予療法之後,如相較於安慰劑治療或其他合適的對照個體,測試個體將展現與所治療之疾病或病症相關之一或多種症狀之約10%到至多約99%減少。
一般而言,抗體或抗原結合片段之治療有效日劑量係(對於70 kg哺乳動物)約0.001 mg/kg(亦即0.07 mg)至約100 mg/kg(亦即7.0 g);較佳地,治療有效劑量係(對於70 kg哺乳動物)約0.01 mg/kg(亦即0.7 mg)至約50 mg/kg(亦即3.5 g);更佳地,治療有效劑量係(對於70 kg哺乳動物)約1 mg/kg(亦即70 mg)至約25 mg/kg(亦即1.75 g)。對於本揭露之多核苷酸、載體、宿主細胞及相關組成物,治療有效劑量可不同於抗體或抗原結合片段的治療有效劑量。
如本文中所述之S2V29-v1.2抗體或其片段,特別是S2V29-v1.2-IgG1m17_Lamda或S2V29-v1.2-IgG1m17,1-LS抗體之年齡及/或體重相稱劑量之單一肌內(IM)投予可足以治療SARS-CoV-2感染或具有在三至六個月之間或至多六個月之預防效益。
在某些具體實施例中,方法包含向個體投予抗體、抗原結合片段、多核苷酸、載體、宿主細胞、或組成物2、3、4、5、6、7、8、9、10次、或更多次。
在某些具體實施例中,方法包含向個體投予抗體、抗原結合片段、或組成物複數次,其中第二次或連續投予係分別在第一次或前次投予後約6、約7、約8、約9、約10、約11、約12、約24、約48、約74、約96小時、或更長時間執行。
在某些具體實施例中,方法包含在個體受嚴重急性呼吸道症候群β型冠狀病毒感染之前投予至少一次的抗體、抗原結合片段、多核苷酸、載體、宿主細胞或組成物。
包含抗體、抗原結合片段、多核苷酸、載體、宿主細胞之組成物、或本揭露之組成物亦可與一或多種其他治療劑之投予同時、在其之前、或在其之後投予。此種組合療法可包括投予含有本發明之化合物及一或多種額外活性劑之單一醫藥劑量配方,以及投予包含呈自身獨立劑量配方之本揭露之抗體或抗原結合片段及各活性劑之組成物。舉例而言,如本文中所述之抗體或其抗原結合片段及其他活性劑可以單一口服劑量組成物(諸如錠劑或膠囊)一起向患者投予,或各劑係以獨立口服劑量配方投予。類似地,如本文中所述之抗體或其抗原結合片段及其他活性劑可以單一腸胃外劑量組成物(諸如鹽水溶液或其他生理上可接受之溶液)一起向患者投予,或各劑係以獨立腸胃外劑量配方投予。在使用獨立劑量配方之情況下,包含抗體或抗原結合片段及一或多種額外活性劑之組成物可以基本上同時,亦即並行地投予,或以分開地交錯時間,亦即依序及按任何順序投予;組合療法應理解為包括所有此等方案。
在某些具體實施例中,提供組合療法,其包含一或多種本揭露之抗嚴重急性呼吸道症候群β型冠狀病毒抗體(或一或多種核酸、宿主細胞、載體、或組成物)及一或多種消炎劑及/或一或多種抗病毒劑。在特定具體實施例中,一或多種消炎劑包含皮質類固醇,諸如例如地塞米松(dexamethasone)、潑尼松(prednisone)等。在一些具體實施例中,一或多種消炎劑包含細胞介素拮抗劑,諸如例如結合至IL6(諸如司妥昔單抗(siltuximab)),或結合至IL-6R(諸如托珠單抗(tocilizumab)),或結合至IL-1β、IL-7、IL-8、IL-9、IL-10、FGF、G-CSF、GM-CSF、IFN-γ、IP-10、MCP-1、MIP-1A、MIP1-B、PDGR、TNF-α、或VEGF的抗體。在一些具體實施例中,使用消炎劑,諸如來羅利單抗(leronlimab)、盧佐替尼(ruxolitinib)及/或阿那白滯素(anakinra)。在一些具體實施例中,一或多種抗病毒劑包含核苷酸類似物或核苷酸類似物前藥,諸如例如瑞德西韋(remdesivir)、索非布韋(sofosbuvir)、阿昔洛韋(acyclovir)、及齊多夫定(zidovudine)。在特定具體實施例中,抗病毒劑包含洛匹那韋(lopinavir)、利托那韋(ritonavir)、法匹拉韋(favipiravir)、或其任何組合。用於本揭露之組合療法的其他消炎劑包括非類固醇消炎藥(NSAIDS)。應瞭解,在此種組合療法中,一或多種抗體(或一或多種核酸、宿主細胞、載體、或組成物)及一或多種消炎劑及/或一或多種抗病毒劑可以任何順序及任何次序投予、或一起投予。
在一些具體實施例中,抗體(或一或多種核酸、宿主細胞、載體、或組成物)係向先前已接受過一或多種消炎劑及/或一或多種抗病毒劑之個體投予。在一些具體實施例中,一或多種消炎劑及/或一或多種抗病毒劑係向先前已接受過抗體(或一或多種核酸、宿主細胞、載體、或組成物)之個體投予。
在某些具體實施例中,提供組合療法,其包含二或更多種本揭露之抗嚴重急性呼吸道症候群β型冠狀病毒抗體。方法可包含向已接受過第二抗體之個體投予第一抗體,或可包含一起投予二或更多種抗體。舉例而言,在特定具體實施例中,提供方法,其包含向個體投予(a)第一抗體或抗原結合片段,當該個體已接受過第二抗體或抗原結合片段時;(b)第二抗體或抗原結合片段,當該個體已接受過第一抗體或抗原結合片段時;或(c)第一抗體或抗原結合片段,及第二抗體或抗原結合片段。
在相關態樣中,提供目前所揭示之抗體、抗原結合片段、載體、宿主細胞、及組成物之用途。
本揭露進一步提供套組,其包含本文中所揭示之任何抗體、抗原結合片段、多核苷酸、核酸、載體、或其他組成物中之一或多者。套組可進一步包括容器(諸如試管、小瓶、或注射器)、活化劑、閥、子容器、或使用說明書(諸如向個體投予)中之一或多者。
在某些具體實施例中,提供抗體、抗原結合片段、多核苷酸、載體、宿主細胞、或組成物,其係用於治療個體之嚴重急性呼吸道症候群β型冠狀病毒感染之方法中。
在某些具體實施例中,提供抗體、抗原結合片段、或組成物,其係用於製造或製備用於治療個體之嚴重急性呼吸道症候群β型冠狀病毒感染之藥物之方法中。
本揭露提供以下特定具體實施例:
具體實施例1. 一種抗體、或其抗原結合片段,其包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(A)(i)該CDRH1包含下列者或由下列者組成:如SEQ ID NO: 24之胺基酸序列、或其功能變體,該功能變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 25之胺基酸序列、或其功能變體,該功能變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 26之胺基酸序列、或其功能變體,該功能變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 28之胺基酸序列、或其功能變體,該功能變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 29之胺基酸序列、或其功能變體,該功能變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 30之胺基酸序列、或其功能變體,該功能變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,(B)(i)該CDRH1包含下列者或由下列者組成:如SEQ ID NO: 32之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 33之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 34之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 38之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 39之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 40之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,(C)(i)該CDRH1包含下列者或由下列者組成:如SEQ ID NO: 84之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 85之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 86或186中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 88或194中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 89之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 90之胺基酸序列、或其序列變體,該序列變體包含具有一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(D)(i)該CDRH1包含下列者或由下列者組成:如SEQ ID NO: 94、198、或208中任一者之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 95之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 96、199、202、或205中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 98、226、229、232中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 39之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 99之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(E)(i)該CDRH1包含下列者或由下列者組成:如SEQ ID NO: 103之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 85之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 104、236、或239中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 106或255中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 107之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 258之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;或(F)(i)該CDRH1包含下列者或由下列者組成:如SEQ ID NO: 112之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 113、126、129、132、135、138、142、146、150、154、267、或270中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 114、139、143、147、151、或155中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 116、273、或283中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 117、274、或287中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 118、122、158、275、280、284、288、或291中任一者之胺基酸序列、或其序列變體,該序列變體包含具有一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,
其中該取代視需要地係如表2或表3之取代,且其中該抗體或抗原結合片段能夠與嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。
具體實施例2. 一種抗體、或其抗原結合片段,其包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,該CDRH1、CDRH2、及CDRH3及該CDRL1、CDRL2、及CDRL3具有如下列之胺基酸序列:(A)分別為SEQ ID NO: 24至26及28至30;(B)分別為SEQ ID NO: 32至34及38至40;(C)分別為SEQ ID NO: 84至86或84、85及186及88至90或194、89、及90;(D)分別為SEQ ID NO: 94至96;198、95及96;208、95及96;94、95、及199;198、95及199;208、95、及199;94、95、及202;198、95、及205;208、95、及199;205、95、及202;或208、95、及205、及98、39、及99;226、39、及99;或229、39、及232;(E)分別為SEQ ID NO: 103、85、及104;103、85、及236;或103、85、及239、及106至108;106、107、及258;255、107、及108;或255、107、或258;及(F)分別為SEQ ID NO: 112至114;112、126、及114;112、129及114;112、132、及114;112、135、及114;112、138、及114;112、142、及114;112、146、及114;112、150、及114;112、154、及114;112、267、及114;112、270、及114;112、113、及139;112、126、及139;112、129及139;112、132、及139;112、135、及139;112、138、及139;112、142、及139;112、146、及139;112、150、及139;112、154、及139;112、267、及139;112、270、及139;112、113、及143;112、126、及143;112、129及143;112、132、及143;112、135、及143;112、138、及143;112、142、及143;112、146、及143;112、150、及143;112、154、及143;112、267、及143;112、270、及143;112、113、及147;112、126、及147;112、129及147;112、132、及147;112、135、及147;112、138、及147;112、142、及147;112、146、及147;112、150、及147;112、154、及147;112、267、及147;112、270、及147;112、113、及151;112、126、及151;112、129 及151;112、132、及151;112、135、及151;112、138、及151;112、142、及151;112、146、及151;112、150、及151;112、154、及151;112、267、及151;112、270、及151;112、113、及155;112、126、及155;112、129及155;112、132、及155;112、135、及155;112、138、及155;112、142、及155;112、146、及1551;112、150、及155;112、154、及155;112、267、及155;或112、270、及155;及116至118;116、274、及118;116、287、及118;116、117、及122;116、274、及122;116、287、及122;116、117、及158;116、274、及275;116、287、及275;116、117、及280;116、274、及280;116、287、及280;116、117、及284;116、274、及284;116、287、及284;116、117、及288;116、274、及288;116、287、及288;116、117、及291;116、274、及291;116、287、及291;273、117、及118;273、274、及118;273、287、及118;273、117、及122;273、274、及122;273、287、及122;273、117、及158;273、274、及275;273、287、及275;273、117、及280;273、274、及280;1273、287、及280;273、117、及284;273、274、及284;273、287、及284;273、117、及288;273、274、及288;273、287、及288;273、117、及291;273、274、及291;273、287、及291;283、117、118;283、274、及118;283、287、及118;283、117、及122;283、274、及122;283、287、及122;283、117、及158;283、274、及275;283、287、及275;283、117、及280;283、274、及280;283、287、及280;283、117、及284;283、274、及284;283、287、及284;283、117、及288;283、274、及288;283、287、及288;283、117、及291;283、274、及291;或283、287、及291。
具體實施例3. 如具體實施例1或2之抗體或抗原結合片段,其中該嚴重急性呼吸道症候群β型冠狀病毒係演化支1b(Clade 1b)嚴重急性呼吸道症候群β型冠狀病毒。
具體實施例4. 如具體實施例3之抗體或抗原結合片段,其中該嚴重急性呼吸道症候群β型冠狀病毒係SARS-CoV-2 WT、SARS-CoV-2 BA.1、RATG13、PANG/GD、或PAND/GX。
具體實施例5. 如具體實施例1至4中任一者之抗體或抗原結合片段,其中當表面醣蛋白在宿主細胞之細胞表面上表現及/或包含在病毒粒子上時,該抗體或抗原結合片段能夠與該表面醣蛋白結合。
具體實施例6. 如具體實施例1至5中任一者之抗體或抗原結合片段,其能夠與來自二或更多種(例如二種、三種、四種、五種、或更多種)嚴重急性呼吸道症候群β型冠狀病毒之表面醣蛋白結合。
具體實施例7. 如具體實施例1至6中任一者之抗體或抗原結合片段,其能夠在感染之體外模式中及/或在感染之體內動物模式中及/或在人類中中和由一或多種嚴重急性呼吸道症候群β型冠狀病毒所致之感染。
具體實施例8. 如具體實施例1至7中任一者之抗體或抗原結合片段,其能夠在感染之體外模式中及/或在感染之體內動物模式中及/或在人類中中和由二或更多種嚴重急性呼吸道症候群β型冠狀病毒所致之感染。
具體實施例9. 如具體實施例1至8中任一者之抗體或抗原結合片段,其中該VH及該VL分別包含下列者或由下列者組成:與以下所述之胺基酸序列具有至少85%、至少86%、至少87%、至少88%、至少89%、至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、或至少99%同一性之胺基酸序列;或分別包含以下所述之胺基酸序列或由以下所述之胺基酸序列組成:(I) 1) SEQ ID NO: 23及27;2) SEQ ID NO: 23及37;3) SEQ ID NO: 31及27;4) SEQ ID NO: 31及37;5) SEQ ID NO: 35及27;6) SEQ ID NO: 35及37;7) SEQ ID NO: 36及27;8) SEQ ID NO: 36及37;9) SEQ ID NO: 43及27;10) SEQ ID NO: 43及37;11) SEQ ID NO: 83及87;12) SEQ ID NO: 83及193;13) SEQ ID NO: 179及87;14) SEQ ID NO: 179及193;15) SEQ ID NO: 181及87;16) SEQ ID NO: 181及193;17) SEQ ID NO: 183及87;18) SEQ ID NO: 183及193;18) SEQ ID NO: 185及87;19) SEQ ID NO: 185及193;20) SEQ ID NO: 188及87;21) SEQ ID NO: 188及193;22) SEQ ID NO: 190及87;23) SEQ ID NO: 190及193;24) SEQ ID NO: 93及97;25) SEQ ID NO: 93及225;26) SEQ ID NO: 93及228;27) SEQ ID NO: 93及231;28) SEQ ID NO: 197及97;29) SEQ ID NO: 197及225;30) SEQ ID NO: 197及228;31) SEQ ID NO: 197及231;32) SEQ ID NO: 201及97;33) SEQ ID NO: 201及225;34) SEQ ID NO: 201及228;35) SEQ ID NO: 201及231;36) SEQ ID NO: 204及97;37) SEQ ID NO: 204及225;38) SEQ ID NO: 204及228;39) SEQ ID NO: 204及231;40) SEQ ID NO: 207及97;41) SEQ ID NO: 207及225;42) SEQ ID NO: 207及228;43) SEQ ID NO: 207及231;44) SEQ ID NO: 210及97;45) SEQ ID NO: 210及225;46) SEQ ID NO: 210及228;47) SEQ ID NO: 210及231;48) SEQ ID NO: 212及97;49) SEQ ID NO: 212及225;50) SEQ ID NO: 212及228;51) SEQ ID NO: 212及231;52) SEQ ID NO: 214及97;53) SEQ ID NO: 214及225;54) SEQ ID NO: 214及228;55) SEQ ID NO: 214及231;56) SEQ ID NO: 216及97;57) SEQ ID NO: 216及225;58) SEQ ID NO: 216及228;59) SEQ ID NO: 216及231;60) SEQ ID NO: 218及97;61) SEQ ID NO: 218及225;62) SEQ ID NO: 218及228;63) SEQ ID NO: 218及231;64) SEQ ID NO: 220及97;65) SEQ ID NO: 220及225;66) SEQ ID NO: 220及228;67) SEQ ID NO: 220及231;68) SEQ ID NO: 222及97;69) SEQ ID NO: 222及225;70) SEQ ID NO: 222及228;71) SEQ ID NO: 222及231;72) SEQ ID NO: 102及105;73) SEQ ID NO: 102及254;74) SEQ ID NO: 102及257;75) SEQ ID NO: 102及260;76) SEQ ID NO: 235及105;77) SEQ ID NO: 235及254;78) SEQ ID NO: 235及257;79) SEQ ID NO: 235及260;80) SEQ ID NO: 238及105;81) SEQ ID NO: 238及254;82) SEQ ID NO: 238及257;83) SEQ ID NO: 238及260;84) SEQ ID NO: 241及105;85) SEQ ID NO: 241及254;86) SEQ ID NO: 241及257;87) SEQ ID NO: 241及260;88) SEQ ID NO: 243及105;89) SEQ ID NO: 243及254;90) SEQ ID NO: 243及257;91) SEQ ID NO: 243及260;92) SEQ ID NO: 245及105;93) SEQ ID NO: 245及254;94) SEQ ID NO: 245及257;95) SEQ ID NO: 245及260;96) SEQ ID NO: 247及105;97) SEQ ID NO: 247及254;98) SEQ ID NO: 247及257;99) SEQ ID NO: 247及260;100) SEQ ID NO: 249及105;101) SEQ ID NO: 249及254;102) SEQ ID NO: 249及257;103) SEQ ID NO: 249及260;104) SEQ ID NO: 251及105;105) SEQ ID NO: 251及254;106) SEQ ID NO: 251及257;107) SEQ ID NO: 251及260;108) SEQ ID NO: 111及115;109) SEQ ID NO: 111及121;110) SEQ ID NO: 111及157;111) SEQ ID NO: 111及272;112) SEQ ID NO: 111及277;113) SEQ ID NO: 111及279;114) SEQ ID NO: 111及282;115) SEQ ID NO: 111及286;116) SEQ ID NO: 111及290;117) SEQ ID NO: 125及115;118) SEQ ID NO: 125及121;119) SEQ ID NO: 125及157;120) SEQ ID NO: 125及272;121) SEQ ID NO: 125及277;122) SEQ ID NO: 125及279;123) SEQ ID NO: 125及282;124) SEQ ID NO: 125及286;125) SEQ ID NO: 125及290;126) SEQ ID NO: 128及115;127) SEQ ID NO: 128及121;128) SEQ ID NO: 128及157;129) SEQ ID NO: 128及272;129) SEQ ID NO: 128及279;130) SEQ ID NO: 128及282;131) SEQ ID NO: 128及286;132) SEQ ID NO: 128及290;133) SEQ ID NO: 131及115;134) SEQ ID NO: 131及121;135) SEQ ID NO: 131及157;136) SEQ ID NO: 131及272;137) SEQ ID NO: 131及277;138) SEQ ID NO: 131及279;139) SEQ ID NO: 131及282;140) SEQ ID NO: 131及286;141) SEQ ID NO: 131及290;142) SEQ ID NO: 134及115;143) SEQ ID NO: 134及121;144) SEQ ID NO: 134及157;145) SEQ ID NO: 134及272;146) SEQ ID NO: 134及277;147) SEQ ID NO: 134及279;148) SEQ ID NO: 134及282;149) SEQ ID NO: 134及286;150) SEQ ID NO: 134及290;151) SEQ ID NO: 137及115;152) SEQ ID NO: 137及121;153) SEQ ID NO: 137及157;154) SEQ ID NO: 137及272;155) SEQ ID NO: 137及277;156) SEQ ID NO: 137及279;157) SEQ ID NO: 137及282;158) SEQ ID NO: 137及286;159) SEQ ID NO: 137及290;160) SEQ ID NO: 141及115;161) SEQ ID NO: 141及121;162) SEQ ID NO: 141及157;162) SEQ ID NO: 141及272;162) SEQ ID NO: 141及277;163) SEQ ID NO: 141及279;164) SEQ ID NO: 141及282;165) SEQ ID NO: 141及286;166) SEQ ID NO: 141 290;167) SEQ ID NO: 145及115;168) SEQ ID NO: 145及121;169) SEQ ID NO: 145及157;170) SEQ ID NO: 145及272;171) SEQ ID NO: 145及277;172) SEQ ID NO: 145及279;173) SEQ ID NO: 145及282;174) SEQ ID NO: 145及282;175) SEQ ID NO: 145及286;176) SEQ ID NO: 145及290;177) SEQ ID NO: 149及115;178) SEQ ID NO: 149及121;179) SEQ ID NO: 149及157;180) SEQ ID NO: 149及272;181) SEQ ID NO: 149及277;182) SEQ ID NO: 149及279;及183) SEQ ID NO: 149及282;184) SEQ ID NO: 149及286;185) SEQ ID NO: 149及290;186) SEQ ID NO: 153及115;187) SEQ ID NO: 153及121;188) SEQ ID NO: 153及157;189) SEQ ID NO: 153及272;190) SEQ ID NO: 153及277;191) SEQ ID NO: 153及279;192) SEQ ID NO: 153及282;193) SEQ ID NO: 153及286;194) SEQ ID NO: 153及290;195) SEQ ID NO: 264及115;196) SEQ ID NO: 264及121;197) SEQ ID NO: 264及157;198) SEQ ID NO: 264及272;199) SEQ ID NO: 264及277;200) SEQ ID NO: 264及279;201) SEQ ID NO: 264及282;202) SEQ ID NO: 264及286;203) SEQ ID NO: 264及290;204) SEQ ID NO: 266及115;205) SEQ ID NO: 266及121;206) SEQ ID NO: 266及157;207) SEQ ID NO: 266及272;208) SEQ ID NO: 266及277;209) SEQ ID NO: 266及279;210) SEQ ID NO: 266及282;211) SEQ ID NO: 266及286;212) SEQ ID NO: 266及290;213) SEQ ID NO: 269及115;214) SEQ ID NO: 269及121;215) SEQ ID NO: 269及157;216) SEQ ID NO: 269及157;217) SEQ ID NO: 269及272;218) SEQ ID NO: 269及277;219) SEQ ID NO: 269及279;219) SEQ ID NO: 269及282;220) SEQ ID NO: 269及286;或221) SEQ ID NO: 269及290,或(II)與表2及表3中所述相同的抗體類型之任何其他組合。
具體實施例10. 如具體實施例1至9中任一者之抗體或抗原結合片段,其中該VH及該VL分別包含以下所述之胺基酸序列或由以下所述之胺基酸序列組成:1) SEQ ID NO: 23及27;2) SEQ ID NO: 23及37;3) SEQ ID NO: 31及27;4) SEQ ID NO: 31及37;5) SEQ ID NO: 35及27;6) SEQ ID NO: 35及37;7) SEQ ID NO: 36及27;8) SEQ ID NO: 36及37;9) SEQ ID NO: 43及27;10) SEQ ID NO: 43及37;11) SEQ ID NO: 83及87;12) SEQ ID NO: 83及193;13) SEQ ID NO: 179及87;14) SEQ ID NO: 179及193;15) SEQ ID NO: 181及87;16) SEQ ID NO: 181及193;17) SEQ ID NO: 183及87;18) SEQ ID NO: 183及193;18) SEQ ID NO: 185及87;19) SEQ ID NO: 185及193;20) SEQ ID NO: 188及87;21) SEQ ID NO: 188及193;22) SEQ ID NO: 190及87;23) SEQ ID NO: 190及193;24) SEQ ID NO: 93及97;25) SEQ ID NO: 93及225;26) SEQ ID NO: 93及228;27) SEQ ID NO: 93及231;28) SEQ ID NO: 197及97;29) SEQ ID NO: 197及225;30) SEQ ID NO: 197及228;31) SEQ ID NO: 197及231;32) SEQ ID NO: 201及97;33) SEQ ID NO: 201及225;34) SEQ ID NO: 201及228;35) SEQ ID NO: 201及231;36) SEQ ID NO: 204及97;37) SEQ ID NO: 204及225;38) SEQ ID NO: 204及228;39) SEQ ID NO: 204及231;40) SEQ ID NO: 207及97;41) SEQ ID NO: 207及225;42) SEQ ID NO: 207及228;43) SEQ ID NO: 207及231;44) SEQ ID NO: 210及97;45) SEQ ID NO: 210及225;46) SEQ ID NO: 210及228;47) SEQ ID NO: 210及231;48) SEQ ID NO: 212及97;49) SEQ ID NO: 212及225;50) SEQ ID NO: 212及228;51) SEQ ID NO: 212及231;52) SEQ ID NO: 214及97;53) SEQ ID NO: 214及225;54) SEQ ID NO: 214及228;55) SEQ ID NO: 214及231;56) SEQ ID NO: 216及97;57) SEQ ID NO: 216及225;58) SEQ ID NO: 216及228;59) SEQ ID NO: 216及231;60) SEQ ID NO: 218及97;61) SEQ ID NO: 218及225;62) SEQ ID NO: 218及228;63) SEQ ID NO: 218及231;64) SEQ ID NO: 220及97;65) SEQ ID NO: 220及225;66) SEQ ID NO: 220及228;67) SEQ ID NO: 220及231;68) SEQ ID NO: 222及97;69) SEQ ID NO: 222及225;70) SEQ ID NO: 222及228;71) SEQ ID NO: 222及231;72) SEQ ID NO: 102及105;73) SEQ ID NO: 102及254;74) SEQ ID NO: 102及257;75) SEQ ID NO: 102及260;76) SEQ ID NO: 235及105;77) SEQ ID NO: 235及254;78) SEQ ID NO: 235及257;79) SEQ ID NO: 235及260;80) SEQ ID NO: 238及105;81) SEQ ID NO: 238及254;82) SEQ ID NO: 238及257;83) SEQ ID NO: 238及260;84) SEQ ID NO: 241及105;85) SEQ ID NO: 241及254;86) SEQ ID NO: 241及257;87) SEQ ID NO: 241及260;88) SEQ ID NO: 243及105;89) SEQ ID NO: 243及254;90) SEQ ID NO: 243及257;91) SEQ ID NO: 243及260;92) SEQ ID NO: 245及105;93) SEQ ID NO: 245及254;94) SEQ ID NO: 245及257;95) SEQ ID NO: 245及260;96) SEQ ID NO: 247及105;97) SEQ ID NO: 247及254;98) SEQ ID NO: 247及257;99) SEQ ID NO: 247及260;100) SEQ ID NO: 249及105;101) SEQ ID NO: 249及254;102) SEQ ID NO: 249及257;103) SEQ ID NO: 249及260;104) SEQ ID NO: 251及105;105) SEQ ID NO: 251及254;106) SEQ ID NO: 251及257;107) SEQ ID NO: 251及260;108) SEQ ID NO: 111及115;109) SEQ ID NO: 111及121;110) SEQ ID NO: 111及157;111) SEQ ID NO: 111及272;112) SEQ ID NO: 111及277;113) SEQ ID NO: 111及279;114) SEQ ID NO: 111及282;115) SEQ ID NO: 111及286;116) SEQ ID NO: 111及290;117) SEQ ID NO: 125及115;118) SEQ ID NO: 125及121;119) SEQ ID NO: 125及157;120) SEQ ID NO: 125及272;121) SEQ ID NO: 125及277;122) SEQ ID NO: 125及279;123) SEQ ID NO: 125及282;124) SEQ ID NO: 125及286;125) SEQ ID NO: 125及290;126) SEQ ID NO: 128及115;127) SEQ ID NO: 128及121;128) SEQ ID NO: 128及157;129) SEQ ID NO: 128及272;129) SEQ ID NO: 128及279;130) SEQ ID NO: 128及282;131) SEQ ID NO: 128及286;132) SEQ ID NO: 128及290;133) SEQ ID NO: 131及115;134) SEQ ID NO: 131及121;135) SEQ ID NO: 131及157;136) SEQ ID NO: 131及272;137) SEQ ID NO: 131及277;138) SEQ ID NO: 131及279;139) SEQ ID NO: 131及282;140) SEQ ID NO: 131及286;141) SEQ ID NO: 131及290;142) SEQ ID NO: 134及115;143) SEQ ID NO: 134及121;144) SEQ ID NO: 134及157;145) SEQ ID NO: 134及272;146) SEQ ID NO: 134及277;147) SEQ ID NO: 134及279;148) SEQ ID NO: 134及282;149) SEQ ID NO: 134及286;150) SEQ ID NO: 134及290;151) SEQ ID NO: 137及115;152) SEQ ID NO: 137及121;153) SEQ ID NO: 137及157;154) SEQ ID NO: 137及272;155) SEQ ID NO: 137及277;156) SEQ ID NO: 137及279;157) SEQ ID NO: 137及282;158) SEQ ID NO: 137及286;159) SEQ ID NO: 137及290;160) SEQ ID NO: 141及115;161) SEQ ID NO: 141及121;162) SEQ ID NO: 141及157;162) SEQ ID NO: 141及272;162) SEQ ID NO: 141及277;163) SEQ ID NO: 141及279;164) SEQ ID NO: 141及282;165) SEQ ID NO: 141及286;166) SEQ ID NO: 141 290;167) SEQ ID NO: 145及115;168) SEQ ID NO: 145及121;169) SEQ ID NO: 145及157;170) SEQ ID NO: 145及272;171) SEQ ID NO: 145及277;172) SEQ ID NO: 145及279;173) SEQ ID NO: 145及282;174) SEQ ID NO: 145及282;175) SEQ ID NO: 145及286;176) SEQ ID NO: 145及290;177) SEQ ID NO: 149及115;178) SEQ ID NO: 149及121;179) SEQ ID NO: 149及157;180) SEQ ID NO: 149及272;181) SEQ ID NO: 149及277;182) SEQ ID NO: 149及279;及183) SEQ ID NO: 149及282;184) SEQ ID NO: 149及286;185) SEQ ID NO: 149及290;186) SEQ ID NO: 153及115;187) SEQ ID NO: 153及121;188) SEQ ID NO: 153及157;189) SEQ ID NO: 153及272;190) SEQ ID NO: 153及277;191) SEQ ID NO: 153及279;192) SEQ ID NO: 153及282;193) SEQ ID NO: 153及286;194) SEQ ID NO: 153及290;195) SEQ ID NO: 264及115;196) SEQ ID NO: 264及121;197) SEQ ID NO: 264及157;198) SEQ ID NO: 264及272;199) SEQ ID NO: 264及277;200) SEQ ID NO: 264及279;201) SEQ ID NO: 264及282;202) SEQ ID NO: 264及286;203) SEQ ID NO: 264及290;204) SEQ ID NO: 266及115;205) SEQ ID NO: 266及121;206) SEQ ID NO: 266及157;207) SEQ ID NO: 266及272;208) SEQ ID NO: 266及277;209) SEQ ID NO: 266及279;210) SEQ ID NO: 266及282;211) SEQ ID NO: 266及286;212) SEQ ID NO: 266及290;213) SEQ ID NO: 269及115;214) SEQ ID NO: 269及121;215) SEQ ID NO: 269及157;216) SEQ ID NO: 269及157;217) SEQ ID NO: 269及272;218) SEQ ID NO: 269及277;219) SEQ ID NO: 269及279;219) SEQ ID NO: 269及282;220) SEQ ID NO: 269及286;或221) SEQ ID NO: 269及290。
具體實施例11. 如具體實施例1至10中任一者之抗體或抗原結合片段,其中:
i) 該VH及該VL包含下列者或由下列者組成:分別與SEQ ID NO: 111及157中所述胺基酸序列具有至少85%、至少86%、至少87%、至少88%、至少89%、至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、或至少99%同一性之胺基酸序列,或分別包含SEQ ID NO: 111及157中所述之胺基酸序列或由SEQ ID NO: 111及157中所述之胺基酸組成。
ii) 該VH及該VL分別包含SEQ ID NO: 111及157中所述之胺基酸序列或由SEQ ID NO: 111及157中所述之胺基酸組成;
iii) i)或ii)之該VH包含CDRH1、CDRH2、及CDRH3,且i)或ii)之該VL包含CDRL1、CDRL2、及CDRL3,其具有由任何VH及VL編號方案所判定之胺基酸序列;
iii) 該VH包含CDRH1、CDRH2、及CDRH3,且VL包含CDRL1、CDRL2、及CDRL3,其分別具有如SEQ ID NO: 112至114、116、117、及158之胺基酸序列;
iv) 該抗體或抗原結合片段包含i)至iv)中任一者與具有如SEQ ID NO: 44至80中任一者之序列的重鏈恆定區及具有如SEQ ID NO: 292之序列的輕鏈恆定區的組合;
v) 該抗體或抗原結合片段包含具有如SEQ ID NO: 293之序列的重鏈及具有如SEQ ID NO: 294之序列的輕鏈;
或
vi) 該抗體或抗原結合片段包含具有如SEQ ID NO: 295之序列的重鏈及具有如SEQ ID NO: 296之序列的輕鏈。
具體實施例12. 如具體實施例1至11中任一者之抗體或抗原結合片段,其中:(i)識別二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒之棘蛋白中之表位;(ii)能夠阻斷在二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒之棘蛋白與其對應的一或多種細胞表面受體之間的交互作用,其中,視需要地,細胞表面受體包含人類ACE2;(iii)識別在二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒之棘蛋白中保留表位;(iv)針對二或更多種、三或更多種、四或更多種、或五或更多種嚴重急性呼吸道症候群β型冠狀病毒、視需要地包含一或多種演化支1b嚴重急性呼吸道症候群β型冠狀病毒具有交叉反應性;或(v)(i)至(iv)之任何組合。
具體實施例13. 如具體實施例1至12中任一者之抗體或抗原結合片段,其係IgG、IgA、IgM、IgE、或IgD同型。
具體實施例14. 如具體實施例13之抗體或抗原結合片段,其係選自IgG1、IgG2、IgG3、及IgG4之IgG同型,且較佳地係IgG1同型。
具體實施例15. 如具體實施例1至14中任一者之抗體或抗原結合片段,其係人類的、人源化的、或嵌合的。
具體實施例16. 如具體實施例1至15中任一者之抗體或抗原結合片段,其中該抗體、或該抗原結合片段包含人類抗體、單株抗體、純化抗體、單鏈抗體、Fab、Fab’、F(ab’)2、Fv、scFv、或scFab。
具體實施例17. 如具體實施例16之抗體或抗原結合片段,其中該scFv包含多於一個VH結構域及多於一個VL結構域。
具體實施例18. 如具體實施例1至17中任一者之抗體或抗原結合片段,其中該抗體或抗原結合片段係多特異性抗體或抗原結合片段。
具體實施例19. 如具體實施例18之抗體或抗原結合片段,其中該抗體或抗原結合片段係雙特異性抗體或抗原結合片段。
具體實施例20. 如具體實施例19之抗體或抗原結合片段,其包含:第一VH及第一VL;及第二VH及第二VL,其中該第一VH及VL包含i)分別與SEQ ID NO: 23及27中所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列;ii)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為31、35、36、或43中任一者及37;分別為14及15;分別為16及17;分別為18及19;分別為20及21;分別為20及22;iii)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為83、179、181、183、185、188、或190中任一者及87或193中任一者;iv)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為93、197、201、204、207、210、212、214、216、218、220、或222中任一者及97、225、228、或231中任一者;v)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為102、235、238、241、243、245、247、249、或251中任一者及105、254、257、或260中任一者;或vi)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及115、121、157、272、277、279、282、286、或290中任一者;且其中該第二VH及VL包含i)分別與SEQ ID NO: 23及27中所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列;ii)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為31、35、36、或43中任一者及37;分別為14及15;分別為16及17;分別為18及19;分別為20及21;分別為20及22;iii)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為83、179、181、183、185、188、或190中任一者及87或193中任一者;iv)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為93、197、201、204、207、210、212、214、216、218、220、或222中任一者及97、225、228、或231中任一者;v)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為102、235、238、241、243、245、247、249、或251中任一者及105、254、257、或260中任一者;或vi)與下列SEQ ID NO.所述之胺基酸序列具有至少85%(亦即85%、86%、87%、88%、89%、90%、91%、92%、93%、94%、95%、96%、97%、98%、99%、或100%)同一性之胺基酸序列:分別為111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及115、121、157、272、277、279、282、286、或290中任一者;其中該第一VH及第二VL不同於該第二VH及VL,且其中該第一VH及該第一VL一起形成第一抗原結合位點,且其中該第二VH及該第二VL一起形成第二抗原結合位點。
具體實施例21. 如具體實施例1至20中任一者之抗體或抗原結合片段,其中該抗體或抗原結合片段包含Fc多肽或其片段。
具體實施例22. 如具體實施例21之抗體或抗原結合片段,其中該Fc多肽或其片段包含:(i)增強與FcRn的結合的突變,其係如相較於不包含該突變的參考Fc多肽;(ii)增強與FcγR的結合的突變,其係如相較於不包含該突變的參考Fc多肽;(iii)增強與人類FcγRIIa的結合及/或降低與人類FcγRIIb的結合的突變,其係如相較於不包含該突變的參考Fc多肽;及/或(iv)增強與人類C1q的結合的突變,其係相較於不包含該突變的參考Fc多肽。
具體實施例23. 如具體實施例22之抗體或抗原結合片段,其中該Fc多肽包含該等取代突變M428L/N434S、M428L/N434A、G236A/A330L/I332E/M428L/N434S、或G236A/A330L/I332E/M428L/N434A,其中,視需要地,該抗體或抗原結合片段係IgG1同型,且包含Fc多肽或其片段或由Fc多肽或其片段組成,該Fc多肽或其片段包含下列者或由下列者組成:與SEQ ID NO: 44至80具有至少85%、至少86%、至少87%、至少88%、至少89%、至少90%、至少91%、至少92%、至少93%、至少94%、至少95%、至少96%、至少97%、至少98%、或至少99%同一性之胺基酸序列,視需要地為其天然存在的變體以外者;或該Fc多肽或其片段包含SEQ ID NO: 52至80中所述之胺基酸序列或由SEQ ID NO: 52至80中所述之胺基酸序列組成。
具體實施例24. 一種單離之多核苷酸,其編碼如具體實施例1至23中任一者之抗體或抗原結合片段。
具體實施例25. 如具體實施例24之多核苷酸,其中該多核苷酸包含下列者或由下列者組成:與如SEQ ID NO: 81、82、91、92、100、101、109、110、119、120、123、127、130、133、136、140、144、148、152、156、159、180、182、184、187、189、191、192、195、196、200、203、206、209、211、213、215、217、219、221、223、224、227、230、233、234、237、240、242、244、246、248、250、252、253、256、259、261、262、263、265、268、271、276、278、281、285、或289中之一或多者之核酸序列具有至少85%(亦即85%、86、87、88、89、90、91、92、93、94、95、96、97、98、99、或100%)同一性之核酸序列。
具體實施例26. 如具體實施例24或具體實施例25之多核苷酸,其中該多核苷酸包含去氧核糖核酸(DNA)或核糖核酸(RNA),其中該RNA視需要地包含傳訊RNA(mRNA)。
具體實施例27. 如具體實施例24至26中任一者之多核苷酸,其經密碼子最佳化以在宿主細胞中表現。
具體實施例28. 一種重組載體,其包含如具體實施例24至27中任一者之多核苷酸。
具體實施例29. 一種宿主細胞,其包含如具體實施例24至27中任一者之多核苷酸及/或如具體實施例28之載體,其中該多核苷酸對該宿主細胞係異源的。
具體實施例30. 一種人類B細胞,其包含如具體實施例24至27中任一者之多核苷酸及/或如具體實施例28之載體,其中多核苷酸對該人類B細胞係異源的及/或其中該人類B細胞係永生化的。
具體實施例31. 一種組成物,其包含:(i)如具體實施例1至23中任一者之抗體或抗原結合片段;(ii)如具體實施例24至27中任一者之多核苷酸;(iii)如具體實施例28之重組載體;(iv)如具體實施例29之宿主細胞;及/或(v)如具體實施例30之人類B細胞,及醫藥上可接受之賦形劑、載劑、或稀釋劑。
具體實施例32. 如具體實施例31之組成物,其包含二或更多種抗體或抗原結合片段,其中該第一抗體或抗原結合片段及第二抗體或抗原結合片段分別包含、或該多特異性抗體或抗原結合片段包含CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3、及視需要地VH及VL,其係根據:(i)任何S3A3抗體及任何S3A19抗體;(ii)任何S3A3抗體及索托韋單抗(sotrovimab);(iii)任何S3A3抗體及S2K146;(iv)任何S3A3抗體及S2X259;(v)任何S3A3抗體及任何S2X324抗體;(vi)任何S3A3抗體及S309;(vi)任何S3A19抗體及索托韋單抗;(vii)任何S3A19抗體及S2K146;(viii)任何S3A19抗體及S2X259;(ix)任何S3A19抗體及任何S2X324抗體;(x)任何S3A19抗體及S309;(xi)任何S3I2抗體及任何S3A3抗體;(xii)任何S3I2抗體及任何S3A19抗體;(xiii)任何S3I2抗體及索托韋單抗;(xiv)任何S3I2抗體及S2K146;(xv)任何S3I2抗體及S2X259;(xvi)任何S3I2抗體及任何S2X324抗體;(xvii)任何S3I2抗體及S309;(xviii)任何S3I2抗體及任何S3O13抗體;(xix)任何S3I2抗體及任何S3L17抗體;(xx)任何S3O13抗體及任何S3A3抗體;(xxi)任何S3O13抗體及任何S3A19抗體;(xxii)任何S3O13抗體及索托韋單抗;(xxiii)任何S3O13抗體及S2K146;(xxiv)任何S3O13抗體及S2X259;(xxv)任何S3O13抗體及任何S2X324抗體;(xxvi)任何S3O13抗體及S309;(xxvii)任何S3O13抗體及任何S3L17抗體;(xxviii)任何S3L17抗體及任何S3A3抗體;(xxix)任何S3L17抗體及任何S3A19抗體;(xxx)任何S3L17抗體及索托韋單抗;(xxxi)任何S3L17抗體及S2K146;(xxxii)任何S3L17抗體及S2X259;(xxxiii)任何S3L17抗體及任何S2X324抗體;(xxxiv)任何S3L17抗體及S309;(xxxv)任何S2V29抗體及任何S3A3抗體;(xxxvi)任何S2V29抗體及任何S3A19抗體;(xxxvii)任何S2V29抗體及索托韋單抗;(xxxviii)任何S2V29抗體及S2K146;(xxxix)任何S2V29抗體及S2X259;(xl)任何S2V29抗體及任何S2X324抗體;(xli)任何S2V29抗體及S309;(lxlii)任何S2V29抗體及任何S3L17抗體;及(xliii)任何S2V29抗體及任何S3O13抗體、或其任何抗原結合片段。
具體實施例33. 如具體實施例31之組成物,其中該第一抗體或抗原結合片段包含S3L17抗體或抗原結合片段且該第二抗體或抗原結合片段包含S2V29抗體。
具體實施例34. 一種如具體實施例33之組成物,其中該第一抗體或抗原結合片段分別包含下列之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列:如SEQ ID NO: 103、85、及、104;103、85、及236;或103、85、及239、及106至108;106、107、及258;255、107、及108;或255、107、或258,且該第二抗體或抗原結合片段分別包含下列之CDRH1、CDRH2、CDRH3、CDRL1、CDRL2、及CDRL3胺基酸序列:如SEQ ID NO: 112至114;112、126、及114;112、129 及114;112、132、及114;112、135、及114;112、138、及114;112、142、及114;112、146、及114;112、150、及114;112、154、及114;112、267、及114;112、270、及114;112、113、及139;112、126、及139;112、129 及139;112、132、及139;112、135、及139;112、138、及139;112、142、及139;112、146、及139;112、150、及139;112、154、及139;112、267、及139;112、270、及139;112、113、及143;112、126、及143;112、129及143;112、132、及143;112、135、及143;112、138、及143;112、142、及143;112、146、及143;112、150、及143;112、154、及143;112、267、及143;112、270、及143;112、113、及147;112、126、及147;112、129及147;112、132、及147;112、135、及147;112、138、及147;112、142、及147;112、146、及147;112、150、及147;112、154、及147;112、267、及147;112、270、及147;112、113、及151;112、126、及151;112、129及151;112、132、及151;112、135、及151;112、138、及151;112、142、及151;112、146、及151;112、150、及151;112、154、及151;112、267、及151;112、270、及151;112、113、及155;112、126、及155;112、129及155;112、132、及155;112、135、及155;112、138、及155;112、142、及155;112、146、及1551;112、150、及155;112、154、及155;112、267、及155;或112、270、及155;及116至118;116、274、及118;116、287、及118;116、117、及122;116、274、及122;116、287、及122;116、117、及158;116、274、及275;116、287、及275;116、117、及280;116、274、及280;116、287、及280;116、117、及284;116、274、及284;116、287、及284;116、117、及288;116、274、及288;116、287、及288;116、117、及291;116、274、及291;116、287、及291;273、117、及118;273、274、及118;273、287、及118;273、117、及122;273、274、及122;273、287、及122;273、117、及158;273、274、及275;273、287、及275;273、117、及280;273、274、及280;1273、287、及280;273、117、及284;273、274、及284;273、287、及284;273、117、及288;273、274、及288;273、287、及288;273、117、及291;273、274、及291;273、287、及291;283、117、118;283、274、及118;283、287、及118;283、117、及122;283、274、及122;283、287、及122;283、117、及158;283、274、及275;283、287、及275;283、117、及280;283、274、及280;283、287、及280;283、117、及284;283、274、及284;283、287、及284;283、117、及288;283、274、及288;283、287、及288;283、117、及291;283、274、及291;或283、287、及291。
具體實施例35. 如具體實施例33之組成物,其中該第一抗體或抗原結合片段包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(i)該CDRH1包含下列者或由下列者組成:如SEQ ID NO: 103之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 85之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 104、236、或239中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 106或255任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 107之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 108或258中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代,且其中該第二抗體或抗原結合片段包含重鏈可變結構域(VH)及輕鏈可變結構域(VL),該重鏈可變結構域包含CDRH1、CDRH2、及CDRH3,該輕鏈可變結構域包含CDRL1、CDRL2、及CDRL3,其中:(i)該CDRH1包含下列者或由下列者組成:如SEQ ID NO: 112之胺基酸序列或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(ii)該CDRH2包含下列者或由下列者組成:如SEQ ID NO: 113、126、129、132、135、138、142、146、150、154、267、或270中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iii)該CDRH3包含下列者或由下列者組成:如SEQ ID NO: 114、139、143、147、151、或155中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(iv)該CDRL1包含下列者或由下列者組成:如SEQ ID NO: 116、273、或283中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;(v)該CDRL2包含下列者或由下列者組成:如SEQ ID NO: 117、274、或287中任一者之胺基酸序列、或其序列變體,該序列變體包含一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代;及/或(vi)該CDRL3包含下列者或由下列者組成:如SEQ ID NO: 118、122、158、275、280、284、288、或291中任一者之胺基酸序列、或其序列變體,該序列變體包含具有一個、二個、或三個胺基酸取代,該等取代之一或多者視需要地係保留取代及/或係對生殖系編碼之胺基酸的取代。
具體實施例36. 如具體實施例33之組成物,其中該第一抗體或抗原結合片段包含下列之VH序列:如SEQ ID NO: 102、235、238、241、243、245、247、249、或251中任一者及下列之VL序列:如SEQ ID NO: 105、254、257、或260中任一者,其中該第二抗體或抗原結合片段包含下列之VH序列:如SEQ ID NO: 111、125、128、131、134、137、141、145、149、153、264、266、或269中任一者及下列之VL序列:如SEQ ID NO: 115、121、157、272、277、279、282、286、或290中任一者。
具體實施例37. 一種組成物,其包含包覆在載劑分子中之如具體實施例24至27中任一者之多核苷酸,其中該載劑分子視需要地包含脂質、脂質衍生之遞送媒劑,諸如脂質體、固體脂質奈米粒子、油性懸浮液、次微米脂質乳劑、脂質微氣泡、逆脂質微胞、耳蝸脂質體、脂質微管、脂質微柱、脂質奈米粒子(LNP)、或奈米級平台。
具體實施例38. 一種治療個體之嚴重急性呼吸道症候群β型冠狀病毒感染(例如由SARS-CoV-2所致之感染)之方法,該方法包含向該個體投予有效量的(i)如具體實施例1至23中任一者之抗體或抗原結合片段;(ii)如具體實施例24至27中任一者之多核苷酸;(iii)如具體實施例28之重組載體;(iv)如具體實施例29之宿主細胞;及/或(v)如具體實施例30之人類B細胞,及/或(vi)如具體實施例31至37中任一者之組成物。
具體實施例39. 如具體實施例1至23中任一者之抗體或抗原結合片段、如具體實施例24至27中任一者之多核苷酸、如具體實施例28之重組載體、如具體實施例29之宿主細胞、如具體實施例30之人類B細胞、及/或如具體實施例31至37中任一者之組成物,其係用於治療個體之嚴重急性呼吸道症候群β型冠狀病毒感染(例如由SARS-CoV-2所致之感染)之方法。
具體實施例40. 如具體實施例1至23中任一者之抗體或抗原結合片段、如具體實施例24至27中任一者之多核苷酸、如具體實施例28之重組載體、如具體實施例29之宿主細胞、如具體實施例30之人類B細胞、及/或如具體實施例31至37中任一者之組成物,其係用於製備用於治療個體之嚴重急性呼吸道症候群β型冠狀病毒感染(例如由SARS-CoV-2所致之感染)之藥物。
具體實施例41. 如具體實施例1至23或39至40中任一者之抗體或抗原結合片段,其中該抗體或抗原結合片段與二或更多種嚴重急性呼吸道症候群β型冠狀病毒S蛋白質結合,如使用生物薄層干涉法所測量。
具體實施例42. 一種套組,其包含液體組成物及其在治療個體之SARS-CoV-2感染中之使用說明書,該液體組成物包含如具體實施例1至23或39至40中任一者之抗體或抗原結合片段。
具體實施例43. 如具體實施例42之套組,其中該使用說明書係針對如具體實施例38之方法或如具體實施例39至40中任一者之用途。
具體實施例44. 一種用於體外診斷嚴重急性呼吸道症候群β型冠狀病毒感染(例如由SARS-CoV-2所致之感染)之方法,該方法包含:(i)使來自個體之樣本與如具體實施例1至23中任一者之抗體或抗原結合片段接觸;及(ii)偵測複合物,其包含抗原及該抗體、或包含抗原及該抗原結合片段。
具體實施例45. 一種用於生產如具體實施例1至23或具體實施例39至40中任一者之抗體或抗原結合片段之方法,其中該方法包含在足以生產該抗體或抗原結合片段之條件及時間下培養表現該抗體或抗原結合片段之宿主細胞。
具體實施例46. 如具體實施例45之用於生產抗體或抗原結合片段之方法,其中該宿主細胞包含如具體實施例28之重組載體。
具體實施例47. 如具體實施例46之用於生產抗體或抗原結合片段之方法,其中該宿主細胞係哺乳動物細胞。
*表2在各對應VH序列中以粗體字按順序指示CDRH1、CDRH2及CDRH3d(IMGT定義);及在各對應VL序列中以粗體字按順序指示CDRL1、CDRL2、CDRL3。
The antibodies and antigen-binding fragments provided herein are capable of binding to SARS beta coronaviruses (e.g., SARS-CoV-2). In some embodiments, the antibodies or antigen-binding fragments are capable of binding to a plurality of SARS beta coronaviruses (e.g., to one or more (e.g., one, two, three, four, five, six, or more) different SARS beta coronaviruses as described herein, optionally contained on virus particles and/or on the surface of cells infected with two or more SARS beta coronaviruses). In certain embodiments, the plurality of SARS beta coronaviruses comprises one or more clade 1b SARS beta coronaviruses. In certain embodiments, the antibodies and antigen-binding fragments disclosed herein can neutralize infection caused by one or more SARS-betacoronaviruses (e.g., one, two, three, four, or more SARS-betacoronaviruses) in an in vitro model of infection and/or in an animal model and/or in a human subject. Polynucleotides encoding antibodies and antigen binding fragments, vectors, host cells, and related compositions are also provided, as well as methods of using antibodies, antigen binding fragments, polynucleotides, vectors, host cells, and related compositions to treat (e.g., reduce, delay, eliminate, or prevent) an individual's infection caused by two or more severe acute respiratory syndrome beta coronaviruses and/or for the manufacture of a drug for treating an individual's infection caused by two or more severe acute respiratory syndrome beta coronaviruses (e.g., one, two, three, four, or more severe acute respiratory syndrome beta coronaviruses). Combinations of two or more antibodies or antigen binding fragments are also provided, for example for use in therapy and/or prevention.
Before describing the present disclosure in more detail, it may be helpful to first provide definitions of certain terms used herein. Additional definitions are set forth throughout this disclosure.
As used herein, an "anti-sarbecovirus antibody or antigen-binding fragment" specifically binds to at least one sarbecovirus and, in some embodiments, may bind to two or more, three or more, four or more, or five or more sarbecoviruses.
As used herein, "sarbecovirus" refers to any betacoronavirus within lineage B, and includes lineage B viruses in clade 1a, clade 1b, clade 2, and clade 3. Examples of clade 1a SARS beta coronaviruses are SARS-CoV and bat SARS-like coronavirus WIV1 (WIV1). Examples of clade 1b SARS beta coronaviruses are SARS-CoV-2, RatG13, pangolin-Guanxi-2017 (PANG/GX) and pangolin-Guangdon-2019 (PANG/GD). Embodiments of clade 1b also include SARS-CoV-2 variants, such as variants having any of the following mutations: A67V, Δ69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, Δ212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K41 7N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (wherein X is any amino acid), Y453F, S477N, T478K, V483A, E484A, E484Q, E484K, E484X (wherein X is any amino acid), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q 613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, or variants in the following genealogies: B.1.1.7 and Q genealogies and subsequent genealogies (Alpha); B.1.351 and subsequent genealogies (Beta); B.1.429 and B.1.427 and subsequent genealogies (Epsilon); P.1 and subsequent genealogies (Gamma); B.1.1. 222; C.37; B.1.617.2; AY.1, AY.2, other AY series and later series (Delta); B.1.525 and later series (Eta); B.1.526 and later series (Iota); B.1.617.1 and later series (Kappa); 1.617.3; B.1.621, and B.1.621.1 and later series (Mu); P.2 (Zeta); and B.1.1.529.1, BA.1, BA.2, BA.2.12, BA.3, BA.4, BA.5 and later series (Omicron). Examples of clade 2 SARS beta coronaviruses are bat ZC45 (ZC45), bat ZXC21 (ZXC21), YN2013, RmYN02, Anlong112, SC2018, and SX2011. Examples of clade 3 SARS beta coronaviruses are BtkY72 and BGR2008.
Figure 1It also explains the evolutionary clades of severe acute respiratory syndrome beta coronavirus and
Figure 2 In some embodiments, the antibody or antigen-binding fragment thereof is capable of binding to a clade 1b SARS beta coronavirus, such as SARS-CoV-2 (including all variants described herein), RatG13, Pangolin-Guanxi-2017 (PANG/GX), Pangolin-Guangdon-209, or any combination thereof. In certain further embodiments, the antibody or antigen-binding fragment thereof is capable of binding to a SARS-CoV-2 variant; for example, embodiments of clade 1b of SARS-CoV-2 variants are also included, such as variants having any one or more of the following mutations: A67V, Δ69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, Δ212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P 384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (wherein X is any amino acid except L), Y453F, S477N, T478K, V483A, E484A, E484Q, E484K, E484X (wherein X is any amino acid except E), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, or variants in the following lineages: B.1.1.7 and Q lineages and subsequent lineages (Alpha); B.1.351 and subsequent lineages (Beta); B.1.429 and B.1.427 and subsequent lineages (Epsilon); P.1 and subsequent lineages (Gamma ); B.1.1.222; C.37; B.1.617.2; AY.1, AY.2, other AY series, and subsequent series (Delta); B.1.525 and subsequent series (Eta); B.1.526 and subsequent series (Iota); B.1.617.1 and subsequent series (Kappa); 1.617.3; B.1.621, and B.1.621.1 and subsequent series (Mu); P.2 (Zeta); and B.1.1.529.1, BA.1, BA.2, BA.2.12, BA.3, BA.4, BA.5 and subsequent series (Omicron), or any combination thereof. In some embodiments, the SARS-Cov-2 variant is an Omicron variant, such as BA.1, BA.2, BA.2.12, BA.3, BA.4, or BA.5. In some embodiments, the antibody is (or the antigen-binding fragment is) S3A3, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3A3 or a variant disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S3A3 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of inhibiting the binding interaction between human ACE2 and severe acute respiratory syndrome beta coronavirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 of about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to about 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 In some embodiments, the antibody is (or the antigen-binding fragment is) S3A19, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3A19 or a variant disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S3A19 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of inhibiting the binding interaction between human ACE2 and severe acute respiratory syndrome beta coronavirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 of about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 18.5 ng/mL to about 100 ng/mL, about 19.5 ng/mL to about 100 ng/mL, about 20.0 ng/mL to about 100 ng/mL, about 21.5 ng/mL to about 100 ng/mL, about 22.5 ng/mL to about 100 ng/mL, about 24.5 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 26.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or about at least about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL. In some embodiments, the antibody is (or the antigen-binding fragment is) S3I2, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3I2 or a variant disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S3I2 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of inhibiting the binding interaction between human ACE2 and severe acute respiratory syndrome beta coronavirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 of about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to about 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL. In some embodiments, the antibody is (or the antigen-binding fragment is) S3O13, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3O13 or variants disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S3O13 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of inhibiting the binding interaction between human ACE2 and severe acute respiratory syndrome beta coronavirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 of about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to about 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL. In some embodiments, the antibody is (or the antigen-binding fragment is) S3L17, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3L17 or a variant disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S3L17 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of inhibiting the binding interaction between human ACE2 and severe acute respiratory syndrome beta coronavirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 of about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to about 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL. As used herein, "S2V29" includes any VH and VL variants disclosed herein. In some embodiments, the antibody is (or the antigen-binding fragment is) S2V29, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S2V29 or a variant disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S2V29 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of inhibiting the binding interaction between human ACE2 and severe acute respiratory syndrome beta coronavirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 of about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to about 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL. As used herein, "SARS-CoV-2" also known as "Wuhan coronavirus", "Wuhan seafood market pneumonia virus", "Wuhan CoV", "novel CoV", "nCoV", "2019 nCoV", "Wuhan nCoV", or its variants, is a lineage B betacoronavirus (severe acute respiratory syndrome betacoronavirus). SARS-CoV-2 was first identified in Wuhan, Hubei Province, China in late 2019 and spread in China and other parts of the world in early 2020. SARS CoV-2 infection can cause a disease called COVID-19; symptoms of COVID-19 include fever or chills, dry cough, difficulty breathing, fatigue, body aches, headache, new loss of taste or smell, sore throat, stuffy or runny nose, nausea or vomiting, diarrhea, persistent chest pressure or pain, new confusion, inability to wake up or stay awake, and bluish lips or face. The genomic sequence of the SARS-CoV-2 isolate Wuhan-Hu-1 is provided in GenBank MN908947.3 (January 23, 2020), and the amino acid transcripts of the genome are provided in GenBank QHD43416.1 (January 23, 2020). These GenBank sequences and the GenBank sequences of all SARS-CoV-2 variants are incorporated herein by reference as describing the severe acute respiratory syndrome beta coronavirus or SARS-CoV-2 to which the antibodies or antigen-binding fragments thereof according to the present disclosure specifically bind. Like other coronaviruses (e.g., SARS-CoV), SARS-CoV-2 contains a "spike" or surface ("S") type I transmembrane glycoprotein containing a receptor binding domain (RBD). The RBD is believed to mediate entry of lineage B SARS coronavirus into respiratory epithelial cells by binding to the cell surface receptor angiotensin-converting enzyme 2 (ACE2). In particular, the receptor binding motif (RBM) in the viral RBD is believed to interact with ACE2. The amino acid sequence of the Wuhan-Hu-1 surface glycoprotein is provided in SEQ ID NO: 1. The amino acid sequence of the Wuhan-Hu-1 RBD is provided in SEQ ID NO: 2. The Wuhan-Hu-1 S protein has approximately 73% amino acid sequence identity with SARS-CoV. The amino acid sequence of the Wuhan-Hu-1 RBM is provided in SEQ ID NO: 3. Many SARS-CoV-2 variants have emerged, which may differ in genome and amino acid sequence, particularly in surface glycoprotein or RBD. Some SARS-CoV-2 variant mutations increase affinity for ACE receptors and/or infectivity of the virus. Important variants of SARS-CoV-2 include embodiments of clade 1b of SARS-CoV-2 variants, such as variants having any of the following mutations: A67V, Δ69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, Δ212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (wherein X is any amino acid except L), Y453F, S477N, T478K, V483A, E484A, E484Q, E484K, E484X (wherein X is any amino acid except E), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E51 6Q, T547K, Q613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, or variants in the following genealogies: B.1.1.7 and Q genealogies and subsequent genealogies (Alpha); B.1.351 and subsequent genealogies (Beta); B.1.429 and B.1.427 and subsequent genealogies (Epsilon); P.1 and subsequent genealogies (Gamma); B.1.1 .222; C.37; B.1.617.2; AY.1, AY.2, other AY series, and subsequent series (Delta); B.1.525 and subsequent series (Eta); B.1.526 and subsequent series (Iota); B.1.617.1 and subsequent series (Kappa); 1.617.3; B.1.621 and B.1.621.1 and subsequent series (Mu); P.2 (Zeta); and B.1.1.529.1, BA.1, BA.2, BA.2.12, BA.3, BA.4, BA.5 and subsequent series (Omicron), or any combination thereof. In some embodiments, the SARS-Cov-2 variant is an Omicron variant, such as BA.1, BA.2, BA.2.12, BA.3, BA.4, or BA.5. SARS-CoV-2 variants circulating in the United States are classified as variants of concern by the Centers for Disease Control and Prevention (see https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html). In some embodiments, antibodies or antigen-binding fragments for treating severe acute respiratory syndrome beta coronavirus infection are provided. In certain embodiments, severe acute respiratory syndrome beta coronavirus infection comprises SARS-CoV-2 infection. Treatment of SARS CoV-2 infection according to the present disclosure includes treatment of infection caused by any one or more of the aforementioned SARS-CoV-2 viruses. In certain embodiments, treating SARS-CoV-2 infection comprises treating any one or more of the following: SARS CoV-2 Wuhan-Hu-1; also including embodiments of clade 1b of SARS-CoV-2 variants, such as variants having any of the following mutations: A67V, Δ69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, Δ212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417 N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (wherein X is any amino acid except L), Y453F, S477N, T478K, V483A, E484A, E484Q, E484K, E484X (wherein X is any amino acid except E), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, D614, E340A, or variants in the following genealogies: B.1.1.7 and Q genealogies and descendant genealogies (Alpha); B.1.351 and descendant genealogies (Beta); B.1.429 and B.1.427 and descendant genealogies (Epsilon); P.1 and descendant genealogies (Gamma); B.1.1.222; C. 37; B.1.617.2; AY.1, AY.2, other AY series, and subsequent series (Delta); B.1.525 and subsequent series (Eta); B.1.526 and subsequent series (Iota); B.1.617.1 and subsequent series (Kappa); 1.617.3; B.1.621 and B.1.621.1 and subsequent series (Mu); P.2 (Zeta); and B.1.1.529.1, BA.1, BA.2, BA.2.12, BA.3, BA.4, BA.5 and subsequent series (Omicron), BQ.1.1, XBB.1, or any combination thereof. In some embodiments, the SARS-CoV-2 variant is an Omicron variant, such as BA.1, BA.2, BA.2.12, BA.3, BA.4, or BA.5. In some embodiments, the SARS-CoV-2 variant is BQ.1.1. In some embodiments, the SARS-CoV-2 is XBB.1. In this specification, unless otherwise indicated, any concentration range, percentage range, ratio range, or integer range should be understood to include any integer value within the range, and (when appropriate) its fraction (such as one tenth and one hundredth of an integer). In addition, unless otherwise indicated, any numerical range described herein related to any physical characteristic (such as polymer subunits, size or thickness) should be understood to include any integer within the range. As used herein, unless otherwise indicated, the term "about" means ±20% of a specified range, value, or structure. It should be understood that, as used herein, the term "a/an" refers to "one or more" of the listed components. The use of alternatives (e.g., "or") should be understood to mean any one, two, or any combination of the alternatives. As used herein, the terms "include," "have," and "comprise" are used synonymously, and these terms and variations thereof are intended to be interpreted as non-restrictive. The term "optional" or "optionally" means that the subsequently described element, component, event, or condition may or may not occur, and the specification includes the occurrence and non-occurrence of the element, component, event, or condition. Furthermore, individual structures, or groups of structures, derived from various combinations of structures or subunits described herein are disclosed by the present application to the same extent as if each structure or group of structures were individually described. Thus, selection of a particular structure or a particular subunit is within the scope of the present disclosure. The term "consisting essentially of" is not equivalent to "comprising" and refers to specified materials or steps within the scope of the application, or materials or steps that do not materially affect the basic characteristics of the claimed subject matter. For example, a protein domain, region, or module (e.g., a binding domain) or protein "consists essentially of a particular amino acid sequence" when the amino acid sequence of the domain, region, module, or protein includes extensions, deletions, mutations, or combinations thereof (e.g., amino acids at the amino or carboxyl termini or between domains) that, taken together, account for up to 20% (e.g., up to 15%, 10%, 8%, 6%, 5%, 4%, 3%, 2%, or 1%) of the length of the domain, region, module, or protein and do not substantially affect (i.e., the activity is reduced by no more than 50%, such as no more than 40%, 30%, 25%, 20%, 15%, 10%, 5%, or 1%) the activity of one or more domains, one or more regions, one or more modules, or one or more proteins (e.g., the target binding affinity of the binding protein). As used herein, "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to naturally occurring amino acids. Naturally occurring amino acids are amino acids encoded by genetic codons, as well as those amino acids that are subsequently modified, such as hydroxyproline, γ-carboxyglutamine, and O-phosphoserine. Amino acid analogs refer to compounds that have the same basic chemical structure (i.e., α-carbon bound to hydrogen, carboxyl, amine, and R groups) as naturally occurring amino acids, such as serine, norleucine, methionine sulfoxide, and methionine methylsulfoxide. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as naturally occurring amino acids. Amino acid analogs refer to chemical compounds that have a structure that is different from the chemical structure of general amino acids, but function in a manner similar to naturally occurring amino acids. As used herein, "mutation" refers to a change in the sequence of a nucleic acid molecule or a polypeptide molecule compared to a reference or wild-type nucleic acid molecule or polypeptide molecule, respectively. Mutations can result in several different types of sequence changes, including substitutions, insertions, or deletions of one or more nucleotides or amino acids. "Reservation substitutions" refer to amino acid substitutions that do not significantly affect or change the binding properties of a particular protein. Generally speaking, a reservation substitution is one in which the substituted amino acid residue is replaced with an amino acid residue with a similar side chain. Conservative substitutions include substitutions found in one of the following groups: Group 1: alanine (Ala or A), glycine (Gly or G), serine (Ser or S), threonine (Thr or T); Group 2: aspartic acid (Asp or D), glutamine (Glu or Z); Group 3: asparagine (Asn or N), glutamine (Gln or Q); Group 4: arginine (Arg or R), lysine (Lys or K), histidine (His or H); Group 5: isoleucine (Ile or I), leucine (Leu or L), methionine (Met or M), valeric acid (Val or V); and Group 6: phenylalanine (Phe or F), tyrosine (Tyr or Y), tryptophan (Trp or W). Additionally or alternatively, amino acids can be grouped into conservative substitution groups by similar function, chemical structure, or composition (e.g., acidic, basic, aliphatic, aromatic, or sulfur-containing). For example, for substitution purposes, an aliphatic group can include Gly, Ala, Val, Leu, and Ile. Other reserved substitution groups include: sulfur-containing: Met and cysteine (Cys or C); acidic: Asp, Glu, Asn, and Gln; small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr, Pro, and Gly; polar, negatively charged residues and their amides: Asp, Asn, Glu, and Gln; polar, positively charged residues: His, Arg, and Lys; large aliphatic, nonpolar residues: Met, Leu, Ile, Val, and Cys; and large aromatic residues: Phe, Tyr, and Trp. Additional information can be found in Creighton (1984) Proteins, W.H. Freeman and Company. As used herein, "protein" or "polypeptide" refers to a polymer of amino acid residues. Proteins are applicable to naturally occurring amino acid polymers, and to amino acid polymers in which one or more amino acid residues are artificial chemical analogs of naturally occurring amino acids, and non-naturally occurring amino acid polymers. Variants of the proteins, peptides, and polypeptides disclosed herein are also contemplated. In certain embodiments, the variant proteins, peptides, and polypeptides comprise or consist of the following: an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.9% identical to a defined amino acid sequence or a reference amino acid sequence as described herein. Any polypeptide disclosed herein (e.g., VH, VL, Fab, Fd, antibody heavy chain, antibody light chain) may be encoded by a polynucleotide sequence comprising a "signal peptide" (also referred to as a leader sequence, leader peptide, or transporter peptide). The signaling peptide targets the newly synthesized polypeptide to its appropriate location inside or outside the cell. The signaling peptide may be removed in whole or in part from the polypeptide during or after localization or secretion is completed. A polypeptide with a (e.g., full-length) signaling peptide may be referred to as a "pre-protein," and a polypeptide from which the signaling peptide has been removed - at least partially removed - may be referred to as a "mature" protein or polypeptide. In certain embodiments, the antibody or antigen-binding fragment is a mature protein or pre-protein. "Nucleic acid molecule" or "polynucleotide" or "polynucleic acid" refers to a polymeric compound comprising covalently linked nucleotides, which nucleotides may be composed of natural subunits (e.g., purine or pyrimidine bases) or non-natural subunits (e.g.,The nucleic acid molecules include polyribonucleic acid (RNA), including mRNA, microRNA, siRNA, viral genomic RNA, and synthetic RNA; and polydeoxyribonucleotide (DNA), including cDNA, genomic DNA, and synthetic DNA, any of which may be single-stranded or double-stranded. If single-stranded, the nucleic acid molecule may be a coding strand or a non-coding (antisense) strand. Nucleic acid molecules encoding amino acid sequences include all nucleotide sequences encoding the same amino acid sequence. Some forms of nucleotide sequences may also include one or more introns by removing one or more introns by co-transcriptional or post-transcriptional mechanisms. In other words, due to redundancy or simplification of the genetic code, or by splicing, different nucleotide sequences can encode the same amino acid sequence.
Variants of the nucleic acid molecules disclosed herein are also contemplated. Variant nucleic acid molecules are at least 70%, 75%, 80%, 85%, 90%, and preferably 95%, 96%, 97%, 98%, 99%, or 99.9% identical to a defined nucleic acid molecule or reference polynucleotide as described herein, or hybridize with a polynucleotide under stringent hybridization conditions of 0.015M sodium chloride, 0.0015M sodium citrate at about 65 to 68°C or 0.015M sodium chloride, 0.0015M sodium citrate, and 50% formamide at about 42°C. Nucleic acid molecule variants retain the functionality described herein, such as the ability of their binding domains to bind to a target molecule.
"Percent sequence identity" refers to the determination of the relationship between two or more sequences by comparing the sequences. The preferred method for determining sequence identity is designed to give the best match between the compared sequences. For example, the sequences are compared for the purpose of optimal comparison (e.g., a spacer can be introduced into one or both of the first and second amino acid or nucleic acid sequences to achieve optimal comparison). In addition, non-homologous sequences can be ignored for comparison purposes. Unless otherwise indicated, the percentage sequence identity mentioned herein is calculated based on the length of the reference sequence. Methods for determining sequence identity and similarity can be found in publicly available computer programs. Sequence alignment and percentage identity calculations can be performed using BLAST programs (e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX). The mathematical algorithms used in the BLAST program can be found in Altschul
et al.,
Nucleic Acids Res.
25:3389-3402, 1997. In the context of this disclosure, it is understood that when sequence analysis software is used for analysis, the analysis results are based on the "default values" of the program mentioned. "Default values" means any value or parameter set that is initially loaded with the software when it is first initialized.
Other embodiments include Clustal W, MAFFT, Clustal Omega, AlignMe, Praline, GAP, BESTFIT, Needle (EMBOSS), Stretcher (EMBOSS), GGEARCH2SEQ, Water (EMBOSS), Matcher (EMBOSS), LALIGN, and SSEARCH2SEQ. Global alignment algorithms such as Needleman and Wunsch algorithms can be used to align two sequences based on their entire lengths to maximize the number of matches and minimize the number of gaps. Default values can be used.
To generate a similarity score for two amino acid sequences, a scoring matrix that assigns positive scores to some non-identical amino acids (e.g., amino acid substitutions that are conserved, amino acids that have similar physicochemical properties, and/or amino acids that exhibit frequent substitutions in heterologs, homologs, or homologs) can be used. Non-limiting examples of scoring matrices include PAM30, PAM70, PAM250, BLOSUM45, BLOSUM50, BLOUM62, BLOSUM80, and BLOSUM90.
The term "isolated" means that a substance is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally occurring nucleic acid or polypeptide present in a living animal is not isolated, but the same nucleic acid or polypeptide isolated from some or all coexisting materials in the natural system is isolated. Such a nucleic acid can be part of a vector and/or such a nucleic acid or polypeptide can be part of a composition (e.g., a cell lysate) and still be isolated in that such a vector or composition is not part of the natural environment of the nucleic acid or polypeptide.
The term "gene" means a segment of a DNA or RNA chain involved in producing a polypeptide chain; in certain contexts, it includes regions preceding or following the coding region (e.g., 5' untranslated regions (UTRs) and 3' UTRs) and intervening sequences (introns) between individual coding segments (exons).
"Functional variant" refers to a compound that is structurally similar or substantially similar to the parent and reference compounds disclosed herein, but slightly different in composition (e.g., a base, atom or functional group is different, added, or removed), such that the polypeptide or the encoded polypeptide is able to perform at least one function of the parent polypeptide with at least 50% efficiency, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% activity level. In other words, when compared to the parent or reference polypeptide, the functional variant has a higher activity in a selected assay (e.g., an assay for measuring binding affinity, such as association (Ka) or dissociation (K
D) constants) in Biacore® or tetramer staining), the polypeptide or the functional variant encoding the polypeptide disclosed herein has "similar binding", "similar affinity" or "similar activity".
As used herein, "functional portion" or "functional fragment" refers to a polypeptide or polynucleotide that only comprises a domain, part or fragment of a parent or reference compound, and the polypeptide or the encoded polypeptide retains at least 50% of the activity associated with the domain, part or fragment of the parent or reference compound, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% of the activity level of the parent polypeptide, or provides a biological benefit (e.g., effector function). When the functional part or fragment exhibits a performance reduction of no more than 50% in the selected assay compared to the parent or reference polypeptide (in terms of affinity, preferably no more than 20% or 10%, or no more than a logarithmic difference compared to the parent or reference), the polypeptide or the "functional part" or "functional fragment" encoding the polypeptide disclosed herein has "similar binding" or "similar activity".
As used herein, the term "engineered", "recombinant", or "non-natural" refers to an organism, microorganism, cell, nucleic acid molecule, or vector that includes at least one genetic alteration or has been modified by the introduction of an exogenous or heterologous nucleic acid molecule, wherein such alteration or modification is introduced by genetic engineering (i.e., human intervention). Genetic alterations include, for example, modifications that introduce expressible nucleic acid molecules encoding functional RNA, proteins, fusion proteins, or enzymes, or additions, deletions, substitutions, or other functional disruptions of the genetic material of the cell by other nucleic acid molecules. Additional modifications include, for example, non-coding regulatory regions, wherein such modifications alter the expression of a polynucleotide, gene, or operator.
As used herein, "heterologous" or "non-endogenous" or "exogenous" refers to any gene, protein, compound, nucleic acid molecule, or activity that is not native to a host cell or individual, or any gene, protein, compound, nucleic acid molecule, or activity that is native to a host cell or individual that has been altered. Heterologous, non-endogenous, or exogenous includes genes, proteins, compounds, or nucleic acid molecules that have been mutated or otherwise altered such that the structure, activity, or both are different between the native and altered genes, proteins, compounds, or nucleic acid molecules. In certain embodiments, heterologous, non-endogenous, or exogenous genes, proteins, or nucleic acid molecules (e.g., receptors, ligands, etc.) may not be endogenous to the host cell or individual, but nucleic acids encoding such genes, proteins, or nucleic acid molecules may be added to the host cell by conjugation, transformation, transfection, electroporation, etc., wherein the added nucleic acid molecule may be integrated into the host cell genome or may exist as extrachromosomal genetic material (e.g., as a plasmid or other self-replicating vector). The term "homologous" or "homolog" refers to a gene, protein, compound, nucleic acid molecule, or activity found in or derived from a host cell, species, or strain. For example, a heterologous or exogenous polynucleotide or gene encoding a polypeptide may be homologous to a native polynucleotide or gene and encode a homologous polypeptide or activity, but the polynucleotide or polypeptide may have an altered structure, sequence, expression level, or any combination thereof. Non-endogenous polynucleotides or genes, and encoded polypeptides or activities may be from the same species, a different species, or a combination thereof.
In certain embodiments, a nucleic acid molecule native to a host cell or a portion thereof is considered heterologous to the host cell if it has been altered or mutated, or a nucleic acid molecule native to a host cell is considered heterologous to the host cell if it has been altered by a heterologous expression control sequence or by an endogenous expression control sequence that is not normally associated with a nucleic acid molecule native to the host cell. In addition, the term "heterologous" may refer to a biological activity that is different from, altered, or not endogenous to the host cell. As described herein, more than one heterologous nucleic acid molecule may be introduced into a host cell as a single nucleic acid molecule, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding a fusion protein, or any combination thereof.
As used herein, the term "endogenous" or "native" refers to a polynucleotide, gene, protein, compound, molecule, or activity that is normally present in a host cell or individual.
As used herein, the term "expression" refers to the process of producing a polypeptide based on the coding sequence of a nucleic acid molecule (such as a gene). Such processes include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post-translational modification, or any combination thereof. The expressed nucleic acid molecule is generally operably linked to an expression control sequence (such as a promoter).
The term "operably linked" refers to the process of producing a polypeptide based on the coding sequence of a nucleic acid molecule (such as a gene). "Linked" means that two or more nucleic acid molecules are attached to a single nucleic acid fragment so that the function of one is affected by the other. For example, when a promoter is able to affect the expression of a coding sequence, the promoter is operably linked to the coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter). "Unlinked" means that the related genetic elements are not closely attached to each other, and the function of one does not affect the other.
As described herein, more than one heterologous nucleic acid molecule can be introduced into a host cell as a single nucleic acid molecule, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding a protein (e.g., the heavy chain of an antibody), or any combination thereof. When two or more heterologous nucleic acid molecules are introduced into a host cell, it is understood that the two or more heterologous nucleic acid molecules can be introduced as a single nucleic acid molecule (e.g., on a single vector) on a separate vector and integrated into a single site or multiple sites in the host chromosome, or any combination thereof. The number of heterologous nucleic acid molecules or protein activities mentioned refers to the number of encoding nucleic acid molecules or the number of protein activities, not the number of individual nucleic acid molecules introduced into the host cell.
The term "construct" refers to any polynucleotide containing a recombinant nucleic acid molecule (or, when the context clearly indicates, a fusion protein of the present disclosure). The (polynucleotide) construct may be present in a vector (e.g., a bacterial vector, a viral vector) or may be integrated into a genome. A "vector" is a nucleic acid molecule capable of transporting another nucleic acid molecule. For example, a vector may be a plasmid, a muscisome, a virus, an RNA vector, or a linear or circular DNA or RNA molecule, which may include chromosomal, non-chromosomal, semisynthetic or synthetic nucleic acid molecules. The vectors of the present disclosure also include transposon systems (e.g., Sleeping Beauty, see, e.g.,
Geurts et al., Mol. Ther. 8:108, 2003: March
et al., Nat. Genet.41:753, 2009). Exemplary vectors are those capable of autonomous replication (episomal vectors), capable of delivering polynucleotides to the cell genome (e.g., viral vectors), or capable of expressing nucleic acid molecules to which they are linked (expression vectors).
As used herein, "expression vector" or "vector" refers to a DNA construct containing a nucleic acid molecule that is operably linked to a suitable control sequence that enables expression of the nucleic acid molecule in a suitable host. Such control sequences include promoters that enable transcription, optional operator sequences that control such transcription, sequences encoding suitable mRNA ribosome binding sites, and sequences that control transcription and translation termination. A vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert. Once transformed into a suitable host, the vector can replicate and function independently of the host genome, or can in some cases integrate into the genome itself or deliver the polynucleotide contained in the vector to a genome that does not have the vector sequence. In this specification, "plastid", "expression plasmid", "virus", and "vector" are often used interchangeably.
The term "introduced" in the context of inserting a nucleic acid molecule into a cell means "transfection", "transformation", or "transduction", and includes reference to the incorporation of a nucleic acid molecule into a eukaryotic cell or a prokaryotic cell, where the nucleic acid molecule can be incorporated into the cell's genome (e.g., chromosome, plastid, chromatin, or mitochondrial DNA), converted into an autonomous replicator, or transiently expressed (e.g., transfected mRNA).
In certain embodiments, the polynucleotides disclosed herein can be operably linked to certain elements of a vector. For example, a polynucleotide sequence required to achieve expression and processing of the coding sequence to which it is joined can be operably linked. Expression control sequences can include appropriate transcriptional initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals, such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequences); sequences that enhance protein stability; and sequences that may enhance protein secretion. An expression control sequence can be operably linked if it is adjacent to the gene of interest and the expression control sequence acts in trans or at a distance to control the gene of interest.
In certain embodiments, the vector comprises a plasmid vector or a viral vector (e.g., a lentiviral vector or a γ-retroviral vector). Viral vectors include retroviruses, adenoviruses, parvoviruses (e.g., adeno-associated viruses), coronaviruses, negative-stranded RNA viruses such as orthomyxoviruses (e.g., influenza virus), rhabdoviruses (e.g., rabies and vesicular stomatitis virus), paramyxoviruses (e.g., measles and Sendai virus), positive-stranded RNA viruses such as picornaviruses and alphaviruses, and double-stranded DNA viruses including adenoviruses, herpes simplex viruses (e.g., herpes simplex virus type 1 and type 2, Epstein-Barr virus, cytomegalovirus), and poxviruses (e.g., vaccinia, fowlpox, and canarypox). Other viruses include, for example, Norwalk virus, togavirus, flavivirus, reovirus, papovavirus, hepadnavirus, and hepatitis virus. Examples of retroviruses include avian leukemic sarcoma, mammalian C-type virus, B-type virus, D-type virus, HTLV-BLV group, lentivirus, foamy virus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
A "retrovirus" is a virus with an RNA genome that is reverse transcribed into DNA using a reverse transcriptase enzyme, which is then incorporated into the host cell genome. A "gammaretrovirus" refers to a genus in the Retroviridae family. Examples of gammaretroviruses include mouse stem cell virus, murine leukemia virus, feline leukemia virus, feline sarcoma virus, and avian reticuloendothelial virus.
"Lentiviral vectors" include HIV-based lentiviral vectors for gene delivery that can be integrating or non-integrating, have relatively large packaging capacity, and can transduce a range of different cell types. Lentiviral vectors are typically produced after three (packaging, envelope, and transfer) or more plasmids are temporarily transfected into production cells. Like HIV, lentiviral vectors enter target cells through the interaction of viral surface glycoproteins with receptors on the cell surface. After entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is double-stranded linear viral DNA, which is the substrate for viral integration into the DNA of infected cells.
In certain embodiments, the viral vector may be a gamma retrovirus, such as a vector derived from Moloney murine leukemia virus (MLV). In other embodiments, the viral vector may be a more complex retrovirus-derived vector, such as a lentivirus-derived vector. HIV-1-derived vectors belong to this category. Other embodiments include lentiviral vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and Maedi-Visna virus (ovine lentivirus). Methods for transducing mammalian host cells with viral particles containing transgenes using retrovirus and lentiviral vectors and packaging cells are known in the art and have been previously described, for example, in the following documents: U.S. Patent No. 8,119,772; Walchli
et al.,
PLoS One 6:327930, 2011; Zhao
et al.,
J. Immunol.174:4415, 2005; Engels
et al.,
Hum. Gene Ther. 14:1155, 2003; Frecha
et al.,
Mol.Ther.
18:1748, 2010; and Verhoeyen
et al.,
Methods Mol. Biol. 506:97, 2009. Retroviral and lentiviral vector constructs and expression systems are also commercially available. Other viral vectors can also be used for polynucleotide delivery including DNA viral vectors, such as adenovirus-based vectors and adeno-associated virus (AAV)-based vectors; vectors derived from herpes simplex virus (HSV), including amplicon vectors, replication-defective HSV and attenuated HSV (Krisky
et al.,
Gene Ther.5:1517, 1998).
Other vectors that can be used with the compositions and methods disclosed herein include vectors derived from bacilli and alpha viruses. (Jolly, DJ. 1999. Emerging Viral Vectors. pp 209-40 in Friedmann T. ed. The Development of Human Gene Therapy. New York: Cold Spring Harbor Lab), or plasmid vectors (such as sleeping beauty or other transposon vectors).
When the viral vector genome comprises a plurality of polynucleotides to be expressed as separate transcripts in a host cell, the viral vector may also comprise additional sequences between two (or more) transcripts that allow bicistronic or polycistronic expression. Examples of such sequences for viral vectors include an internal ribosome entry site (IRES), a furin cleavage site, a viral 2A peptide, or any combination thereof.
Further described herein are plasmid vectors, including plasmid vectors encoding DNA-based antibodies or antigen-binding fragments for direct administration to an individual.
As used herein, the term "host" refers to a cell or microorganism targeted for genetic modification with a heterologous nucleic acid molecule to produce a polypeptide of interest, such as an antibody of the present disclosure.
A host cell may include any individual cell or cell culture that can accept a vector or incorporate a nucleic acid or express a protein. The term also encompasses progeny of the host cell, whether genetically or phenotypically identical or different. Suitable host cells may depend on the vector and may include mammalian cells, animal cells, human cells, monkey cells, insect cells, yeast cells, and bacterial cells. These cells may be induced to incorporate vectors or other substances by the use of viral vectors, transformation by calcium phosphate precipitation, DEAE-polydextrose, electroporation, microinjection, or other methods. See, e.g., Sambrook
et al.,
Molecular Cloning: A Laboratory Manual2d ed.(Cold Spring Harbor Laboratory, 1989).
In the context of SARS-betacoronavirus infection, "host" refers to a cell or individual infected with SARS-betacoronavirus.
As used herein, "antigen" or "Ag" refers to an immunogenic molecule that elicits an immune response. This immune response may involve antibody production, activation of specific immunologically competent cells, activation of complements, antibody-dependent cellular cytotoxicity, or any combination thereof. Antigens (immunogenic molecules) may be, for example, peptides, glycopeptides, polypeptides, glycopolypeptides, polynucleotides, polysaccharides, lipids, etc. Obviously, antigens may be synthetic, recombinantly produced, or derived from biological samples. Exemplary biological samples that may contain one or more antigens include tissue samples, fecal samples, cells, biological fluids, or combinations thereof. Antigens may be produced by cells that have been modified or genetically engineered to express the antigen. Antigens may also be present in SARS-betacoronavirus (surface glycoproteins or portions thereof), such as in viral particles, or expressed or presented on the surface of cells infected with SARS-betacoronavirus.
The term "epitope" or "antigenic epitope" includes any molecule, structure, amino acid sequence, or protein determinant that is recognized and specifically bound by a cognate binding molecule such as an immunoglobulin, or other binding molecule, domain, or protein. Epitope determinants usually contain chemically active surface molecular groups (such as amino acids or sugar side chains) and may have specific three-dimensional structural properties as well as specific charge properties. When the antigen is or comprises a peptide or protein, the epitope may comprise consecutive amino acids (e.g., a linear epitope); or may comprise amino acids from different parts or regions of the protein that are brought into close proximity by protein folding (e.g., a discontinuous or conformational epitope); or non-adjacent amino acids in close proximity that are not associated with protein folding.
Antibodies, antigen-binding fragments, and compositions In one aspect, the disclosure provides an isolated antibody, or an antigen-binding fragment thereof, that is capable of binding to a surface glycoprotein of a severe acute respiratory syndrome beta coronavirus (e.g., SARS-CoV-2). In some embodiments, the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of two or more severe acute respiratory syndrome beta coronaviruses, three or more severe acute respiratory syndrome beta coronaviruses, four or more severe acute respiratory syndrome beta coronaviruses, or five or more severe acute respiratory syndrome beta coronaviruses. In some embodiments, the antibody or antigen-binding fragment comprises a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3.
In some embodiments, two or more, three or more, four or more, or five or more severe acute respiratory syndrome beta coronaviruses comprise or one or more, or are selected from clade 1b severe acute respiratory syndrome beta coronaviruses or naturally occurring variants thereof, and any combination thereof. In certain embodiments, the antibody or antigen-binding fragment is capable of binding to the surface glycoproteins of two or more, three or more, four or more, or five or more severe acute respiratory syndrome beta coronaviruses; for example, it is capable of binding when the surface glycoproteins of severe acute respiratory syndrome beta coronaviruses are expressed on the cell surface of host cells and/or on severe acute respiratory syndrome beta coronavirus virus particles. In certain embodiments, two or more, three or more, four or more, or five or more severe acute respiratory syndrome beta coronaviruses are selected from SARS-CoV-2, PANG/GD, PANG/GX, RatG13, and naturally occurring variants thereof. In some embodiments, two or more, three or more, four or more, or five or more severe acute respiratory syndrome beta coronaviruses include one or more of the SARS-CoV-2 variants. In certain further embodiments, the antibody or antigen-binding fragment thereof is capable of binding to one or more SARS-CoV-2 variants. Embodiments of clade 1b also include SARS-CoV-2 variants, such as variants having any of the following mutations: A67V, Δ69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, Δ212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (wherein X is any amino acid except L), Y453F, S477N, T478K, V483A, E484A, E484Q, E484K, E484X (wherein X is any amino acid except E), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q613H, D61 4G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, D614, E340A, or variants in the following genealogies: B.1.1.7 and Q genealogies and subsequent genealogies (Alpha); B.1.351 and subsequent genealogies (Beta); B.1.429 and B.1.427 and subsequent genealogies (Epsilon); P.1 and subsequent genealogies (Gamma); B.1.1.222; C .37; B.1.617.2; AY.1, AY.2, other AY series and later series (Delta); B.1.525 and later series (Eta); B.1.526 and later series (Iota); B.1.617.1 and later series (Kappa); 1.617.3; B.1.621 and B.1.621.1 and later series (Mu); P.2 (Zeta); and B.1.1.529.1, BA.1, BA.2, BA.2.12, BA.3, BA.4, BA.5 and later series (Omicron); BQ.1.1; XBB.1.
In some embodiments, two or more, three or more, four or more, or five or more SARS-CoV-2 beta coronaviruses include one or more SARS-CoV-2 variants with the following S protein mutations: D614G, Q493R, G496S, Q498R, N501Y, Y453F, N439K, K417V, E484K, or any combination thereof. In some embodiments, two or more SARS-CoV-2 beta coronaviruses include one or more SARS-CoV-2 variants with the following S protein mutations: K417N, Q493K, G496S, or any combination thereof.
In certain embodiments, the antibody or antigen-binding fragment disclosed herein binds or associates with a severe acute respiratory syndrome beta coronavirus surface glycoprotein epitope or an antigen comprising the epitope, but does not significantly bind or associate with any other molecule or component in the sample. In some embodiments, the epitope is contained in the S1 subunit of the S protein. In further embodiments, the epitope is contained in the RBD of the S protein. In some embodiments, the epitope is a conformational epitope or a linear epitope.
In certain embodiments, the antibody or antigen-binding fragment disclosed herein binds or associates (e.g., binds) with a first severe acute respiratory syndrome beta coronavirus surface glycoprotein epitope, and may also bind or associate with an epitope from another severe acute respiratory syndrome beta coronavirus present in the sample, but does not significantly bind or associate with any other molecule or component in the sample. In other words, in certain embodiments, the antibody or antigen-binding fragment disclosed herein is cross-reactive and specifically binds to two or more severe acute respiratory syndrome beta coronaviruses (e.g., SARS-CoV-2 Wuhan-Hu-1 and one or more variants thereof).
In certain embodiments, the antibody or antigen-binding fragment disclosed herein specifically binds to severe acute respiratory syndrome beta coronavirus surface glycoprotein. As used herein, "specifically bind" refers to the affinity or K of an antibody or antigen-binding fragment to bind or associate with an antigen.a(i.e., the equilibrium constant of a specific binding interaction, expressed in 1/M) equal to or greater than 10
5M
-1(It is equal to the on-rate of this on-reaction [K
on] for the dissociation rate (off rate) [K
off] ratio), but does not significantly bind or associate with any other molecule or component in the sample. Alternatively, affinity can be defined as the equilibrium dissociation constant (K) of a specific binding interaction.d), the unit is M (for example 10
-5M to 10
-13M). Antibodies can be classified as either "high affinity" antibodies or "low affinity" antibodies. "High affinity" antibodies are antibodies with at least 10
7M
-1, at least 10
8M
-1, at least 10
9M
-1, at least 10
10M
-1, at least 10
11M
-1, at least 10
12M
-1, or at least 10
13M
-1K
a"Low affinity" antibodies are antibodies with a binding affinity of at most 10
7M
-1, up to 10
6M
-1, up to 10
5M
-1K
aof those antibodies. Alternatively, affinity can be defined as the equilibrium dissociation constant (K
d), the unit is M (for example 10
-5M to 10
-13M).
Various assays are known for identifying antibodies disclosed herein that bind to specific targets, and for determining the affinity of binding domains or binding proteins, such as Western blots, ELISA (e.g., direct, indirect, or sandwich), analytical ultracentrifugation, spectroscopy, and surface plasmon resonance (Biacore®) analysis (see, e.g., Scatchard
et al.,
Ann. NY Acad. Sci. 51:660, 1949; Wilson,
Science 295:2103, 2002; Wolff
et al.,
Cancer Res.53:2560, 1993; and U.S. Patent Nos. 5,283,173, 5,468,614, or equivalents). Assays for assessing affinity or apparent affinity or relative affinity are also known.
In certain embodiments, the antibodies or antigen-binding fragments of the present disclosure bind to one or more, or two or more clade 1b SARS-CoV-2 with an EC50 of about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 16.0 ng/mL to about 100 ng/mL, about 18.0 ng/mL to about 100 ng/mL, about 19.0 ng/mL to about 100 ng/mL, about 20.0 ng/mL to about 100 ng/mL, about 21.0 ng/mL to about 100 ng/mL, about 23.0 ng/mL to about 100 ng/mL, about 24.0 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to about 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, which can be measured by ELISA. In some embodiments, the antibody or antigen-binding fragment binds to the spike (S) protein RBD from one, two, three, four, or five severe acute respiratory syndrome beta coronaviruses.
In some embodiments, the antibody or antigen-binding fragment is capable of binding to the first and second severe acute respiratory syndrome beta coronaviruses each independently selected from clade 1b, wherein the antibody or antigen-binding fragment is capable of binding to the first severe acute respiratory syndrome beta coronavirus with an EC50 of about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, and is capable of binding to SARS-CoV-2 beta coronavirus with the following EC50: about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, the antibody is (or the antigen-binding fragment is) S3A3, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3A3 or variants disclosed herein. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3A3 or variants disclosed herein to confer similar specific binding, or fragments thereof, and is capable of binding to SARS-CoV-2 RBD with a KD of about 1.0 x 10
-09M and about 1.0 x 10
-08M, about 1.2 x 10
-09M and about 1.0 x 10
-08M, about 1.5 x 10
-09M and about 1.0 x 10
-08M, about 2.0 x 10
-09M and about 1.0 x 10
-08M, about 2.25 x 10
-09M and about 1.0 x 10
-08M, about 2.5 x 10
-09M and about 1.0 x 10
-08M, about 3.0 x 10
-09M and about 1.0 x 10
-08M, about 3.5 x 10
-09M and about 1.0 x 10
-08M, about 4.0 x 10
-09M and about 1.0 x 10
-08M, about 4.5 x 10
-09M and about 1.0 x 10
-08M, or about 5.0 x 10
-09M and about 1.0 x 10
-08M, about 1.0 x 10
-09M, or about 1.2 x 10
-09M, about 1.5 x 10
-09M, about 2.0 x 10
-09M, about 2.25 x 10
-09M, about 2.5 x 10
-09M, about 3.0 x 10
-09M, about 4.0 x 10
-09M, about 4.5 x 10
-09M, or about 5.0 x 10
-09M, or not more than approximately 1.0 x 10
-09M, or about 1.2 x 10
-09M, about 1.5 x 10
-09M, about 2.0 x 10
-09M, about 2.25 x 10
-09M, about 2.5 x 10
-09M, about 3.0 x 10
-09M, about 4.0 x 10
-09M, about 4.5 x 10
-09M, or about 5.0 x 10
-09M, as can be determined by biotin interferometry (e.g., using Octet).
In some embodiments, the antibody is (or the antigen-binding fragment is) S3A19, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S3A19 or variants disclosed herein. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3A19 or variants disclosed herein to confer similar specific binding, or fragments thereof, and is capable of binding to SARS-CoV-2 RBD with a KD of about 1.0 x 10
-12M and about 5.0 x 10
-08M, about 1.5 x 10
-12M and about 5.0 x 10
-08M, about 2.0 x 10
-12M and about 5.0 x 10
-08M, about 2.25 x 10
-12M and about 5.0 x 10
-08M, about 2.5 x 10
-12M and about 5.0 x 10
-08M, about 1.0 x 10
-11M and about 5.0 x 10
-08M, about 1.0 x 10
-10M and about 5.0 x 10
-08M, about 1.0 x 10
-09M and about 5.0 x 10
-08M, about 1.0 x 10
-08M and about 5.0 x 10
-08M, about 1.0 x 10
-12M, or about 1.5 x 10
-12M, about 2.0 x 10
-12M, about 2.25 x 10
-12M, about 2.5 x 10
-12M, about 1.0 x 10
-11M, about 1.0 x 10
-10M, about 1.0 x 10
-09M, or not more than approximately 1.0 x 10
-12M, or about 1.5 x 10
-12M, about 2.0 x 10
-12M, about 2.25 x 10
-12M, about 2.5 x 10
-12M, about 1.0 x 10
-11M, about 1.0 x 10
-10M, about 1.0 x 10
-09M, as can be determined by biotin interferometry (e.g., using Octet).
In some embodiments, the antibody is (or the antigen-binding fragment is) S3I2, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S3I2 or variants disclosed herein. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 or variants disclosed herein to confer similar specific binding, or fragments thereof, and is capable of binding to an antigen at about 1.0 x 10
-12M and about 5.0 x 10
-08M and bind to SARS-CoV-2 RBD with a KD in the range of about 1.0 x 10.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3O13, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S3O13 or variants disclosed herein. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 or variants disclosed herein to confer similar specific binding, or fragments thereof, and is capable of binding to SARS-CoV-2 RBD at about 1.0 x 10-12M and about 5.0 x 10
-08M and bind to SARS-CoV-2 RBD with a KD in the range of about 1.0 x 10
In some embodiments, the antibody is (or the antigen-binding fragment is) S3L17, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S3L17 or variants disclosed herein. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 or variants disclosed herein to confer similar specific binding, or fragments thereof, and is capable of binding to SARS-CoV-2 RBD at about 1.0 x 10
-12M and about 5.0 x 10
-08M for binding to the SARS-CoV-2 RBD.
In certain embodiments, binding can be determined by recombinantly expressing SARS-CoV-2 antigens in host cells (e.g., by transfection) and immunostaining the host cells with the antibody (e.g., fixed, or fixed and pre-permeabilized), and analyzing by flow cytometry (e.g., using a ZE5 cytometer (BioRad®) and FlowJo software (TreeStar)). In some specific embodiments, positive binding can be defined by differential staining of cells expressing SARS-CoV-2 versus control (e.g., mock) cells with the antibody.
In some embodiments, the antibodies or antigen-binding fragments of the present disclosure bind to SARS-CoV-2 spike proteins (i.e., from two or more, three or more, four or more, or five or more SARS-CoV-2 beta-coronaviruses) expressed on the surface of host cells (e.g., Expi-CHO cells) as measured by flow cytometry.
In some embodiments, the antibodies or antigen-binding fragments of the present disclosure bind to SARS-CoV-2 S protein as measured using bio-thin layer interferometry.
In certain embodiments, the antibodies of the present disclosure are capable of neutralizing infection caused by one or more, or by two or more SARS-CoV-2 beta-coronaviruses. As used herein, a "neutralizing antibody" is an antibody that neutralizes, i.e., prevents, inhibits, reduces, blocks or interferes with the ability of a pathogen to initiate and/or maintain infection in a host. The terms "neutralizing antibody" and "an antibody that neutralizes/antibodies that neutralize" are used interchangeably herein. In any of the currently disclosed embodiments, the antibody or antigen-binding fragment is capable of preventing and/or neutralizing infection caused by one or more, or by two or more, SARS-beta coronaviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in humans.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3A3, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3A3 or a variant disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S3A3 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) at about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 11.0 ng/mL to about 11.0 ng/mL ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to about 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, the antibody is (or the antigen-binding fragment is) S3A19, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3A19 or a variant disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S3A19 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) at about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25 ng/mL to about 100 ng/mL, about 26 ng/mL to about 100 ng/mL, about 28 ng/mL to about 100 ng/mL, about 29 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 31 ng/mL to about 100 ng/mL, about 32 ng/mL to about 100 ng/mL, about 33 ng/mL to about 100 ng/mL, about 34 ng/mL to about 100 ng/mL, about 35 ng/mL to about 100 ng/mL, about 36 ng/mL to about 100 ng/mL, about 37 ng/mL to about 100 ng/mL, about 38 ng/mL to about 100 ng/mL ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to about 50 ng/mL, or in the range of about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3I2, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3I2 or a variant disclosed herein. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 or variants disclosed herein to confer similar specific binding, or fragments thereof, and is capable of neutralizing infection caused by SARS-CoV-2 in a pseudoviral system (e.g., MLV-pp-based or VSV-pp-based) in the range of about 0.5 ng/mL to about 100 ng/mL.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3O13, or the antibody or antigen-binding fragment comprises CDRs and, optionally, VH and VL of S3O13 or variants disclosed herein. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 or variants disclosed herein to confer similar specific binding, or fragments thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudoviral system (e.g., MLV-pp-based or VSV-pp-based) in the range of about 0.5 ng/mL to about 100 ng/mL.
In some embodiments, the antibody is (or the antigen-binding fragment is) S3L17, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S3L17 or variants disclosed herein. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 or variants disclosed herein to confer similar specific binding, or fragments thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudoviral system (e.g., MLV-pp-based or VSV-pp-based) in the range of about 0.5 ng/mL to about 100 ng/mL.
In some embodiments, the antibody is (or the antigen-binding fragment is from) S2V29, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S2V29 or variants disclosed herein. In some embodiments, the antibodies comprise sufficient CDR, VH, and/or VL identity to S2V29 or variants disclosed herein to confer similar specific binding, or fragments thereof, and are capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) within a range of about 0.5 ng/mL to about 100 ng/mL.
In certain embodiments, the antibody or antigen-binding fragment (i) recognizes an epitope in the spike protein of two or more severe acute respiratory syndrome beta coronaviruses; (ii) is capable of blocking the interaction between the spike protein of one or more severe acute respiratory syndrome beta coronaviruses and a cell surface receptor; (iii) recognizes an epitope retained in the spike protein of two or more severe acute respiratory syndrome beta coronaviruses; (iv) is cross-reactive against two or more severe acute respiratory syndrome beta coronaviruses; or (v) any combination of (i) to (iv).
Unless otherwise expressly defined herein, terms in the field of antibody technology that are understood by a person of ordinary skill in the art each have the meaning given to them in the art. For example, the term "antibody" refers to an intact antibody comprising at least two heavy (H) chains and two light (L) chains interconnected by disulfide bonds, and any antigen-binding portion or fragment of an intact antibody that has or retains the ability to bind to an antigen target molecule recognized by the intact antibody, such as a scFv, Fab, or Fab'2 fragment. Therefore, the term "antibody" herein is used in the broadest sense and includes polyclonal and monoclonal antibodies, including intact antibodies and functional (antigen-binding) antibody fragments thereof, including fragment antigen-binding fragment (Fab) fragments, F(ab')2 fragments, Fab' fragments, Fv fragments, recombinant IgG (rIgG) fragments, single-chain antibody fragments, including single-chain variable fragments (scFv), and single-domain antibody (e.g., sdAb, sdFv, nanobody) fragments. The term covers genetically engineered and/or otherwise modified forms of immunoglobulins, such as intrabodies, peptibodies, chimeric antibodies, fully human antibodies, humanized antibodies, and heteroconjugate antibodies, multispecific (e.g., bispecific) antibodies, bifunctional antibodies, trifunctional antibodies, tetrafunctional antibodies, tandem di-scFvs, and tandem tri-scFvs. Unless otherwise specified, the term "antibody" should be understood to cover functional antibody fragments thereof. The term also covers intact or full-length antibodies, including antibodies of any class or subclass, including IgG and its subclasses (IgG1, IgG2, IgG3, IgG4), IgM, IgE, IgA, and IgD.
The term "V
L" or "VL" and "V
H" or "VH" refers to the variable binding region from the antibody light chain and the antibody heavy chain, respectively. In some embodiments, the VL is of the kappa class (also referred to herein as "VK"). In some embodiments, the VL is of the lambda class. The variable binding region comprises discrete, well-defined subregions, referred to as "complementarity determining regions" (CDRs) and "framework regions" (FRs). The terms "complementarity determining region" and "CDR" are synonymous with "hypervariable region" or "HVR", and refer to amino acid sequences within the variable region of an antibody that generally together confer antigen specificity and/or binding affinity to the antibody, wherein in the primary structure, consecutive CDRs (i.e., CDR1 and CDR2, CDR2 and CDR3) are separated from each other by framework regions. There are three CDRs in each variable region (HCDR1, HCDR2, HCDR3; LCDR1, LCDR2, LCDR3; also referred to as CDRH and CDRL, respectively). In certain embodiments, the antibody VH comprises the following four FRs and three CDRs: FR1-HCDR1-FR2-HCDR2-FR3-HCDR3-FR4, and the antibody VL comprises the following four FRs and three CDRs: FR1-LCDR1-FR2-LCDR2-FR3-LCDR3-FR4. Typically, VH and VL together form an antigen binding site through their individual CDRs.
In any of the currently disclosed embodiments, the antibody or antigen-binding fragment is capable of preventing and/or neutralizing infection caused by one or more, or by two or more severe acute respiratory syndrome beta coronaviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in humans.
In certain embodiments, antibodies or antigen-binding fragments comprising VH and VL are provided, wherein the VH and VL respectively comprise or consist of the following amino acid sequences: 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 17) SEQ ID NO: 181 and 87; 18) SEQ ID NO: 181 and 87; 19) SEQ ID NO: 183 and 193; 20) SEQ ID NO: 185 and 87; 21) SEQ ID NO: 185 and 87; 22) SEQ ID NO: 190 and 87; 23) SEQ ID NO: 190 and 193; 24) SEQ ID NO: 93 and 97; 25) SEQ ID NO: 93 and 225; 26) SEQ ID NO: 93 and 228; 27) SEQ ID NO: 93 and 231; 28) SEQ ID NO: 41) SEQ ID NO: 207 and 225; 42) SEQ ID NO: 207 and 228; 43) SEQ ID NO: 54) SEQ ID NO: 214 and 228; 55) SEQ ID NO: 214 and 231; 56) SEQ ID NO: 216 and 97; 57) SEQ ID NO: 216 and 225; 58) SEQ ID NO: 69) SEQ ID NO: 222 and 225; 70) SEQ ID NO: 222 and 228; 71) SEQ ID NO: 222 and 231; 72) SEQ ID NO: 102 and 105; 73) SEQ ID NO: 106 and 107; 74) SEQ ID NO: 108 and 109; 75) SEQ ID NO: 112 and 113; 76) SEQ ID NO: 114 and 115; 77) SEQ ID NO: 115 and 116; 78) SEQ ID NO: 116 and 228; 79) SEQ ID NO: 216 and 231; 80) SEQ ID NO: 218 and 97; 81) SEQ ID NO: 218 and 225; 82) SEQ ID NO: 218 and 228; 83) SEQ ID NO: 218 and 231; 84) SEQ ID NO: 220 and 97; 85) SEQ ID NO: 220 and 225; 86) SEQ ID NO: 220 and 228; 87) SEQ ID NO: 220 and 231; 88) SEQ ID NO: 222 and 97; 7) SEQ ID NO: 235 and 260; 80) SEQ ID NO: 238 and 105; 81) SEQ ID NO: 238 and 254; 82) SEQ ID NO: 238 and 257; 83) SEQ ID NO: 238 and 260; 84) SEQ ID NO: 241 and 105; 85) SEQ ID NO: 241 and 254; 86) SEQ ID NO: 241 and 257; 87) SEQ ID NO: 97) SEQ ID NO: 247 and 254; 98) SEQ ID NO: 247 and 257; 99) SEQ ID NO: 247 and 260; 100) SEQ ID NO: 249 and 105; 101) SEQ ID NO: 10) SEQ ID NO: 111 and 121; 110) SEQ ID NO: 111 and 157; 111) SEQ ID NO: 111 and 272; 112) SEQ ID NO: 111 and 277; 113) SEQ ID NO: 111 and 279; 114) SEQ ID NO: 111 and 282; 115) SEQ ID NO: 111 and 282; 125) SEQ ID NO: 125 and 290; 126) SEQ ID NO: 128 and 115; 127) SEQ ID NO: 128 and 121; 128) SEQ ID NO: 128 and 157; 129) SEQ ID NO: 129 and 272; 130) SEQ ID NO: 129 and 277; 131) SEQ ID NO: 129 and 279; 132) SEQ ID NO: 129 and 282; 133) SEQ ID NO: 129 and 286; 134) SEQ ID NO: 129 and 290; 135) SEQ ID NO: 128 and 115; 136) SEQ ID NO: 128 and 121; 137) SEQ ID NO: 128 and 157; 138) SEQ ID NO: 128 and 157; 139) SEQ ID NO: 129 and 272; 140) SEQ ID NO: 129 and 277; 141) SEQ ID NO: 129 and 279; 142) SEQ ID NO: 129 and 282; 143) SEQ ID NO: 129 and 286; 144) SEQ ID NO: 129 and 290; 145) SEQ ID NO: 129 and 291; 146) SEQ ID NO: 12 136) SEQ ID NO: 131 and 272; 137) SEQ ID NO: 131 and 277; 138) SEQ ID NO: 131 and 279; 139) SEQ ID NO: 131 and 282; 140) SEQ ID NO: 131 and 286; 141) SEQ ID NO: 131 and 290; 142) SEQ ID NO: 134 and 115; 143) SEQ ID NO: 134 and 121; 144) SEQ ID NO: 134 and 157; 145) SEQ ID NO: 134 and 272; 146) SEQ ID NO: 134 and 277; 147) SEQ ID NO: 134 and 279; 148) SEQ ID NO: 134 and 282; 149) SEQ ID NO: 134 and 286; 150) SEQ ID NO: 134 and 290; 151) SEQ ID NO: 137 and 115; 152) SEQ ID NO: 137 and 121; 153) SEQ ID NO: 137 and 157; 154) SEQ ID NO: 137 and 272; 155) SEQ ID NO: 156) SEQ ID NO: 137 and 279; 157) SEQ ID NO: 137 and 282; 158) SEQ ID NO: 137 and 286; 159) SEQ ID NO: 137 and 290; 160) SEQ ID NO: 141 and 115; 161) SEQ ID NO: 141 and 121; 162) SEQ ID NO: 141 and 157; 162) SEQ ID NO: 141 and 272; 162) SEQ ID NO: 141 and 277; 163) SEQ ID NO: 141 and 279; 164) SEQ ID NO: 141 and 282; 165) SEQ ID NO: 141 and 286; 166) SEQ ID NO: 141 290; 167) SEQ ID NO: 141 176) SEQ ID NO: 145 and 290; 177) SEQ ID NO: 149 and 115; 178) SEQ ID NO: 149 and 121; 179) SEQ ID NO: 149 and 157; 170) SEQ ID NO: 149 and 272; 171) SEQ ID NO: 149 and 277; 172) SEQ ID NO: 149 and 279; 173) SEQ ID NO: 149 and 282; 174) SEQ ID NO: 149 and 282; 175) SEQ ID NO: 149 and 286; 176) SEQ ID NO: 149 and 290; 177) SEQ ID NO: 149 and 115; 178) SEQ ID NO: 149 and 121; 179) SEQ ID NO: 149 and 157; 180) SEQ ID NO: 149 and 272; 181) SEQ ID NO: 149 and 277; 190) SEQ ID NO: 153 and 277; 191) SEQ ID NO: 153 and 279; 192) SEQ ID NO: 153 and 282; 193) SEQ ID NO: 153 and 286; 194) SEQ ID NO: 153 and 290; 195) SEQ ID NO: 153 and 115; 187) SEQ ID NO: 153 and 121; 188) SEQ ID NO: 153 and 157; 189) SEQ ID NO: 153 and 272; 190) SEQ ID NO: 153 and 277; 191) SEQ ID NO: 153 and 279; 192) SEQ ID NO: 153 and 282; 193) SEQ ID NO: 153 and 286; 194) SEQ ID NO: 153 and 290; 195) SEQ ID NO: 264 and 115; 196) SEQ ID NO: 264 and 121; 197) SEQ ID NO: 264 and 157; 198) SEQ ID NO: 264 and 272; 199) SEQ ID NO: 264 and 277; 200) SEQ ID NO: 264 and 279; 201) SEQ ID NO: 264 and 282; 202) SEQ ID NO: 264 and 286; 203) SEQ ID NO: 264 and 290; 204) SEQ ID NO: 266 and 115; 205) SEQ ID NO: 266 and 121; 206) SEQ ID NO: 266 and 157; 207) SEQ ID NO: 266 and 272; 208) SEQ ID NO: 269 and 272; 218) SEQ ID NO: 269 and 277; 219) SEQ ID NO: 269 and 279; 220) SEQ ID NO: 269 and 282; 221) SEQ ID NO: 269 and 286; 222) SEQ ID NO: 269 and 290; 223) SEQ ID NO: 269 and 115; 224) SEQ ID NO: 269 and 121; 225) SEQ ID NO: 269 and 157; 226) SEQ ID NO: 269 and 157; 227) SEQ ID NO: 269 and 272; 228) SEQ ID NO: 269 and 277; 229) SEQ ID NO: 269 and 279; 230) SEQ ID NO: 269 and 282; 231) SEQ ID NO: 269 and 286; or 232) SEQ ID NO: 269 and 286 NO: 269 and 290.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3A3, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3A3. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3A3 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences of SEQ ID NOs: 23 and 27, respectively.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3A19, or the antibody or antigen-binding fragment comprises the CDRs and optionally VH and VL of S3A19. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3A19 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the following: such as SEQ ID NO: 31 and 37, respectively; 35 and 37, respectively; 36 and 37, respectively; and any one of 43 and 37, respectively.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3I2, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S3I2. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 to confer similar specific binding, or a fragment thereof, and VH and VL comprise or consist of amino acid sequences such as SEQ ID NOs: 83 and 87, respectively.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3O13, or the antibody or antigen-binding fragment comprises CDRs and, optionally, VH and VL of S3O13. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of amino acid sequences such as SEQ ID NOs: 93 and 97, respectively.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S3L17, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S3L17. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 to confer similar specific binding, or a fragment thereof, and VH and VL comprise or consist of amino acid sequences such as SEQ ID NOs: 102 and 105, respectively.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S2V29a, or the antibody or antigen-binding fragment comprises the CDRs and, optionally, VH and VL of S2V29a. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S2V29a (to confer similar specific binding), or a fragment thereof, and VH and VL comprise or consist of amino acid sequences such as SEQ ID NOs: 111 and 115, respectively.
In some embodiments, the antibody is (or the antigen-binding fragment is derived from) S2V29b, or the antibody or antigen-binding fragment comprises CDRs and, optionally, VH and VL of S2V29b. In some embodiments, the antibody comprises sufficient CDR, VH, and/or VL identity to S2V29b to confer similar specific binding, or a fragment thereof, and VH and VL comprise or consist of amino acid sequences such as SEQ ID NOs: 111 and 121, respectively.
In certain embodiments, an antibody or antigen-binding fragment comprising a heavy chain variable domain (VH) is provided, wherein the heavy chain variable domain comprises or consists of: an amino acid sequence of any one of SEQ ID NO: 23, 31, 35, 36, 43, 83, 93, 102, 111, 125, 128, 131, 137, 141, 145, 149, 453, 179, 181, 183, 185, 188, 190, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, 222, 235, 238, 241, 243, 245, 247, 249, 251, 264, 266, or 269.
In certain embodiments, an antibody or antigen-binding fragment comprising a light chain variable domain (VL) is provided, wherein the light chain variable domain comprises or consists of an amino acid sequence of any one of SEQ ID NOs: 27, 37, 87, 97, 105, 115, 121, 157, 193, 225, 228, 231, 254, 257, 260, 272, 277, 279, 282, 286, 290.
As used herein, a "variant" of a CDR refers to a functional variant of a CDR sequence having up to 1 to 3 amino acid substitutions (e.g., conserved or non-conserved substitutions), deletions, or a combination thereof.
CDRs and framework regions may be coded according to any known method or scheme, such as the Kabat, Chothia, EU, IMGT, Contact, North, Martin, AbM, and AHo numbering schemes (see, e.g., Kabat et al., "Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, Public Health Service National Institutes of Health, 1991, 5th ed.; Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987)); Lefranc et al., Dev. Comp. Immunol. 27:55, 2003; Honegger and Plückthun, J. Mol. Bio. 309:657-670 (2001); North et al. J Mol Biol. (2011) 406:228-56; doi:10.1016/j.jmb.2010.10.030; Abhinandan and Martin, Mol Immunol.(2008)45:3832-9. 10.1016/j.molimm.2008.05. 022). The antibody and CDR numbering systems of these references are incorporated herein by reference. Equivalent residue positions can be identified using the Antigen receptor Numbering and Receptor Classification (ANARCI) software tool (2016, Bioinformatics 15:298-300) to annotate and compare different molecules. Therefore, identifying the CDRs of the exemplary variable region (VH or VL) sequences as provided herein according to one numbering scheme does not include antibodies comprising CDRs of the same variable region as determined using a different numbering scheme. In certain embodiments, antibodies or antigen-binding fragments are provided that comprise one or more CDRs of the following VH sequences: as shown in SEQ ID NO: any of 23, 31, 35, 36, 43, 83, 93, 102, 111, 125, 128, 131, 137, 141, 145, 149, 453, 179, 181, 183, 185, 188, 190, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, 222, 235, 238, 241, 243, 245, 247, 249, 251, 264, 266, or 269; and/or one or more CDRs in the following VL sequences: such as SEQ ID NO: 27, 37, 87, 97, 105, 115, 121, 157, 193, 225, 228, 231, 254, 257, 260, 272, 277, 279, 282, 286, 290, according to any known CDR numbering method, including Kabat, Chothia, North, EU, IMGT, Martin (enhanced Chothia), Contact, AbM, and AHo numbering methods, or according to a combination of two or more of these methods (e.g., including those residues that fall within a CDR as defined by any or all of the numbering methods). In certain embodiments, the CDR is according to the IMGT numbering method (optionally using a combined definition of the CDR3 amino acid sequence). In some embodiments, the CDRs are numbered according to the antibody numbering method developed by the Chemical Computing Group (CCG); for example, using the Molecular Operating Environment (MOE) software (chemcomp.com). In some embodiments, the CDRs are numbered according to the IMGT numbering method.
S3A3 Antibodies, antigen-binding fragments, and variantsIn certain embodiments, an antibody or antigen-binding fragment is provided, comprising a VH sequence such as SEQ ID NO: 23 and a VL sequence such as SEQ ID NO: 27.
In certain embodiments, the amino acid sequence changes relative to SEQ ID NO: 23 or SEQ ID NO: 27 are limited to changes in one or more framework regions (FRs) relative to SEQ ID NO: 23 or SEQ ID NO: 27, respectively.
The framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more thereof). CDRs can be identified within variable structural domains or within heavy or light chains based on a numbering scheme or combination of numbering schemes, and preferably, FRs can be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, the antibody or antigen-binding fragment comprises a VH comprising FR1, FR2, FR3, and/or FR4 of the VH amino acid sequence set forth in SEQ ID NO: 23 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions); and a VL comprising FR1, FR2, FR3, and/or FR4 of the VL amino acid sequence set forth in SEQ ID NO: 27 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions). In some embodiments, FR is defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or according to any combination thereof. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence described in SEQ ID NO: 23; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence described in SEQ ID NO: 27.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence described in SEQ ID NO: 23; and (ii) a light chain variable domain (VL) comprising the amino acid sequence described in SEQ ID NO: 27.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence described in SEQ ID NO: 23; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence described in SEQ ID NO: 27.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence described in SEQ ID NO: 23; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence described in SEQ ID NO: 27.
In certain embodiments, an antibody or antigen-binding fragment is provided, comprising CDRs identified in the VH sequence of SEQ ID NO: 23 and in the VL sequence of SEQ ID NO: 27, wherein the CDRs are defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or according to any combination thereof.
In certain embodiments, antibodies or antigen-binding fragments are provided, comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein: (i) CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 24 or a sequence variant thereof, wherein the sequence variant comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: (iii) the CDRH3 comprises or consists of an amino acid sequence such as SEQ ID NO: 26, or a sequence variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence such as SEQ ID NO: 28, or a sequence variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence such as SEQ ID NO: 30, or a sequence variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; NO: 29, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retained substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of the following: such as SEQ ID NO: 30, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retained substitutions and/or substitutions of germline-encoded amino acids, wherein the antibody or antigen-binding fragment is capable of binding to one or more or two or more surface glycoproteins of severe acute respiratory syndrome beta coronaviruses expressed on the cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises the amino acid sequences of CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 as shown in SEQ ID NOs: 24 to 26 and 28 to 30, respectively.
S3A19 Antibodies, antigen-binding fragments, and variantsIn certain embodiments, antibodies or antigen-binding fragments are provided, comprising a VH sequence as any one of SEQ ID NOs: 31, 35, 36, and 43 and a VL sequence as SEQ ID NO: 37.
In certain embodiments, the amino acid sequence variations relative to any one of SEQ ID NOs: 31, 35, 36, and 43 or SEQ ID NO: 37 are limited to variations in one or more framework regions (FRs) relative to any one of SEQ ID NOs: 31, 35, 36, and 43 or SEQ ID NO: 37, respectively.
Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more thereof). CDRs can be identified within variable structural domains or within heavy or light chains based on a numbering scheme or combination of numbering schemes, and preferably, FRs can be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, the antibody or antigen-binding fragment comprises a VH comprising the following: FR1, FR2, FR3, and/or FR4 of the VH amino acid sequence described in any one of SEQ ID NOs: 31, 35, 36, and 43 (or variants of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions); and a VL comprising FR1, FR2, FR3, and/or FR4 of the VL amino acid sequence described in SEQ ID NO: 37 (or variants of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions). In some embodiments, FR is defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or according to any combination thereof. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence described in any one of SEQ ID NOs: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence described in SEQ ID NO: 37.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the following: an amino acid sequence described in any one of SEQ ID NOs: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) comprising the amino acid sequence described in SEQ ID NO: 37.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the following: an amino acid sequence described in any one of SEQ ID NOs: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence described in SEQ ID NO: 37.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence described in any one of SEQ ID NOs: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence described in SEQ ID NO: 37.
The S3A19 antibody may be as described in Table 3.
In certain embodiments, antibodies or antigen-binding fragments are provided, comprising CDRs identified in: a VH sequence such as any one of SEQ ID NOs: 31, 35, 36, and 43 and a VL sequence such as SEQ ID NO: 37, wherein the CDRs are defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering systems, or according to any combination thereof.
In certain embodiments, antibodies or antigen-binding fragments are provided, which comprise a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein: (i) CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 32 or a sequence variant thereof, wherein the sequence variant comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: (iii) the CDRH3 comprises or consists of an amino acid sequence such as SEQ ID NO: 34, or a sequence variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence such as SEQ ID NO: 38, or a sequence variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence such as SEQ ID NO: 39, or a sequence variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; NO: 39, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retained substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of the following: such as SEQ ID NO: 40, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retained substitutions and/or substitutions of germline-encoded amino acids, wherein the antibody or antigen-binding fragment is capable of binding to one or more or two or more surface glycoproteins of severe acute respiratory syndrome beta coronaviruses expressed on the cell surface of a host cell.
In any of the currently disclosed embodiments, the antibody or antigen-binding fragment comprises the amino acid sequences of CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 as shown in SEQ ID NOs: 32 to 34 and 38 to 40, respectively.
S3I2 Antibodies, antigen-binding fragments, and variantsIn certain embodiments, antibodies or antigen-binding fragments are provided, comprising a VH sequence as in any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, 190 and a VL sequence as in any one of SEQ ID NOs: 87 or 193.
In certain embodiments, the amino acid sequence changes relative to any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, 190 or any one of SEQ ID NOs: 87 or 193 are limited to changes in one or more framework regions (FRs) relative to any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, 190 or any one of SEQ ID NOs: 87 or 193, respectively.
Framework regions may be identified according to a numbering scheme such as IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these. CDRs may be identified within variable domains or within heavy or light chains according to a numbering scheme or combination of numbering schemes, and preferably, FRs may be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, the antibody or antigen-binding fragment comprises a VH comprising the following: FR1, FR2, FR3, and/or FR4 of the VH amino acid sequence described in any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, 190 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions); and a VL comprising FR1, FR2, FR3, and/or FR4 of the VL amino acid sequence described in any one of SEQ ID NOs: 87 or 193 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions). In some embodiments, FR is defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or according to any combination thereof. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence of any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence of any one of SEQ ID NOs: 87 or 193.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the following: an amino acid sequence described in any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) comprising an amino acid sequence described in any one of SEQ ID NOs: 87 or 193.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence of any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence of any one of SEQ ID NOs: 87 or 193.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of an amino acid sequence described in any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) consisting of an amino acid sequence described in any one of SEQ ID NOs: 87 or 193.
In certain embodiments, antibodies or antigen-binding fragments are provided, comprising CDRs identified in: a VH sequence such as any one of SEQ ID NOs: 83, 179, 181, 183, 185, 190 and a VL sequence such as any one of SEQ ID NOs: 87 or 193, wherein the CDRs are defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering systems, or according to any combination thereof.
In certain embodiments, antibodies or antigen-binding fragments are provided, which comprise a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein: (i) CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 84 or a sequence variant thereof, wherein the sequence variant comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 85, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) the CDRH3 comprises or consists of the following: an amino acid sequence as any one of SEQ ID NO: 86 or 186, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of the following: an amino acid sequence as any one of SEQ ID NO: 88 or 194, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence such as SEQ ID NO: 89, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of an amino acid sequence such as SEQ ID NO: 90, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids, wherein the antibody or antigen-binding fragment is capable of binding to one or more or two or more surface glycoproteins of severe acute respiratory syndrome beta coronaviruses expressed on the cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences of SEQ ID NO: 84 to 86 or 84, 85 and 186 and 88 to 90 or 194, 89, and 90, respectively.
S3O13 Antibodies, antigen-binding fragments, and variantsIn certain embodiments, an antibody or antigen-binding fragment is provided, comprising a VH sequence as set forth in any one of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and a VL sequence as set forth in any one of SEQ ID NOs: 97, 225, 228, or 231.
In some embodiments, the amino acid sequence changes relative to any one of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 or any one of SEQ ID NOs: 97, 225, 228, or 231 are limited to changes in one or more framework regions (FRs) relative to any one of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 or any one of SEQ ID NOs: 97, 225, 228, or 231, respectively.
Framework regions may be identified according to a numbering scheme such as IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these. CDRs may be identified within variable domains or within heavy or light chains according to a numbering scheme or combination of numbering schemes, and preferably, FRs may be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, the antibody or antigen-binding fragment comprises a VH comprising the following: FR1, FR2, FR3, and/or FR4 of the VH amino acid sequence described in any one of SEQ ID NO: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions); and a VL comprising the following: SEQ ID NO: 97, 225, 228, or 231 of any of the VL amino acid sequences described in FR1, FR2, FR3, and/or FR4 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions). In some embodiments, FR is defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or according to any combination thereof. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of an amino acid sequence as set forth in any one of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of an amino acid sequence as set forth in any one of SEQ ID NOs: 97, 225, 228, or 231.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the following: an amino acid sequence described in any one of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) comprising the following: an amino acid sequence described in any one of SEQ ID NOs: 97, 225, 228, or 231.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence of any one of SEQ ID NO: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence of any one of SEQ ID NO: 97, 225, 228, or 231.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence of any one of SEQ ID NO: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence of any one of SEQ ID NO: 97, 225, 228, or 231.
In certain embodiments, antibodies or antigen-binding fragments are provided, comprising CDRs identified in: a VH sequence such as any one of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and a VL sequence such as any one of SEQ ID NOs: 97, 225, 228, or 231, wherein the CDRs are defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering systems, or according to any combination thereof.
In certain embodiments, antibodies or antigen-binding fragments are provided, comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein: (i) CDRH1 comprises or consists of the following: an amino acid sequence as set forth in any one of SEQ ID NOs: 94, 198, or 208, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence as set forth in SEQ ID NOs: 95, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) the CDRH3 comprises or consists of an amino acid sequence as any one of SEQ ID NO: 96, 199, 202, or 205, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence as any one of SEQ ID NO: 98, 226, 229, 232, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 39, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 99, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids, wherein the antibody or antigen-binding fragment is capable of binding to one or more or two or more surface glycoproteins of severe acute respiratory syndrome beta coronaviruses expressed on the cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises the following CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences, respectively: such as SEQ ID NO: 94 to 96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202; or 208, 95, and 205, and 98, 39, and 99; 226, 39, and 99; or 229, 39, and 232.
S3L17 Antibodies, antigen-binding fragments, and variantsIn certain embodiments, an antibody or antigen-binding fragment is provided, which comprises a VH sequence as shown in any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence as shown in any one of SEQ ID NOs: 105, 254, 257, or 260.
In some embodiments, amino acid sequence variations relative to any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 or any one of SEQ ID NOs: 105, 254, 257, or 260 are limited to variations in one or more framework regions (FRs) relative to any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 or any one of SEQ ID NOs: 105, 254, 257, or 260, respectively.
Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more thereof). CDRs can be identified within variable structural domains or within heavy or light chains based on a numbering scheme or combination of numbering schemes, and preferably, FRs can be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, the antibody or antigen-binding fragment comprises a VH comprising FR1, FR2, FR3, and/or FR4 of the VH amino acid sequence described in any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions); and a VL comprising FR1, FR2, FR3, and/or FR4 of the VL amino acid sequence described in any one of SEQ ID NOs: 105, 254, 257, or 260 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions). In some embodiments, FR is defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or according to any combination thereof. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence of any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence of any one of SEQ ID NOs: 105, 254, 257, or 260.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the following: an amino acid sequence described in any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) comprising the following: an amino acid sequence described in any one of SEQ ID NOs: 105, 254, 257, or 260.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence of any one of SEQ ID NO: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence of any one of SEQ ID NO: 105, 254, 257, or 260.
In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence of any one of SEQ ID NO: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence of any one of SEQ ID NO: 105, 254, 257, or 260.
In certain embodiments, antibodies or antigen-binding fragments are provided, comprising CDRs identified in: a VH sequence such as any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence such as any one of SEQ ID NOs: 105, 254, 257, or 260, wherein the CDRs are defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering systems, or according to any combination thereof.
In certain embodiments, antibodies or antigen-binding fragments are provided, which comprise a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein: (i) CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 103 or a sequence variant thereof, wherein the sequence variant comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 85, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) the CDRH3 comprises or consists of an amino acid sequence as in any one of SEQ ID NOs: 104, 236, or 239, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence as in SEQ ID NOs: 106 or 255, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence such as SEQ ID NO: 107, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of an amino acid sequence such as SEQ ID NO: An amino acid sequence of any one of 108 or 258, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids, wherein the antibody or antigen-binding fragment is capable of binding to the surface glycoproteins of one or more or two or more severe acute respiratory syndrome beta coronaviruses expressed on the cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises the following CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences, respectively: such as SEQ ID NO: 103, 85, and 104; 103, 85, and 236; or 103, 85, and 239, and 106 to 108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258.
In some embodiments, the antibody or antigen-binding fragment comprises the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences of S3A3, S3A19 VH.1, S3A19 VH.2, S3A19 VH.3, S3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as described in Table 3. In certain embodiments, the antibody or antigen-binding fragment comprises a VH and VL amino acid sequence that is at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the VH and VL amino acid sequence of (each) S3A3, S3A19 VH.1, S3A19 VH.2, S3A19 VH.3, o3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as described in Table 3, or comprises S3A3, S3A19 VH.1, S3A19 VH.2, S3A19 VH.3, o3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as described in Table 3. VH.1-VH.3 common antibody, S3I2, S3O13, or S3L17 (each) VH and VL amino acid sequence. In certain embodiments, the antibody or antigen-binding fragment comprises the VH and VL amino acid sequence of S3A3, S3A19 VH.1, S3A19 VH.2, S3A19 VH.3, S3A19 VH.1-VH.3 common antibody, S3I2, S3O13, or S3L17 (each) as described in Table 3.
S2V29 Antibodies, antigen-binding fragments, and variants In certain embodiments, an antibody or antigen-binding fragment is provided, which comprises a VH sequence as any one of SEQ ID NO: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence as any one of SEQ ID NO: 115, 121, 157, 272, 277, 279, 282, 286, or 290. In some embodiments, amino acid sequence variations relative to any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 or any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290 are limited to variations in one or more framework regions (FRs) relative to any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 or any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively. Framework regions can be identified according to a numbering scheme, such as IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these. CDRs can be identified within variable structural domains or within heavy or light chains according to a numbering scheme or combination of numbering schemes, and preferably, FRs can be identified using the same numbering scheme or combination of numbering schemes. In certain embodiments, the antibody or antigen-binding fragment comprises a VH comprising the following: FR1, FR2, FR3, and/or FR4 of the VH amino acid sequence described in any one of SEQ ID NO: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 (or a variant of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions); and a VL comprising the following: SEQ ID NO: 115, 121, 157, 272, 277, 279, 282, 286, or 290. FR1, FR2, FR3, and/or FR4 (or variants of FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions). In some embodiments, FR is defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or according to any combination thereof. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence depicted in any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence depicted in any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence of any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) comprising the amino acid sequence of any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence of any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence of any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290. In some embodiments, the antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence of any one of SEQ ID NO: 1 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence of any one of SEQ ID NO: 115, 121, 157, 272, 277, 279, 282, 286, or 290. In certain embodiments, antibodies or antigen-binding fragments are provided that comprise CDRs identified in: a VH sequence of any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence of any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, wherein the CDRs are defined according to the IMGT, Kabat, Chothia, North, EU, Martin (enhanced Chothia), Contact, AbM, CCG, or AHo numbering systems, or according to any combination thereof. In certain embodiments, antibodies or antigen-binding fragments are provided, which comprise a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein: (i) CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 112 or a sequence variant thereof, wherein the sequence variant comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 113, 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) the CDRH3 comprises or consists of an amino acid sequence as any one of SEQ ID NO: 114, 139, 143, 147, 151, or 155, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence as any one of SEQ ID NO: 116, 273, or 283, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence as described in any of SEQ ID NOs: 117, 274, or 287, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of an amino acid sequence as described in SEQ ID NOs: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids, wherein the antibody or antigen-binding fragment is capable of binding to one or more or two or more surface glycoproteins of severe acute respiratory syndrome beta coronaviruses expressed on the cell surface of a host cell. In certain embodiments, the antibody or antigen-binding fragment comprises the following CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences, respectively: such as SEQ ID NO: 112 to 114; 112, 126, and 114; 112, 129, and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112, 267, and 114; 112, 270, and 114; 112, 113, and 139 ; 112, 126, and 139; 112, 129, and 139; 112, 132, and 139; 112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112, 150, and 139; 112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112, 12 6, and 143; 112, 129, and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129, and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 147; 112, 154, and 147; 112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112, 129 and 151; 112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and 151; 112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 151; 112, 113, and 155; 1 12, 126, and 155; 112, 129, and 155; 112, 132, and 155; 112, 135, and 155; 112, 138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270 , and 155; and 116 to 118; 116, 274, and 118; 116, 287, and 118; 116, 117, and 122; 116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116, 287, and 275; 116, 117, and 280; 116, 2 74, and 280; 116, 287, and 280; 116, 117, and 284; 116, 274, and 284; 116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 116, 117, and 291; 116, 274, and 291; 116, 287, and 291 ; 273, 117, and 118; 273, 274, and 118; 273, 287, and 118; 273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and 275; 273, 287, and 275; 273, 117, and 280; 273, 27 4, and 280; 1273, 287, and 280; 273, 117, and 284; 273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273, 287, and 288; 273, 117, and 291; 273, 274, and 291; 273, 287, and 291 ; 283, 117, 118; 283, 274, and 118; 283, 287, and 118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 283, 117, and 158; 283, 274, and 275; 283, 287, and 275; 283, 117, and 280; 283, 274 , and 280; 283, 287, and 280; 283, 117, and 284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288; 283, 287, and 288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291. In certain embodiments, the antibody or antigen-binding fragment comprises the following CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences, respectively: as SEQ ID NO: 112 to 114 and 116 to 118, respectively (S2V29a); 112 to 114 and 116, 117, and 122, respectively (S2V29b). In certain embodiments, the antibody or antigen-binding fragment comprises a VH or VL comprising or consisting of SEQ ID NOs: 111 and 157, or having at least 85%, 90%, or 95% identity to these sequences, particularly with framework mutations as disclosed herein. In still further embodiments, the antibody or antigen-binding fragment comprises the CDRs described in the VH and VL of SEQ ID NOs: 111 and 157, according to any numbering scheme as described herein. In some embodiments, the antibody or antigen-binding fragment comprises the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences of SEQ ID NOs: 112 to 114 and 116 to 117, and 158, respectively. Any of these antibodies may include an Fc modification as described herein, or may have an unmodified human IgG1 constant region. Specifically, the antibody may have a VH as in SEQ ID NO: 111, a CH as in SEQ ID NO: 44 to 80, a VL as in SEQ ID NO: 157, and a CL as in SEQ ID NO: 292. In certain embodiments, the heavy chain of the antibody or antigen-binding fragment comprises or consists of a sequence that is at least 85%, 90%, 95%, or 99% identical to SEQ ID NO: 293, and the light chain comprises or consists of a sequence that is at least 85%, 90%, 95%, or 99% identical to SEQ ID NO: 294. In some embodiments, the heavy chain of the antibody or antigen-binding fragment comprises or consists of the amino acid sequence of SEQ ID NO: 293 and the light chain comprises or consists of the amino acid sequence of SEQ ID NO: 294. In specific embodiments, the heavy chain of the antibody or antigen-binding fragment comprises or consists of a sequence that is at least 85%, 90%, 95%, or 99% identical to SEQ ID NO: 295, and the light chain comprises or consists of a sequence that is at least 85%, 90%, 95%, or 99% identical to SEQ ID NO: 296. In some embodiments, the heavy chain of the antibody or antigen-binding fragment comprises or consists of the amino acid sequence of SEQ ID NO: 295 and the light chain comprises or consists of the amino acid sequence of SEQ ID NO: 296. The term "CL" refers to "immunoglobulin light chain constant region" or "light chain constant region", i.e., the constant region from the antibody light chain. The term "CH" refers to "immunoglobulin heavy chain constant region" or "heavy chain constant region", which can be further divided into CH1, CH2, and CH3 (IgA, IgD, IgG); or CH1, CH2, CH3, and CH4 domains (IgE, IgM) according to the antibody isotype. The Fc region of the antibody heavy chain is further described herein. In any currently disclosed specific embodiment, the antibody or antigen-binding fragment of the present disclosure comprises any one or more of CL, CH1, CH2, and CH3. In any currently disclosed specific embodiment, the antibody or antigen-binding fragment of the present disclosure may comprise any one or more of CL, CH1, CH2, and CH3. In certain embodiments, CL comprises an amino acid sequence having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the amino acid sequence of SEQ ID NO: 292. In certain embodiments, CL comprises an amino acid sequence having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the human lambda light chain constant domain. The term "CH" refers to "immunoglobulin heavy chain constant region" or "heavy chain constant region", which can be further divided into CH1, CH2, and CH3 (IgA, IgD, IgG); or CH1, CH2, CH3, and CH4 domains (IgE, IgM) according to the antibody isotype. The Fc region of the antibody heavy chain is further described herein. In any of the currently disclosed embodiments, the antibody or antigen-binding fragment of the present disclosure comprises any one or more of CL, CH1, CH2, and CH3. In some embodiments, the antibody or antigen-binding fragment comprises (e.g., human) IgG (e.g., IgG1, IgG2, IgG3, or IgG4), IgA, IgD, IgE, or IgM isotype, or comprises an amino acid sequence from two or more of these isotypes. In some embodiments, the antibody or antigen-binding fragment comprises an IgG1 isotype; it is understood that such an antibody or antigen-binding fragment may comprise one or more amino acid substitutions in the heavy chain constant domain and still be considered an "IgG1" isotype. In some embodiments, IgG1 comprises or consists of an amino acid sequence having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence set forth in SEQ ID NOs: 44 to 80, or comprises or consists of the amino acids set forth in SEQ ID NOs: 44 to 80. It is understood that, for example, production in mammalian cell lines can remove one or more C-terminal lysines of the antibody heavy chain (see, e.g., Liu et al. mAbs 6(5):1145-1154 (2014)). Therefore, the antibodies or antigen-binding fragments disclosed herein may include heavy chains, CH1-CH3, CH3, or Fc polypeptides in which a C-terminal lysine residue or a C-terminal glycine-lysine residue is present or absent; in other words, embodiments in which the C-terminal residue of the heavy chain, CH1-CH3, or Fc polypeptide is not lysine, and embodiments in which lysine is the C-terminal residue are encompassed. In certain embodiments, the composition comprises a plurality of antibodies and/or antigen-binding fragments of the present disclosure, wherein one or more of the antibodies or antigen-binding fragments do not contain a lysine residue or a C-terminal glycine-lysine at the C-terminal end of the heavy chain, CH1-CH3, or Fc polypeptide, and wherein one or more of the antibodies or antigen-binding fragments contain a lysine residue at the C-terminal end of the heavy chain, CH1-CH3, or Fc polypeptide. "Fab" (fragment antigen binding) is the portion of an antibody that binds to an antigen and includes the variable region and CH1 of the heavy chain linked to the light chain via an interchain disulfide bond. Each Fab fragment is monovalent with respect to antigen binding, i.e., it has a single antigen binding site. Pepsin treatment of an antibody yields a single large F(ab')2 fragment, which roughly corresponds to two disulfide-linked Fab fragments, has divalent antigen-binding activity and is still capable of cross-linking antibodies. Both Fab and F(ab')2 are examples of "antigen-binding fragments". Fab' fragments differ from Fab fragments in having an additional small number of residues at the carboxyl terminus of the CH1 domain, which includes one or more cysteines from the antibody hinge region. Fab'-SH is the designation used herein for Fab' in which the cysteine residue(s) of the invariant domains bear a free thiol group. F(ab')2 antibody fragments were originally produced as pairs of Fab' fragments with tethered cysteines between them. Other chemical couplings of antibody fragments are also known. Fab fragments can be joined, for example, by a peptide linker to form a single chain Fab, also referred to herein as "scFab". In these embodiments, the interchain disulfide bonds present in native Fab may not be present, and the linker is used completely or partially to link or connect the Fab fragments in a single polypeptide chain. A heavy chain derived Fab fragment (e.g., comprising, consisting of, or consisting essentially of VH+CH1, or "Fd") and a light chain derived Fab fragment (e.g., comprising, consisting of, or consisting essentially of VL+CL) can be linked in any arrangement to form a scFab. For example, the scFab can be arranged in the N-terminal to C-terminal direction according to (heavy chain Fab fragment-linker-light chain Fab fragment) or (light chain Fab fragment-linker-heavy chain Fab fragment). Peptide linkers and exemplary linker sequences for scFab are discussed in further detail herein. "Fv" is a small antibody fragment containing complete antigen recognition and antigen binding sites. This fragment is typically composed of a dimer of one heavy chain variable region and one light chain variable region in tight, non-covalent association. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although generally with a lower affinity than the entire binding site. "Single-chain Fv" is also abbreviated as "sFv" or "scFv" and is comprised of V and V domains linked into a single polypeptide chain.Hand V
LAntibody fragment of antibody domain. In some specific embodiments, the scFv polypeptide comprises a V
HWith VL A polypeptide linker between and connecting the domains enables the scFv to retain or form the desired structure for antigen binding. Such a peptide linker can be incorporated into the fusion polypeptide using standard methods well known in the art. For a general description of scFv, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994); Borrebaeck 1995, see below. In certain embodiments, the antibody or antigen-binding fragment comprises an scFv comprising a VH domain, a VL domain, and a peptide linker connecting the VH domain to the VL domain. In certain embodiments, the scFv comprises a VH domain connected to a VL domain via a peptide linker, which scFv may be in a VH-linker-VL orientation or in a VL-linker-VH orientation. Any scFv disclosed herein may be engineered such that the C-terminal end of the VL domain is connected to the N-terminal end of the VH domain via a short peptide sequence, or vice versa (i.e., (N)VL(C)-linker-(N)VH(C) or (N)VH(C)-linker-(N)VL(C)). Alternatively, in some embodiments, the linker may be connected to the N-terminal portion or end of the VH domain, the VL domain, or both. The peptide linker sequence can be selected, for example, based on: (1) its ability to present a flexible extended conformation; (2) its inability or lack of ability to present a secondary structure that can interact with a functional epitope on the first and second polypeptides and/or on the target molecule; and/or (3) the lack or relative lack of hydrophobic or charged residues that may react with the polypeptides and/or the target molecule. Other considerations for linker design (e.g., length) may include the conformation or range of conformations in which VH and VL may form a functional antigen binding site. In certain embodiments, the peptide linker sequence contains, for example, Gly, Asn, and Ser residues. Other nearly neutral amino acids (such as Thr and Ala) may also be included in the linker sequence. Other amino acid sequences that may be advantageously used as linkers include those disclosed in Maratea et al., Gene 40:39 46 (1985); Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258 8262 (1986); U.S. Patent No. 4,935,233; and U.S. Patent No. 4,751,180. Other illustrative and non-limiting examples of linkers can include, for example, Glu-Gly-Lys-Ser-Ser-Gly-Ser-Gly-Ser-Glu-Ser-Lys-Val-Asp (SEQ ID NO: 19) (Chaudhary et al., Proc. Natl. Acad. Sci. USA 87: 1066-1070 (1990)) and Lys-Glu-Ser-Gly-Ser-Val-Ser-Ser-Glu-Gln-Leu-Ala-Gln-Phe-Arg-Ser-Leu-Asp (SEQ ID NO: 20) (Bird et al., Science 242: 423-426 (1988)) and the pentamer Gly-Gly-Gly-Gly-Ser (SEQ ID NO: 21), when present in a single iteration or in repeats of 1 to 5 or more times, or more. Any suitable linker can be used, and will generally be about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60, 70, 80, 90, 100 amino acids in length, or less than about 200 amino acids in length, and will preferably comprise a flexible structure (to provide flexibility and space for conformational movement between the two regions, domains, motifs, fragments, or modules connected by the linker), and will preferably be biologically inert and/or have a low risk of human immunogenicity. Exemplary linkers include or consist of the amino acid sequences described in any one or more of SEQ ID NOs: 4 to 13 and linkers SEQ A and B. In certain embodiments, the linker comprises or consists of an amino acid sequence that is at least 75% (i.e., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identical to the amino acid sequence described in any one of SEQ ID NOs: 4 to 13 and linkers SEQ A and B. scFvs can be constructed using any combination of VH and VL sequences disclosed herein or any combination of CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences. In some embodiments, a linker sequence is not required; for example, when the first and second polypeptides have non-essential N-terminal (or C-terminal) amino acid regions that can be used to separate the functional domains and prevent stereointerference. During antibody development, DNA in the germline variable (V), joining (J), and diversity (D) gene loci may rearrange, and insertions and/or deletions of nucleotides may occur in the coding sequence. Somatic mutations may be encoded by the resulting sequence and may be identified by reference to corresponding known germline sequences. In some cases, a somatic mutation that is not essential for a desired property of the antibody (e.g., binding to a SARS-CoV-2 antigen), or that imparts an undesirable property to the antibody (e.g., increases the risk of immunogenicity in an individual to whom the antibody is administered), or both, can be replaced by a corresponding germline-encoded amino acid, or by a different amino acid, such that the desired property of the antibody is improved or maintained and the undesirable property of the antibody is reduced or eliminated. Thus, in some embodiments, the antibodies or antigen-binding fragments of the present disclosure comprise at least one additional germline-encoded amino acid in the variable region as compared to the parent antibody or antigen-binding fragment, provided that the parent antibody or antigen-binding fragment comprises one or more somatic mutations. The variable region and CDR amino acid sequences of the exemplary anti-severe acute respiratory syndrome beta coronavirus antibodies disclosed herein are provided in Table 1 and Table 3 herein. In certain embodiments, the antibody or antigen-binding fragment comprises amino acid modifications (e.g., substitution mutations) to remove the risk of undesired oxidation, deamination, and/or isomerization. Variants comprising one or more amino acid changes in a variable region (e.g., VH, VL, framework, or CDR) are provided herein, which are compared to the currently disclosed S3A3, S3A19, S3I2, S3O13, S3L17, or S2V29 ("parent") antibodies, wherein the variant antibody is capable of binding to a SARS-CoV-2 antigen. In certain embodiments, VH comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to the amino acid sequence of SEQ ID NO: 23, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline-encoded amino acids; and/or (ii) VL comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to the amino acid sequence of SEQ ID NO: An amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to an amino acid sequence of 27, wherein the variations are optionally limited to one or more framework regions and/or the variations comprise one or more substitutions to germline encoded amino acids. In certain embodiments, VH comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as one or more of SEQ ID NOs: 31, 35, 36, and 43, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline-encoded amino acids; and/or (ii) VL comprises or consists of an amino acid sequence as one or more of SEQ ID NOs: An amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence of SEQ ID NO: 37, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline encoded amino acids. In certain embodiments, VH comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as set forth in one or more of SEQ ID NOs: 83, 179, 181, 183, 185, 188, and 190, wherein the alterations are optionally confined to one or more framework regions and/or the alterations comprise one or more substitutions of germline-encoded amino acids; and/or (ii) VL comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as set forth in SEQ ID NOs: An amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to one or more of 87 and 193, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline encoded amino acids. In certain embodiments, VH comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as one or more of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, and 222, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline encoded amino acids; and/or (ii) VL comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as SEQ ID NOs: An amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to one or more of 97, 225, 228, and 231, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline encoded amino acids. In certain embodiments, VH comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as one or more of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, and 251, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline encoded amino acids; and/or (ii) VL comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as SEQ ID NOs: An amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to one or more of 105, 254, 257, and 260, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline encoded amino acids. In certain embodiments, VH comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as one or more of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, and 269, wherein the changes are optionally limited to one or more framework regions and/or the changes comprise one or more substitutions of germline encoded amino acids; and/or (ii) VL comprises or consists of an amino acid sequence that is at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical to an amino acid sequence as SEQ ID NOs: In some embodiments, the antibody or antigen-binding fragment is an IgG (e.g., IgG1, IgG2, IgG3, or IgG4), IgA, IgM, IgE, or IgD isotype, or comprises an amino acid sequence from two or more of these. In some embodiments, the antibody or antigen-binding fragment thereof is human, humanized, or chimeric. The antibody or antigen-binding fragment may be any allotype or combination of allotypes. "Isotype" refers to the allelic variation found within the IgG subclass. For example, an allotype may include G1m1 (or G1m(a)), G1m2 (or G1m(x)), G1m3 (or G1m(f)), G1m17 (or Gm(z))m), G1m27, and/or G1m28 (G1m27 and G1m28 have been described as "alloallotypes"). The G1m3 and G1m17 allotypes are located at the same position in the CH1 domain (position 214 according to EU numbering). G1m3 includes R214 (EU), and G1m17 includes K214 (EU). The G1m1 isoform is located in the CH3 domain (at positions 356 and 358 (EU)) and refers to the substitutions of E356D and M358L. The G1m2 isoform refers to the substitution of alanine for glycine at position 431 (EU). G1m allotypes, isomeric isoforms, and their properties are known in the art and described, for example, in www.imgt.org/IMGTrepertoire/Proteins/allotypes/human/IGH/IGHC/G1m_allotypes.html and Lefranc, M.-P. and Lefranc, G.Human Gm, Km and Am allotypes and their molecular characterization: a remarkable demonstration of polymorphism In: B.Tait, F.Christiansen (Eds.), Immunogenetics, chap.34, Humana Press, Springer, New York, USA.Methods Mol.Biol.2012; 882, 635-680.PMID: 22665258, LIGM: 406, the contents of which and information on isotypes and isoforms are incorporated herein by reference. The G1m1 allotype can be combined, for example, with G1m3, G1m17, G1m27, G1m2, and/or G1m28 allotypes. In some embodiments, the allotype is G1m3, and there is no G1m1 (G1m3,-1). In some embodiments, the allotype is the G1m17,1 allotype. In some embodiments, the allotype is G1m3,1. In some embodiments, the allotype is G1m17, and there is no G1m1 (G1m17,-1). Optionally, these allotypes can be combined (or not combined) with G1m2, G1m27, or G1m28 allotypes. For example, the allotype can be G1m17,1,2. In some embodiments, the antibodies or antigen-binding fragments disclosed herein comprise a G1m3 allotype or a G1m3,1 allotype. In some embodiments, the antibodies or antigen-binding fragments disclosed herein comprise a G1m3 allotype and comprise M428L and N434S or M428L and N434A mutations or any other one or more mutations that enhance binding to human FcRn, as described herein. In some embodiments, the antibodies or antigen-binding fragments disclosed herein comprise a G1m3,1 allotype and comprise M428L and N434S or M428L and N434A mutations or any other one or more mutations that enhance binding to human FcRn, as described herein. In some embodiments, the antibodies or antigen-binding fragments disclosed herein comprise the G1m17,1 allotype. In some embodiments, the antibodies or antigen-binding fragments disclosed herein comprise the G1m17,1 allotype and comprise the M428L and N434S or M428L and N434A mutations or any other one or more mutations that enhance binding to human FcRn, as further described herein. In some embodiments, the antibodies or antigen-binding fragments disclosed herein comprise human antibodies, monoclonal antibodies, purified antibodies, single-chain antibodies, Fab, Fab', F(ab')2, Fv, scFv, or scFab. In certain embodiments, the antibodies or antigen-binding fragments disclosed herein are monospecific (e.g., bind to a single epitope) or multispecific (e.g., bind to multiple epitopes and/or target molecules). Antibodies and antigen-binding fragments can be constructed in a variety of formats. Exemplary antibody formats are disclosed in Spiess et al., Mol. Immunol. 67(2):95 (2015), and in Brinkmann and Kontermann, mAbs 9(2):182-212 (2017), which formats and methods of making the same are incorporated herein by reference, and include, for example, bispecific T cell engagers (BiTEs), DARTs, knobs-into-holes (KIH) assemblies, scFv-CH3-KIH assemblies, KIH common light chain antibodies, TandAbs, triplet, TriBi minibody, Fab-scFv, scFv-CH-CL-scFv, F(ab')2-scFv2, tetravalent HCab, endobody, CrossMab, dual action Fab, DAF) (two-in-one or four-in-one), DutaMab, DT-IgG, charge pairing, Fab-arm exchange, strand exchange engineered body (SEEDbody), trifunctional antibody (Triomab), LUZ-Y assembly, Fcab, κλ body, orthogonal Fab, DVD-Igs (e.g., U.S. Patent No. 8,258,268, the entire text of which is incorporated herein by reference), IgG(H)-scFv, scFv-(H)IgG, IgG(L)-scFv, scFv-(L)IgG, IgG(L,H)-Fv, IgG(H)-V, V(H)-IgG, IgG(L)-V, V(L)-IgG, KIH IgG-scFab, 2scFv-IgG, IgG-2scFv, scFv4-Ig, Zybody, and DVI-IgG (four-in-one), and so-called FIT-Ig (e.g., PCT Publication No. WO 2015/103072, the form of which is incorporated herein by reference in its entirety), the so-called WuxiBody form (e.g., PCT Publication No. WO 2019/057122, the form of which is incorporated herein by reference in its entirety), and the so-called In-Elbow-Insert Ig form (IEI-Ig; e.g., PCT Publication Nos. WO 2019/024979 and WO 2019/025391, the form of which is incorporated herein by reference in its entirety). In certain embodiments, the antibody or antigen-binding fragment comprises two or more VH domains, two or more VL domains, or both (i.e., two or more VH domains and two or more VL domains). In certain embodiments, the antigen-binding fragment comprises the format (N-terminal to C-terminal direction) VH-linker-VL-linker-VH-linker-VL, wherein the two VH sequences may be the same or different and the two VL sequences may be the same or different. Such linked scFvs may include any combination of VH and VL domains arranged to bind to a given target, and in a format comprising two or more VH and/or two or more VL, may bind to one, two, or more different epitopes or antigens. It should be understood that formats incorporating multiple antigen-binding domains may include VH and/or VL sequences in any combination or orientation. For example, the antigen-binding fragment may comprise the form VL-linker-VH-linker-VL-linker-VH, VH-linker-VL-linker-VL-linker-VH, or VL-linker-VH-linker-VH-linker-VL. The monospecific or multispecific antibodies or antigen-binding fragments of the present disclosure constructed comprise any combination of VH and VL sequences disclosed herein and/or any combination of CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences. In some embodiments, the bispecific or multispecific antibodies or antigen-binding fragments may comprise one, two, or more antigen-binding domains (e.g., VH and VL) of the present disclosure. There may be two or more binding domains that bind to the same or different SARS-CoV-2 epitopes, and in some embodiments, a bispecific or multispecific antibody or antigen-binding fragment as provided herein may comprise additional SARS-CoV-2 binding domains, and/or may comprise binding domains that bind to different antigens or pathogens. In any of the presently disclosed embodiments, the antibody or antigen-binding fragment may be multispecific; e.g., bispecific, trispecific, etc. In certain embodiments, the antibody or antigen-binding fragment comprises: (i) a first VH and a first VL; and (ii) a second VH and a second VL, wherein the first VH and the second VH are different. In some embodiments, the first VH and VL comprise i) an amino acid sequence that is at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identical to the amino acid sequence depicted in SEQ ID NOs: 23 and 27, respectively; ii) an amino acid sequence that is at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identical to the amino acid sequence depicted in SEQ ID NOs: The amino acid sequence of NO. has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 83, 179, 181, 183, 185, 188, or 190 and any one of 87 or 193; iv) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and any one of 97, 225, 228, or 231; v) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of 105, 254, 257, or 260; or vi) with the following SEQ ID NO. The amino acid sequence described has at least 85% (i.e. 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with an amino acid sequence: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of 115, 121, 157, 272, 277, 279, 282, 286, or 290; and wherein the second VH and VL comprise i) respectively with SEQ ID NO: 23 and 27 have at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequences described in the following SEQ ID NOs.; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequences described in the following SEQ ID NOs.: 31, 35, 36, or 43, respectively, and 37; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequences described in the following SEQ ID NOs. NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 83, 179, 181, 183, 185, 188, or 190 and any one of 87 or 193; iv) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and any one of 97, 225, 228, or 231; v) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of 105, 254, 257, or 260; or vi) with the following SEQ ID NO. has an amino acid sequence with at least 85% (i.e. 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity: any one of 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively; wherein the first VH and the second VL are different from the second VH and VL, and wherein the first VH and the first VL together form a first antigen-binding site, and wherein the second VH and the second VL together form a second antigen-binding site. In some embodiments, the antibody or antigen-binding fragment may further comprise an Fc polypeptide or fragment thereof, comprising or consisting of an amino acid sequence having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence set forth in SEQ ID NOs: 44 to 80, or comprising or consisting of the amino acids set forth in SEQ ID NOs: 44 to 80. In certain embodiments, the antibody or antigen-binding fragment comprises an Fc polypeptide, or fragment thereof. An "Fc" fragment or Fc polypeptide comprises the carboxyl terminal portion of two antibody H chains (i.e., the CH2 and CH3 domains of IgG) held together by disulfide bonds. Fc may comprise a dimer composed of two Fc polypeptides (i.e., two CH2-CH3 polypeptides). Antibody "effector functions" refer to those biological activities attributable to the Fc region (a native sequence Fc region or an amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype. Examples of antibody effector functions include: C1q binding and complement-dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; downregulation of cell surface receptors (e.g., B cell receptors); and B cell activation. As discussed herein, the Fc domain may be modified (e.g., amino acid substitutions) to modify (e.g., improve, reduce, or ablate) one or more functionalities of an Fc-containing polypeptide (e.g., an antibody of the present disclosure). Such functions include, for example, Fc receptor (FcR) binding, antibody half-life modulation (e.g., by binding to FcRn), ADCC function, protein A binding, protein G binding, and complement binding. Amino acid modifications that modify (e.g., improve, reduce, or ablate) Fc functionality include, for example, T250Q/M428L, M252Y/S254T/T256E, H433K/N434F, M428L/N434S, M428L/N434A, E233P/L234V/L235A/ G236+A327G/A330S/P331S, E333A, S239D/A330L/I332E, P257I/Q311, K326W/E333S, S239D/I332E/G236A, N297Q, K322A, S228P, L235E+E318A/K320A/K322A, L234A/L235A (also referred to herein as "LALA"), and L234A/L235A/P329G mutations, which are summarized and annotated in "Engineered Fc Regions" and is available online at: invivogen.com/PDF/review/review-Engineered-Fc-Regions-invivogen.pdf?utm_source=review&utm_medium=pdf&utm_campaign=review&utm_content=Engineered-Fc-Regions, and is incorporated herein by reference. For example, to activate the complement cascade, when one or more immunoglobulin molecules are attached to the antigen target, the C1q protein complex can bind to at least two IgG1 molecules or one IgM molecule (Ward, E. S., and Ghetie, V., Ther. Immunol. 2 (1995) 77-94). Burton, D. R. described (Mol. Immunol. 22 (1985) 161-206) that a heavy chain region containing amino acid residues 318 to 337 is involved in complement fixation. Duncan, A. R. and Winter, G. (Nature 332 (1988) 738-740) used site-directed mutagenesis to report that Glu318, Lys320, and Lys322 form a binding site for C1q. The role of the Glu318, Lys320, and Lys322 residues in the binding of C1q was confirmed by the ability of short synthetic peptides containing these residues to inhibit complement-mediated cleavage. For example, FcR binding can be mediated by the interaction of the Fc portion (of an antibody) with an Fc receptor (FcR), which is a specialized cell surface receptor on cells including hematopoietic cells. Fc receptors belong to the immunoglobulin superfamily and have been shown to mediate the removal of antibody-coated pathogens by phagocytosis of immune complexes and the lysis of erythrocytes and various other cellular targets (e.g., tumor cells) coated with the corresponding antibody by antibody-dependent cell-mediated cytotoxicity (ADCC; Van de Winkel, J. G., and Anderson, C. L., J. Leukoc. Biol. 49 (1991) 511-524). FcRs are defined by their specificity for immunoglobulin classes; the Fc receptor for IgG antibodies is called FcγR, the Fc receptor for IgE is called FcεR, the Fc receptor for IgA is called FcαR, and so on, and the neonatal Fc receptor is called FcRn. Fc receptor binding is described, for example, in Ravetch, J. V., and Kinet, J. P., Annu. Rev. Immunol. 9 (1991) 457-492; Capel, P. J., et al., Immunomethods 4 (1994) 25-34; de Haas, M., et al., J Lab. Clin. Med. 126 (1995) 330-341; and Gessner, J. E., et al., Ann. Hematol. 76 (1998) 231-248. Crosslinking of receptors by the Fc domain of native IgG antibodies (FcγRs) triggers various effector functions, including phagocytosis, antibody-dependent cellular cytotoxicity, and release of inflammatory mediators, as well as regulation of immune complex clearance and antibody production. It is contemplated herein to provide a crosslinked Fc portion of a receptor (e.g., FcγR). In humans, three types of FcγRs have been characterized so far, which are: (i) FcγRI (CD64), which binds monomeric IgG with high affinity and is expressed on macrophages, monocytes, neutrophils, and eosinophils; (ii) FcγRII (CD32), which binds complexed IgG with moderate to low affinity, is widely expressed, especially on leukocytes, is believed to be a central player in antibody-mediated immunity, and can be divided into FcγRIIA, FcγRIIB, and FcγRIIC, which play different functions in the immune system but bind to IgG-Fc with similar low affinity, and the extracellular domains of these receptors are highly homologous; and (iii) FcγRIII (CD16), which binds IgG with medium to low affinity and has been found in two forms: FcγRIIIA, which has been found on NK cells, macrophages, eosinophils, and some monocytes and T cells, and is believed to mediate ADCC; and FcγRIIIB, which is highly expressed on neutrophils. FcγRIIA is found on many cells involved in killing (e.g., macrophages, monocytes, neutrophils) and appears to be able to activate the killing process. FcγRIIB appears to play a role in the inhibitory process and is found on B cells, macrophages, and on mast cells and eosinophils. Importantly, 75% of all FcγRIIB has been shown to be found in the liver (Ganesan, L. P. et al., 2012: "FcγRIIb on liver sinusoidal endothelium clears small immune complexes," Journal of Immunology 189: 4981-4988). FcγRIIB is abundantly expressed on liver sinusoidal endothelial cells called LSECs and in Kupffer cells in the liver, and LSECs are the major site of clearance of small immune complexes (Ganesan, L. P. et al., 2012: FcγRIIb on liver sinusoidal endothelium clears small immune complexes. Journal of Immunology 189: 4981-4988). In some embodiments, the antibodies and antigen-binding fragments thereof disclosed herein comprise an Fc polypeptide or fragment thereof that binds to FcγRIIb, in particular the Fc region, such as, for example, an IgG-type antibody. Furthermore, the Fc portion can be engineered by introducing mutations S267E and L328F to enhance FcγRIIB binding, as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies. Molecular Immunology 45, 3926-3933. Thereby, the clearance of immune complexes can be enhanced (Chu, S., et al., 2014: Accelerated Clearance of IgE In Chimpanzees Is Mediated By Xmab7195, An Fc-Engineered Antibody With Enhanced Affinity For Inhibitory Receptor FcγRIIb. Am J Respir Crit, American Thoracic Society International Conference Abstracts). In some specific embodiments, the antibody or antigen-binding fragment thereof disclosed herein comprises an engineered Fc portion having mutations S267E and L328F, in particular as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies. Molecular Immunology 45, 3926-3933. On B cells, FcγRIIB may act to suppress further immunoglobulin production and switch isotypes to, for example, the IgE class. On macrophages, FcγRIIB is thought to inhibit phagocytosis mediated by FcγRIIA. On eosinophils and mast cells, the B form may help suppress activation of these cells by binding of IgE to its independent receptors. With respect to FcγRI binding, modifications in native IgG of at least one of E233 to G236, P238, D265, N297, A327, and P329 reduce binding to FcγRI. Substitution of IgG2 residues at positions 233 to 236 into the corresponding positions in IgG1 and IgG4 reduced the binding of IgG1 and IgG4 to FcγRI by 103-fold and abolished the response of human monocytes to antibody-sensitized erythrocytes (Armour, K. L., et al. Eur. J. Immunol. 29 (1999) 2613-2624). With regard to FcγRII binding, IgG mutations such as E233 to G236, P238, D265, N297, A327, P329, D270, Q295, A327, R292, and K414 were found to reduce binding to FcγRIIA. The two allelic forms of human FcγRIIA are the "H131" variant, which binds to IgG1 Fc with higher affinity, and the "R131" variant, which binds to IgG1 Fc with lower affinity. See, e.g., Bruhns et al., Blood 113:3716-3725 (2009). With respect to FcγRIII binding, mutations in, e.g., at least one of E233 to G236, P238, D265, N297, A327, P329, D270, Q295, A327, S239, E269, E293, Y296, V303, A327, K338, and D376 were found to reduce binding to FcγRIIIA. The location of binding sites for Fc receptors on human IgG1, the mutation sites mentioned above, and methods for measuring binding to FcγRI and FcγRIIA are described in Shields, R. L., et al., J. Biol. Chem. 276 (2001) 6591-6604. The two allelic forms of human FcγRIIA are the "F158" variant, which binds to IgG1 Fc with lower affinity and the "V158" variant, which binds to IgG1 Fc with higher affinity. See, e.g., Bruhns et al., Blood 113: 3716-3725 (2009). With regard to binding to FcγRII, two regions of native IgG Fc appear to be involved in the interaction between FcγRII and IgG, namely (i) the lower hinge site of IgG Fc, particularly amino acid residues L, L, G, G (234 to 237, EU numbering), and (ii) adjacent regions of the CH2 domain of IgG Fc, particularly the upper CH2 domain adjacent to the lower hinge region, such as the loop and strand in the region of P331 (Wines, B.D., et al., J. Immunol. 2000; 164: 5313 - 5318). Furthermore, FcγRI appears to bind to the same site on IgG Fc, while FcRn and protein A bind to different sites on IgG Fc, which appear to be located at the CH2 to CH3 interface (Wines, B.D., et al., J. Immunol. 2000; 164: 5313-5318). Mutations that increase the binding affinity of the Fc polypeptides or fragments thereof disclosed herein to (i.e., one or more) Fcγ receptors are also contemplated (e.g., as compared to a reference Fc polypeptide or fragment thereof or containing a reference Fc polypeptide or fragment thereof that does not contain one or more mutations). See, e.g., Delillo and Ravetch, Cell 161(5):1035-1045(2015) and Ahmed et al., J. Struc. Biol. 194(1):78(2016), Fc mutations and techniques thereof are incorporated herein by reference. In any of the embodiments disclosed herein, the antibody or antigen-binding fragment may comprise an Fc polypeptide or fragment thereof comprising a mutation selected from the group consisting of G236A; S239D; A330L; and I332E; or a combination of any two or more of these mutations; for example, S239D/I332E; S239D/A330L/I332E; G236A/S239D/I332E; G236A/A330L/I332E (also referred to herein as "GAALIE"); or G236A/S239D/A330L/I332E. In some embodiments, the Fc polypeptide or fragment thereof does not comprise S239D. In some embodiments, the Fc polypeptide or fragment thereof comprises S at position 239 (EU numbering). In some embodiments, the Fc polypeptide or fragment thereof comprises an amino acid sequence set forth in SEQ ID NOs: 52 to 58. In certain embodiments, the Fc polypeptide or fragment thereof may comprise or consist of at least a portion of an Fc polypeptide or fragment thereof that participates in FcRn binding. In certain embodiments, the Fc polypeptide or fragment thereof comprises one or more amino acid modifications that improve (e.g., enhance binding to) FcRn (e.g., at a pH of about 6.0) and, in some embodiments, thereby extend the in vivo half-life of a molecule comprising the Fc polypeptide or fragment thereof (e.g., compared to an otherwise identical reference Fc polypeptide or fragment thereof or antibody that does not comprise the modification(s)). In certain embodiments, the Fc polypeptide or fragment thereof comprises or is derived from IgG Fc and the half-life-extending mutation comprises any one or more of the following: M428L; N434S; N434H; N434A; N434S; M252Y; S254T; T256E; T250Q; P257I; Q311I; D376V; T307A; E380A (EU numbering). In certain embodiments, the half-life-extending mutation comprises M428L/N434S (also referred to herein as "MLNS", "LS", "-LS", and "-LS"). In certain embodiments, the half-life-extending mutation is in an Fc polypeptide or fragment thereof comprising or consisting of the amino acid sequence set forth in SEQ ID NOs: 59 to 64. In some embodiments, the half-life-extending mutations comprise M252Y/S254T/T256E. In some embodiments, the half-life-extending mutations comprise T250Q/M428L. In some embodiments, the mutation that extends the half-life comprises P257I/Q311I. In some embodiments, the mutation that extends the half-life comprises P257I/N434H. In some embodiments, the mutation that extends the half-life comprises D376V/N434H. In some embodiments, the mutation that extends the half-life comprises T307A/E380A/N434A. In some embodiments, the mutation that extends the half-life comprises M428L/N434A (also referred to herein as "MLNA", "LA", "-LA", and "-LA"). In some embodiments, the mutation that extends the half-life is in an Fc polypeptide or a fragment thereof comprising the amino acid sequence described in SEQ ID NO: 65 to 70 or consisting of the amino acid sequence described in SEQ ID NO: 65 to 70. In some embodiments, the antibody or antigen-binding fragment comprises an Fc portion comprising the substitution mutations M428L/N434S or M428L/N434A. In some embodiments, the antibody or antigen-binding fragment comprises an Fc polypeptide or fragment thereof comprising the substitution mutations G236A/A330L/I332E. In certain embodiments, the antibody or antigen-binding fragment comprises an (e.g., IgG) Fc portion comprising a G236A mutation, an A330L mutation, and an I332E mutation (GAALIE), and does not comprise an S239D mutation (e.g., comprising a native S at position 239). In a specific embodiment, the antibody or antigen-binding fragment comprises an Fc polypeptide or fragment thereof comprising the following substitution mutations: M428L/N434S and G236A/A330L/I332E, (and may comprise or consist of the amino acid sequence set forth in SEQ ID NOs: 71 to 75), and optionally does not comprise S239D (e.g., comprises S at 239). In a specific embodiment, the antibody or antigen-binding fragment comprises an Fc polypeptide or fragment thereof comprising the following substitution mutations: M428L/N434A and G236A/A330L/I332E, (and may comprise or consist of the amino acid sequence set forth in SEQ ID NOs: 76 to 80), and optionally does not comprise S239D (e.g., comprises S at 239). In certain embodiments, the antibody or antigen-binding fragment comprises an Fc polypeptide or fragment thereof comprising the following substitution mutations: M428L/N434S (or M428L/N434A) and G236A/S239D/A330L/I332E. In some embodiments, antibodies or antigen-binding fragments (described further herein) are provided that comprise one or more amino acid mutations described in any one of (i) to (xviii) in a (e.g., human) IgG1 heavy chain: (i) G236A, L328V, and Q295E; (ii) G236A, P230A, and Q295E; (iii) G236A, R292P, and I377N; (iv) G236A, K334A, and Q295E; (v) G236S, R292P, and Y300L; (vi) G236A and Y300L; (vii) G236A, R292P, and Y300L; (viii) G236S, G420V, G446E, and L309T; (ix) (x) R292P and Y300L; (xi) G236A and R292P; (xii) Y300L; (xiii) E345K, G236S, L235Y, and S267E; (xiv) E272R, L309T, S219Y, and S267E; (xv) G236Y; (xvi) G236W; (xvii) F243L, G446E, P396L, and S267E; (xviii) G236A, S239D, and H268E, wherein the numbering of the amino acid residues is according to the EU index as described in Kabat. In certain embodiments, the antibody or antigen-binding fragment is afucosylated. In some embodiments, the antibody or antigen-binding fragment further comprises one or more mutations that enhance binding to human FcRn, such as M428L and N434S mutations or M428L and N434A mutations (EU numbering) or any other mutation(s) that enhance binding to human FcRn, such as those described herein. In certain embodiments, the antibody or antigen-binding fragment is defucosylated. In certain embodiments, the antibody or antigen-binding fragment comprises I) VH and VL having an amino acid sequence as set forth in any one of the following SEQ ID NOs: 23 and 27, respectively; 31 and 37, respectively; 35 and 37, respectively; and 36 and 37, respectively; II) CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 as set forth in VH and VL having an amino acid sequence as set forth in any one of the following: 1) SEQ ID NOs: 23 and 27, respectively; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 87; 21) SEQ ID NO: 188 and 193; 22) SEQ ID NO: 190 and 87; 23) SEQ ID NO: 191 and 87; 24) SEQ ID NO: 192 and 87; 25) SEQ ID NO: 193 and 87; 26) SEQ ID NO: 194 and 87; 27) SEQ ID NO: 195 and 87; 28) SEQ ID NO: 196 and 87; 29) SEQ ID NO: 197 and 87; 30) SEQ ID NO: 198 and 87; 31) SEQ ID NO: 198 and 87; 32) SEQ ID NO: 199 and 87; 33) SEQ ID NO: 190 and 193; 24) SEQ ID NOs: 93 and 97; 25) SEQ ID NOs: 93 and 225; 26) SEQ ID NOs: 93 and 228; 27) SEQ ID NOs: 93 and 231; 28) SEQ ID NOs: 197 and 97; 29) SEQ ID NOs: 197 and 225; 30) SEQ ID NOs: 197 and 228; 31) SEQ ID NOs: 197 and 231; 32) SEQ ID NOs: 201 and 97; 33) SEQ ID NOs: 201 and 225; 34) SEQ ID NOs: 201 and 228; 35) SEQ ID NOs: 201 and 231; 36) SEQ ID NOs: 204 and 97; 37) SEQ ID NOs: 204 and 225; 38) SEQ ID NOs: 49) SEQ ID NO: 212 and 225; 50) SEQ ID NO: 212 and 228; 51) SEQ ID NO: 212 and 231; 52) SEQ ID NO: 214 and 97; 53) SEQ ID NO: 64) SEQ ID NO: 220 and 97; 65) SEQ ID NO: 220 and 225; 66) SEQ ID NO: 220 and 228; 67) SEQ ID NO: 220 and 231; 68) SEQ ID NO: 220 and 231; 79) SEQ ID NO: 235 and 260; 80) SEQ ID NO: 238 and 105; 81) SEQ ID NO: 238 and 254; 82) SEQ ID NO: 238 and 257; 83) SEQ ID NO: 238 and 260; 84) SEQ ID NO: 241 and 105; 85) SEQ ID NO: 241 and 254; 86) SEQ ID NO: 241 and 257; 87) SEQ ID NO: 241 and 260; 88) SEQ ID NO: 243 and 105; 89) SEQ ID NO: 243 and 254; 90) SEQ ID NO: 243 and 257; 91) SEQ ID NO: 243 and 260; 92) SEQ ID NO: 245 and 105; 93) SEQ ID NO: 245 and 254; 94) SEQ ID NO: 245 and 257; 95) SEQ ID NO: 245 and 260; 96) SEQ ID NO: 247 and 105; 97) SEQ ID NO: 108) SEQ ID NO: 111 and 115; 109) SEQ ID NO: 111 and 121; 110) SEQ ID NO: 111 and 157; 111) SEQ ID NO: 111 and 157; 112) SEQ ID NO: 111 and 157; 113) SEQ ID NO: 111 and 157; 114) SEQ ID NO: 111 and 157; 115) SEQ ID NO: 111 and 157; 116) SEQ ID NO: 111 and 157; 117) SEQ ID NO: 111 and 157; 118) SEQ ID NO: 111 and 157; 119) SEQ ID NO: 112 and 113; 120) SEQ ID NO: 113 and 114; 121) SEQ ID NO: 114 and 1157; 115) SEQ ID NO: 115 11) SEQ ID NO: 111 and 272; 112) SEQ ID NO: 111 and 277; 113) SEQ ID NO: 111 and 279; 114) SEQ ID NO: 111 and 282; 115) SEQ ID NO: 111 and 286; 116) SEQ ID NO: 111 and 290; 117) SEQ ID NO: 125 and 115; 118) SEQ ID NO: 125 and 121; 119) SEQ ID NO: 125 and 157; 120) SEQ ID NO: 125 and 272; 121) SEQ ID NO: 125 and 277; 122) SEQ ID NO: 125 and 279; 123) SEQ ID NO: 125 and 282; 124) SEQ ID NO: 125 and 286; 125) SEQ ID 134) SEQ ID NO: 131 and 121; 135) SEQ ID NO: 131 and 157; 136) SEQ ID NO: 131 and 272; 137) SEQ ID NO: 131 and 277; 138) SEQ ID NO: 131 and 279; 139) SEQ ID NO: 128 and 282; 140) SEQ ID NO: 128 and 286; 141) SEQ ID NO: 128 and 290; 142) SEQ ID NO: 128 and 115; 143) SEQ ID NO: 131 and 121; 144) SEQ ID NO: 131 and 121; 145) SEQ ID NO: 131 and 157; 146) SEQ ID NO: 131 and 272; 147) SEQ ID NO: 131 and 277; 148) SEQ ID NO: 131 and 279 147) SEQ ID NO: 134 and 279; 148) SEQ ID NO: 134 and 282; 149) SEQ ID NO: 134 and 286; 150) SEQ ID NO: 134 and 290; 151) SEQ ID NO: 137 and 115; 152) SEQ ID NO: 137 and 121; 153) SEQ ID NO: 137 and 157; 154) SEQ ID NO: 137 and 272; 155) SEQ ID NO: 137 and 277; 156) SEQ ID NO: 137 and 279; 157) SEQ ID NO: 137 and 282; 158) SEQ ID NO: 137 and 286; 159) SEQ ID NO: 137 and 290; 160) SEQ ID NO: 141 and 115; 161) SEQ ID NO: 141 and 121; 162) SEQ ID NO: 141 and 157; 162) SEQ ID NO: 141 and 272; 162) SEQ ID NO: 141 and 277; 163) SEQ ID NO: 164) SEQ ID NO: 141 and 282; 165) SEQ ID NO: 141 and 286; 166) SEQ ID NO: 141 and 290; 167) SEQ ID NO: 145 and 115; 168) SEQ ID NO: 145 and 121; 169) SEQ ID NO: 145 and 157; 170) SEQ ID NO: 145 and 272; 171) SEQ ID NO: 145 and 277; 172) SEQ ID NO: 145 and 279; 173) SEQ ID NO: 145 and 282; 174) SEQ ID NO: 145 and 282; 175) SEQ ID NO: 145 and 286; 176) SEQ ID NO: 145 and 290; 177) SEQ ID NO: 145 and 115; 168) SEQ ID NO: 145 and 121; 169) SEQ ID NO: 145 and 157; 170) SEQ ID NO: 145 and 272; 171) SEQ ID NO: 145 and 277; 172) SEQ ID NO: 145 and 279; 173) SEQ ID NO: 145 and 282; 174) SEQ ID NO: 145 and 282; 175) SEQ ID NO: 145 and 286; 176) SEQ ID NO: 145 and 290; 177) SEQ ID 186) SEQ ID NO: 149 and 290; 187) SEQ ID NO: 153 and 115; 188) SEQ ID NO: 153 and 121; 189) SEQ ID NO: 153 and 157; 180) SEQ ID NO: 149 and 272; 181) SEQ ID NO: 149 and 277; 182) SEQ ID NO: 149 and 279; and 183) SEQ ID NO: 149 and 282; 184) SEQ ID NO: 149 and 286; 185) SEQ ID NO: 149 and 290; 186) SEQ ID NO: 153 and 115; 187) SEQ ID NO: 153 and 121; 188) SEQ ID NO: 153 and 157; 189) SEQ ID NO: 153 and 272; 190) SEQ ID NO: 153 and 277; 191) SEQ ID NO: 153 and 279; 192) SEQ ID NO: 153 and 282; 193) SEQ ID NO: 153 and 286; 194) SEQ ID NO: 153 and 290; 195) SEQ ID NO: 264 and 115; 196) SEQ ID NO: 264 and 121; 197) SEQ ID NO: 264 and 157; 198) SEQ ID NO: 264 and 272; 199) SEQ ID NO: 264 and 277; 200) SEQ ID NO: 264 and 279; 201) SEQ ID NO: 264 and 282; 202) SEQ ID NO: 264 and 286; 203) SEQ ID NO: 264 and 290; 204) SEQ ID NO: 20) SEQ ID NO: 266 and 115; 205) SEQ ID NO: 266 and 121; 206) SEQ ID NO: 266 and 157; 207) SEQ ID NO: 266 and 272; 208) SEQ ID NO: 266 and 277; 209) SEQ ID NO: 266 and 279; 210) SEQ ID NO: 266 and 282; 211) SEQ ID NO: 266 and 286; 212) SEQ ID NO: 266 and 290; 213) SEQ ID NO: 269 and 115; 214) SEQ ID NO: 269 and 121; 215) SEQ ID NO: 269 and 157; 216) SEQ ID NO: 269 and 157; 217) SEQ ID NO: 269 and 272; 218) SEQ ID NO: 269 and 277; 219) SEQ ID NO: 269 and 279; 219) SEQ ID NO: 269 and 282; 220) SEQ ID NO: 269 and 286; or 221) SEQ ID NO: 269 and 290, as determined by any CDL determination scheme disclosed herein; or (III) CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 having an amino acid sequence as follows (i) SEQ ID NO: 24 to 26 or 32 to 34 and 28 to 30 or 38 to 40, respectively; (ii) SEQ ID NO: 32 to 34 and 38 to 40, respectively; (iii) SEQ ID NO: 84 to 86 or 84, 85 and 186 and 88 to 90 or 194, 89, and 90, respectively; (iv) SEQ ID NO: 94 to 96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202; or 208, 95, and 205, and 98, 39, and 99; 226, 39, and 99; or 229, 39, and 232; (v) * SEQ ID NO: 112 to 114; 112, 126, and 114; 112, 129, and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112, 267, and 114; 112, 270, and 114; 112, 113, and 139 ; 112, 126, and 139; 112, 129, and 139; 112, 132, and 139; 112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112, 150, and 139; 112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112, 12 6, and 143; 112, 129, and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129, and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 147; 112, 154, and 147; 112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112, 129 and 151; 112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and 151; 112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 151; 112, 113, and 155; 11 2, 126, and 155; 112, 129, and 155; 112, 132, and 155; 112, 135, and 155; 112, 138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270, and 155; and 116 to 118; 116, 274, and 118; 116, 287, and 118; 116, 117, and 122; 116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116, 287, and 275; 116, 117, and 280; 116, 27 4, and 280; 116, 287, and 280; 116, 117, and 284; 116, 274, and 284; 116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 116, 117, and 291; 116, 274, and 291; 116, 287, and 291; 2 73, 117, and 118; 273, 274, and 118; 273, 287, and 118; 273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and 275; 273, 287, and 275; 273, 117, and 280; 273, 274, and 280; 1273, 287, and 280; 273, 117, and 284; 273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273, 287, and 288; 273, 117, and 291; 273, 274, and 291; 273, 287, and 291; 28 3, 117, 118; 283, 274, and 118; 283, 287, and 118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 283, 117, and 158; 283, 274, and 275; 283, 287, and 275; 283, 117, and 280; 283, 274, and 2 80; 283, 287, and 280; 283, 117, and 284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288; 283, 287, and 288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291; and (A) The Fc portion comprises the following substitution mutations: (i) G236A, L328V, and Q295E; (ii) G236A, P230A, and Q295E; (iii) G236A, R292P, and I377N; (iv) G236A, K334A, and Q295E; (v) G236S, R292P, and Y300L; (vi) G236A and Y300L; (vii) G236A, R292P, and Y300L; (viii) G236S, G420V, G446E, and L309T; (ix) G236A and R292P; (x) R292P and Y300L; (xi) G236A and R292P; (xii) Y300L; (xiii) E345K, G236S, L235Y, and S267E; (xiv) E272R, L309T, S219Y, and S267E; (xv) G236Y; (xvi) G236W; (xvii) F243L, G446E, P396L, and S267E; (xviii) G236A, S239D, and H268E; (xix) M428L/N434S; (xx) M428L/N434A; (xxi) G236A/A330L/I332E/ M428L/N434S; (xxii) or (xxiii) any two or more of (i) to (xxii); or (B) an Fc portion comprising or consisting of an Fc polypeptide or fragment thereof comprising or consisting of an amino acid sequence having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NOs: 44 to 80, optionally not a naturally occurring variant thereof, or comprising or consisting of an amino acid sequence as set forth in SEQ ID NOs: 52 to 80. In certain embodiments, the antibody or antigen-binding fragment comprises a mutation that alters glycosylation, wherein the mutation that alters glycosylation comprises N297A, N297Q, or N297G, and/or the antibody or antigen-binding fragment is partially or completely aglycosylated and/or partially or completely defucosylated. Host cell cell lines and methods for producing partially or completely deglycosylated or partially or completely defucosylated antibodies and antigen-binding fragments are known (see, e.g., PCT Publication No. WO 2016/181357; Suzuki et al. Clin. Cancer Res. 13(6): 1875-82 (2007); Huang et al. MAbs 6: 1-12 (2018)). The antibodies or antigen-binding fragments of the present disclosure may be fucosylated (e.g., comprise one or more fucosyl moieties, and generally comprise a native (wild-type) fucosylation pattern or a fucosylation pattern comprising one or more additional, or fewer, fucosyl moieties than native), or may be defucosylated. In particular, native IgG1 antibodies carry a glycan site at N297, and this is generally the only site in the antibody where a core fucosyl moiety can be found, although some glycan sites may be generated by mutation during antibody development (e.g., in a variable domain). Fucosylation of Fc polypeptides or fragments thereof, or antibodies can be achieved by introducing amino acid mutations to introduce or disrupt the fucosylation site (e.g., mutations at N297, such as N297Q or N297A, to disrupt the formation of a glycan that may include a core fucosylation portion), however it is generally preferred to maintain N297 and its glycans, such as by expressing the polypeptide in a host cell that has been genetically engineered to lack the ability to fucosylate the polypeptide (or to have an inhibitory or impaired ability); by expressing the polypeptide under conditions in which the host cell's ability to fucosylate the polypeptide is impaired (e.g., in the presence of 2-fluoro-L-fucose (2FF)), or similar conditions. The defucosylated polypeptide may comprise a fucosylation moiety, or substantially a fucosylation moiety, and/or may be expressed by a host cell that is genetically engineered to lack the ability to fucosylate the polypeptide (or to have an inhibitory ability or an impaired ability) and/or may be expressed under conditions in which the host cell's ability to fucosylate the polypeptide is impaired (e.g., in the presence of 2-fluoro-L-fucose (2FF)). In some embodiments, the polypeptide does not comprise a core fucosylation moiety at Asn297. In some embodiments, the defucosylated polypeptide has increased binding to FcγRIIIA. In some cases, adding 2FF to a culture medium comprising host cells expressing an antibody produces about 85% or more of the antibody without the fucosylation moiety. Thus, when a plurality of antibodies are produced in the presence of 2FF or a similar reagent, the plurality of antibodies may be described as "defucosylated". In some cases, a plurality of polypeptides or antibodies may be described as, for example, defucosylated, meaning that about 85% or more of the individual polypeptides or antibody molecules of the plurality of polypeptides or antibodies do not contain a fucosyl moiety. In certain preferred embodiments, the defucosylated antibody or polypeptide or a population or plurality of antibodies or polypeptides thereof comprises asparagine (N) at EU position 297. Fucosylation or lack of fucosylation may be assessed using, for example, mass spectrometry, such as electrospray mass spectrometry (ESI-MS). In some embodiments, a composition comprising any one or more of a plurality of the presently disclosed polypeptides is provided, wherein the composition comprises a defucosylated polypeptide. In certain embodiments, the antibody or antigen-binding fragment is able to induce sustained protection in an individual even once no detectable levels of the antibody or antigen-binding fragment are found in the individual (i.e., when the antibody or antigen-binding fragment has been cleared from the individual after administration). Such protection is referred to herein as a vaccine effect. Without wishing to be bound by theory, it is believed that dendritic cells can internalize the complex of antibody and antigen and then induce or promote an endogenous immune response to the antigen. In certain embodiments, the antibody or antigen-binding fragment comprises one or more modifications, such as, for example, mutations in Fc, which comprise G236A, A330L, and I332E, which can activate dendritic cells that can induce, for example, T cell immunity to the antigen. In certain embodiments, the antibodies or antigen-binding fragments of the present disclosure comprise an Fc variant selected from the Fc variants summarized in Table 1 (see also PCT Publication No. WO 2022/251119). In certain embodiments, the Fc variant, or antibody or antigen-binding fragment is fucosylated. In other embodiments, the Fc variant, or antibody or antigen-binding fragment is defucosylated. Table 1. Fc variants (fucosylated unless otherwise indicated) and their properties Variants ( one or more substitution mutations vs. wild-type human IgG1 Fc) Certain properties of one or more of the variants shown, such as compared to fucosylated wild-type human IgG1
G236A_L328V_Q295E Increased binding to human FcγRIIa (H131 allele and R131 allele); comparable or reduced binding to human FcγRIIb (e.g., as determined by MSD and/or surface plasmon resonance); increased ratio of binding to human FcγRIIa (H131 allele or R131 allele) to binding to human FcγRIIb; comparable binding to human FcRn; comparable production titer; increased signaling through FcγRIIa in host cells and/or decreased signaling through FcγRIIb in host cells; Tm differs by 12 ⸰ C or less from wild type; G236S_R292P_Y300L has improved binding to C1q
G236A_P230A_Q295E
G236A_R292P_I377N
G236A_K334A_Q295E
G236S_R292P_Y300L
G236A_Y300L Increased binding to human FcγRIIa (H131 (greater than 18-fold) and R131 (greater than 4-fold)); similar binding to human FcγRIIb or decreased binding to human FcγRIIb (e.g., as measured by surface plasmon resonance); increased ratio of binding to human FcγRIIa (H131 or R131) versus binding to human FcγRIIb; comparable binding to human FcRn; comparable production titer; increased signaling through FcγRIIa in host cells and/or decreased signaling through FcγRIIb in host cells; Tm differs by 4.5 ⸰ C from wild-type
G236A_R292P_Y300L Increased binding to human FcγRIIa (H131 (over 14-fold) and R131 (over 2.7-fold)); similar binding to human FcγRIIb; increased ratio of binding to human FcγRIIa (H131 or R131) to human FcγRIIb; binding to human FcγRIIIa (V158 allele and F158 allele); comparable binding to human FcRn; comparable production titer; increased signaling via FcγRIIa and/or FcγRIIIa in host cells and/or reduced signaling via FcγRIIb in host cells; increased signaling via FcγRIIa in host cells and/or reduced signaling via FcγRIIb in host cells; Tm differs by 4 ⸰ C from wild type; comparable binding to human C1q
G236S_G420V_G446E_L309T Increased binding to human FcγRIIa; decreased binding to human FcγRIIb (less than 0.5-fold); increased ratio of binding to human FcγRIIa (H131 or R131) to binding to human FcγRIIb; comparable binding to human FcRn; comparable production titer; increased signaling through FcγRIIa and/or FcγRIIIa in host cells, and/or decreased signaling through FcγRIIb in host cells; Tm differs by 4 ⸰ C or less from wild type
G236A_R292P
R292P_Y300L Increased binding to human FcγRIIIa (V158 and F158); increased binding to human C1q; Tm differs by 4 ⸰ C from wild type
Y300L Increased binding to human C1q
E345K_G236S_L235Y_S267E
E272R_L309T_S219Y_S267E
G236Y
G236W
F243L_G446E_P396L_S267E
G236A (defucosylated) Increased binding to human FcγRIIa (H131) and mouse FcγRIIa (R131), decreased binding to human FcγRIIb, increased binding to human FcγRIIIa (V158) and mouse FcγRIIIa (F158), increased binding to human FcγRIIIb, somewhat decreased binding to human FcRn, Tm 0.15 ⸰ C different from wild type or 0.9 ⸰ C different from wild type or 0.8 ⸰ C different from wild type or 0.7 ⸰ C different from wild type
S239D_H268E_G236A Increased binding to and signaling through all tested human FcγRs: FcγRIIA (H131); FcγRIIA (R131); FcγRIIB; FcγRIIIA (V158); FcγRIIIA (F158); FcγRIIIB; In addition, when anti-HBV antibodies with S239D_H268E_G236A_M428L_N434S were bound to hBsAg, the resulting immune complexes were incubated with MoDCs; MoDCs were subsequently incubated with donor CD4+ T cells, resulting in an increase in the percentage of NFAT+CD69+CD3+CD4+ T cells compared to antibodies with M428L_N434S alone.
In some embodiments, an anti-parvovirus antibody or antigen-binding fragment is provided, which comprises one or more amino acid mutations described in any of the following (i) to (xviii) in the (e.g., human) IgG1 heavy chain: (i) G236A, L328V, and Q295E; (ii) G236A, P230A, and Q295E; (iii) G236A, R292P, and I377N; (iv) G236A, K334A, and Q295E; (v) G236S, R292P, and Y300L; (vi) G236A and Y300L; (vii) G236A, R292P, and Y300L; (viii) G236S, G420V, G446E, and L309T; (ix) G236A and R292P; (x) R292P and Y300L; (xi) G236A and R292P; (xii) Y300L; (xiii) E345K, G236S, L235Y, and S267E; (xiv) E272R, L309T, S219Y, and S267E; (xv) G236Y; (xvi) G236W; (xvii) F243L, G446E, P396L, and S267E; (xviii) G236A, S239D, and H268E, wherein the numbering of the amino acid residues is according to the EU index as described in Kabat. In certain embodiments, the antibody or antigen-binding fragment is defucosylated. In some embodiments, the antibody or antigen-binding fragment further comprises one or more mutations that enhance binding to human FcRn, such as M428L and N434S mutations or M428L and N434A mutations (EU numbering) or any other mutation or mutations that enhance binding to human FcRn, such as those described herein. In certain embodiments, the antibody or antigen-binding fragment is defucosylated.
In any of the currently disclosed embodiments, the antibody or antigen-binding fragment comprises an Fc polypeptide or fragment thereof, which includes CH2 (or a fragment thereof), CH3 (or a fragment thereof), or CH2 and CH3, wherein the CH2, the CH3, or both may be of any isotype and may contain amino acid substitutions or other modifications as compared to the corresponding wild-type CH2 or CH3, respectively. In certain embodiments, the Fc disclosed herein comprises two CH2-CH3 polypeptides that are combined to form a dimer.
In any of the currently disclosed embodiments, the antibody or antigen-binding fragment comprises an Fc polypeptide or a fragment thereof, which includes CH2 (or a fragment thereof), CH3 (or a fragment thereof), or CH2 and CH3, wherein the CH2, the CH3, or both may be of any isotype and may contain amino acid substitutions or other modifications as compared to the corresponding wild-type CH2 or CH3, respectively. In certain embodiments, the Fc disclosed herein comprises two CH2-CH3 polypeptides that are combined to form a dimer.
In any of the currently disclosed embodiments, the antibody or antigen-binding fragment may be monoclonal. As used herein, the term "monoclonal antibody" (mAb) refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present (in some cases in small amounts). Monoclonal antibodies are highly specific for being directed to a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations that include different antibodies directed to different epitopes, each monoclonal antibody is directed to a single epitope of the antigen. In addition to their specificity, monoclonal antibodies are advantageous in that they can be synthesized without contamination by other antibodies. The term "monoclonal" should not be interpreted as requiring that the antibody be produced by any particular method. For example, monoclonal antibodies useful in the present invention may be prepared by first synthesizing the monoclonal antibody described by Kohler
et al.,
Nature256:495 (1975), or can be prepared using recombinant DNA methods in bacteria, eukaryotic animals, or plant cells (see, e.g., U.S. Patent No. 4,816,567). Monoclonal antibodies can also be prepared using methods described, e.g., in Clacksonet al.,
Nature,
352:624-628(1991) and Marks
et al.,
J. Mol. Biol.,
222:581-597 (1991) from the phage antibody library. Monoclonal antibodies can also be obtained using the method disclosed in PCT Publication No. WO 2004/076677A2.
The antibodies and antigen-binding fragments disclosed herein include "chimeric antibodies" in which a portion of the heavy chain and/or light chain is identical or homologous to a corresponding sequence in an antibody derived from a specific species or belonging to a specific antibody class or subclass, and the remaining portion of the chain(s) is identical or homologous to a corresponding sequence in an antibody derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, as long as they exhibit the desired biological activity (see U.S. Patent Nos. 4,816,567; 5,530,101 and 7,498,415; and Morrison
et al., Proc.Natl.Acad.Sci.USA,
81:6851-6855(1984)). For example, chimeric antibodies can contain human and non-human residues. In addition, chimeric antibodies can contain residues that are not found in the recipient antibody or in the donor antibody. Such modifications are made to further improve the performance of the antibody. For further details, see Jones
et al.,
Nature321:522-525(1986); Riechmann
et al.,
Natur e332:323-329(1988); and Presta,Curr. Op. Struct. Biol. 2:593-596(1992). Chimeric antibodies also include primatized and humanized antibodies.
"Humanized antibodies" are generally considered to be human antibodies that have one or more amino acid residues introduced into them from non-human sources. These non-human amino acid residues are generally taken from variable domains. Humanization can be carried out according to the method of Winter and colleagues (Jones
et al.,
Nature, 321:522-525(1986); Reichmann
et al.,
Nature, 332:323-327(1988); Verhoeyen
et al.,
Science, 239:1534-1536(1988)), by replacing the corresponding sequence of a human antibody with a non-human variable sequence. Therefore, such "humanized" antibodies are chimeric antibodies (U.S. Patents Nos. 4,816,567; 5,530,101 and 7,498,415) in which substantially less than the entire human variable domain has been replaced by the corresponding sequence from a non-human species. In some cases, a "humanized" antibody is an antibody produced by non-human cells or animals and contains human sequences, such as H
Cdomain.
A "human antibody" is an antibody that contains only sequences present in antibodies produced by humans. However, as used herein, a human antibody may include residues or modifications not found in naturally occurring human antibodies (e.g., antibodies isolated from humans), including those modifications and variant sequences described herein. These generally further improve or enhance antibody performance. In some cases, human antibodies are produced by genetically modified animals. For example, see U.S. Patents Nos. 5,770,429; 6,596,541 and 7,049,426.
In certain embodiments, the antibodies or antigen-binding fragments disclosed herein are chimeric, humanized, or human.
Polynucleotides, vectors, and host cells In another aspect, the present disclosure provides isolated polynucleotides encoding any of the antibodies disclosed herein or their antigen-binding fragments, or portions thereof (e.g., CDR, VH, VL, heavy chain, or light chain). In certain embodiments, the polynucleotide sequence is codon-optimized for expression in a host cell. Once the coding sequence is known or identified, codon optimization can be performed using known techniques and tools, such as using GenScript® Optimium GeneTMTool; see also Scholten
et al.,
Clin.Immunol.119:135, 2006). Codon-optimized sequences include partially codon-optimized sequences (i.e., one or more codons are optimized for expression in host cells) and fully codon-optimized sequences.
It should be understood that, due to, for example, the degeneracy of genetic coding, splicing, etc., the polynucleotides encoding the antibodies and antigen-binding fragments disclosed herein may have different nucleotide sequences while still encoding the same antibodies and antigen-binding fragments.
In some specific embodiments, the polynucleotide comprises or consists of the following: and SEQ ID NO: 81, 82, 91, 92, 100, 101, 109, 110, 119, 120, 123, 127, 130, 133, 136, 140, 144, 148, 152, 156, 159, 180, 182, 184, 187, 189, 191, 192, 195, 196, 200, 203, 206, 209, 211, 213, 94, 95, 96, 97, 98, 99, or 100%) identity to one or more of SEQ ID NOs: 123 and 159, in particular to a nucleic acid sequence having at least 85% (i.e. 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity. In more specific embodiments, the single polynucleotide comprises or consists of: and one or more of SEQ ID NOs: 81, 91, 100, 109, 119, 123, 127, 130, 133, 136, 140, 144, 152, 180, 182, 184, 187, 189, 191, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 262, 263, 265, and 268 and SEQ ID NO: 82, 92, 101, 110, 120, 159, 192, 195, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, 261, 271, 276, 278, 281, 285, and 289, in particular a nucleic acid sequence having at least 85% (i.e. 85%, 86, 87, 88, 89, 90, 91, 92, 92, 101, 110, 120, 159, 192, 195, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, 261, 271, 276, 278, 281, 285, and 289, in particular a nucleic acid sequence of SEQ ID NO: 123 and 159. In other more specific embodiments, at least two polynucleotides are provided, wherein the first polynucleotide comprises or consists of: and one or more of SEQ ID NO: 81, 91, 100, 109, 119, 123, 127, 130, 133, 136, 140, 144, 152, 180, 182, 184, 187, 189, 191, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 262, 263, 265, and 268, in particular SEQ ID NO: 82, 92, 101, 110, 120, 159, 192, 195, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, 261, 271, 276, 278, 281, 285, and 289, in particular SEQ ID NO: 159 has at least 85% (i.e. 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity with the nucleic acid sequence.
In some embodiments, a single polynucleotide or a combination of polynucleotides comprises or consists of a combination of two nucleic acid sequences, which are as follows: i) 81 and 82; ii) any one of 91, 180, 182, 184, 187, 189, or 191 and any one of 92, 192, or 195; iii) any one of 100, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, or 223 and any one of 101, 224, 227, 230, or 233; iv) 109 and any one of 110, 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, or 261; or v) any one of 119, 123, 127, 130, 133, 136, 140, 144, 148, 152, 156, 262, 263, 265, or 268 and any one of 120, 159, 271, 276, 178, 281, 285, or 289, in particular 123 and 159, the nucleic acid sequences are at least 85% (i.e. 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identical.
In any of the currently disclosed embodiments, the polynucleotide may comprise deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). In some embodiments, the RNA comprises a messaging RNA (mRNA).
Also provided are vectors, wherein the vector comprises or contains a polynucleotide as disclosed herein (e.g., a polynucleotide encoding an antibody or antigen binding fragment that binds to two or more severe acute respiratory syndrome beta coronaviruses). The vector may comprise any one or more of the vectors disclosed herein. In a specific embodiment, a vector comprising a DNA plasmid construct encoding an antibody or antigen binding fragment, or a portion thereof (e.g., a so-called "DMAb", see, e.g., Muthumani
et al.,
J Infect Dis.214(3):369-378(2016);Muthumani
et al.,
Hum Vaccin Immunother 9:2253-2262 (2013)); Flingai
et al.,
Sci Rep.5:12616(2015); and Elliott
et al.,
NPJ Vaccines18 (2017), which antibody-encoding DNA constructs and methods of use thereof, including administration thereof, are incorporated herein by reference. In certain embodiments, the DNA plasmid construct comprises a single open reading frame encoding the heavy chain and light chain (or VH and VL) of the antibody or antigen-binding fragment, wherein the sequence encoding the heavy chain and the sequence encoding the light chain are optionally separated by a polynucleotide encoding a protease cleavage site and/or by a polynucleotide encoding a self-cleaving peptide. In some embodiments, the substituent component of the antibody or antigen-binding fragment is encoded by a polynucleotide contained in a single plasmid. In other embodiments, the substituent components of the antibody or antigen-binding fragment are encoded by polynucleotides contained in two or more plasmids (e.g., the first plasmid contains a polynucleotide encoding a heavy chain, VH, or VH+CH, and the second plasmid contains a polynucleotide encoding a cognate light chain, VL, or VL+CL). In certain embodiments, a single plasmid contains polynucleotides encoding heavy chains and/or light chains of two or more antibodies or antigen-binding fragments from the present disclosure. An exemplary expression vector is pVax1, available from Invitrogen®. The DNA plasmids of the present disclosure can be delivered to an individual by, for example, electroporation (e.g., intramuscular electroporation), or with an appropriate formulation (e.g., hyaluronidase).
In another aspect, the present disclosure also provides host cells expressing antibodies or antigen-binding fragments according to the present disclosure; or containing or comprising vectors or polynucleotides according to the present disclosure.
Examples of such cells include, but are not limited to, eukaryotic cells, such as yeast cells, animal cells, insect cells, plant cells; and prokaryotic cells, including Escherichia coli. In some specific embodiments, the cell is a mammalian cell. In certain such specific embodiments, the cell is a mammalian cell line, such as a CHO cell (e.g., a DHFR-CHO cell (Urlaub
et al., PNAS 77:4216 (1980)), human embryonic kidney cells (e.g., HEK293T cells), PER.C6 cells, Y0 cells, Sp2/0 cells. NS0 cells, human liver cells, such as Hepa RG cells, myeloma cells, or fusion tumor cells. Other examples of mammalian host cell lines include mouse Sertoli cells (e.g., TM4 cells); monkey kidney CV1 line transformed by SV40 (COS-7); baby hamster kidney cells (BHK); African green monkey kidney cells (VERO-76); monkey kidney cells (CV1); human cervical carcinoma cells (HELA); human lung cells (W138); human liver cells (Hep G2); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); mouse mammary tumor (MMT 060562); TRI cells;
MRC5 cells; and FS4 cells. Mammalian host cell lines suitable for antibody production are also included in, for example, Yazaki and Wu,
Methods in Molecular Biology, Vol. 248 (B. K. C. Lo, ed., Humana Press, Totowa, N.J.), pp. 255-268 (2003).
In certain embodiments, the host cell is a prokaryotic cell, such as E. coli. The expression of peptides in prokaryotic cells such as E. coli is well established (see, e.g., Pluckthun, A.
Bio/Technology 9:545-551 (1991). For example, antibodies can be produced in bacteria, particularly when glycosylation and Fc effector functions are not required. For expression of antibody fragments and polypeptides in bacteria, see, e.g., U.S. Patent Nos. 5,648,237; 5,789,199; and 5,840,523.
In certain embodiments, cells can be transfected with expression vectors according to the present description. The term "transfection" refers to the introduction of a nucleic acid molecule, such as a DNA or RNA (e.g., mRNA) molecule, into a cell, such as into a eukaryotic cell. In the context of this specification, the term "transfection" encompasses any method known to those skilled in the art for introducing nucleic acid molecules into cells, such as into eukaryotic cells, including into mammalian cells. Such methods include, for example, electroporation, lipofection (e.g., based on cationic lipids and/or liposomes), calcium phosphate precipitation, nanoparticle-based transfection, virus-based transfection, or cationic polymer-based transfection (such as DEAE-dextran or polyethyleneimine). In certain specific embodiments, the introduction is non-viral.
Furthermore, the host cells of the present disclosure can be stably or temporarily transfected with the vectors according to the present disclosure, for example, for expressing antibodies, or antigen-binding fragments thereof, according to the present disclosure. In such embodiments, the cells may be stably transfected with a vector as described herein. Alternatively, as disclosed herein, the cells may be temporarily transfected with a vector according to the present disclosure encoding an antibody or antigen binding fragment. In any of the presently disclosed embodiments, the polynucleotide may be heterologous to the host cell.
Thus, the present disclosure also provides recombinant host cells heterologously expressing an antibody or antigen binding fragment of the present disclosure. For example, the cell may be a species different from the species from which the antibody is obtained in whole or in part (e.g., a CHO cell expressing a human antibody or an engineered human antibody). In some embodiments, the cell type of the host cell does not essentially express the antibody or antigen binding fragment. Furthermore, host cells may impart post-translational modifications (PTMs; e.g., glycosylation or fucosylation) to antibodies or antigen-binding fragments that are not present in the native state of the antibody or antigen-binding fragment (or in the native state of the parent antibody from which the antibody or antigen-binding fragment is engineered or derived). Such PTMs may result in functional differences (e.g., reduced immunogenicity). Thus, antibodies or antigen-binding fragments of the present disclosure produced by host cells as disclosed herein may include one or more post-translational modifications that are different from the antibody (or parent antibody) in its native state (e.g., human antibodies produced by CHO cells may contain more post-translational modifications than antibodies when isolated from humans and/or produced by native human B cells or plasma cells).
Insect cells that can be used to express the binding proteins disclosed herein are known in the art and include, for example, Spodoptera frugiperda (
Spodoptera frugipera)Sf9 cells, Trichoplusia in BTI-TN5B1-4 cells, and Spodoptera frugiperda SfSWT01 "Mimic
TM"Cell. See for example Palmberger
et al.,
J. Biotechnol.152(3-4):160-166(2011). A number of bacillivirus strains have been identified that can be used with insect cells, particularly for transfection of Spodoptera frugiperda cells.
Eukaryotic microorganisms (such as filamentous fungi or yeast) are also suitable hosts for the propagation or expression of protein-encoding vectors, and include fungal and yeast strains with "humanized" glycosylation pathways, resulting in the production of antibodies with partially or fully human glycosylation patterns. See Gerngross,
Nat. Biotech.22: 1409-1414(2004); Li
et al.,
Nat. Biotech.24:210-215 (2006).
Plant cells can also be used as hosts for expressing the binding proteins disclosed herein. For example, the PLANTIBODIES™ technology (described in, e.g., U.S. Patent Nos. 5,959,177; 6,040,498; 6,420,548; 7,125,978; and 6,417,429) employs genetically modified plants to produce antibodies.
In certain embodiments, the host cell comprises a mammalian cell. In certain specific embodiments, the host cell is a CHO cell, a HEK293 cell, a PER.C6 cell, a Y0 cell, a Sp2/0 cell, a NS0 cell, a human liver cell, a myeloma cell, or a fusion tumor cell.
In a related aspect, the present disclosure provides a method for producing an antibody or an antigen binding fragment, wherein the method comprises culturing a host cell disclosed herein under conditions and for a time sufficient to produce the antibody or the antigen binding fragment. For example, a method for isolating and purifying a recombinantly produced antibody may include obtaining a supernatant from a suitable host cell/vector system that secretes the recombinant antibody into a culture medium, and then concentrating the culture medium using a commercially available filter. After concentration, the concentrate may be applied to a single suitable purification matrix or a series of suitable matrices, such as an affinity matrix or an ion exchange resin. One or more reverse phase HPLC steps may be used to further purify the recombinant polypeptide. These purification methods can also be used when isolating an immunogen from its natural environment. Methods for large-scale production of one or more of the isolated/recombinant antibodies described herein include batch cell cultures that are monitored and controlled to maintain appropriate culture conditions. Purification of soluble antibodies can be performed according to methods described herein and known in the art, and in accordance with the laws and guidelines of domestic and foreign regulatory agencies.
Composition Also provided herein are compositions comprising any one or more of the antibodies, antigen-binding fragments, polynucleotides, vectors, or host cells disclosed herein, alone or in any combination, and may further comprise a pharmaceutically acceptable carrier, excipient, or diluent. Carriers, excipients, and diluents are discussed in further detail herein.
In certain embodiments, the composition comprises two or more different antibodies or antigen-binding fragments according to the present disclosure. In certain embodiments, the antibodies or antigen-binding fragments used in the combination each independently have one or more of the following properties: neutralize one, two, three, four, five, or more naturally occurring SARS beta coronavirus variants; do not compete with each other for spike protein binding; bind to different SARS beta coronavirus spike protein epitopes; reduce the development of resistance to SARS beta coronavirus; when combined, reduce the ability to resist SARS beta coronavirus; The invention relates to a novel composition comprising an antibody or antigen binding fragment of the present invention that is effective in neutralizing one, two, three, four, five or more live SARS beta coronaviruses; when used in combination, exhibits an additive or synergistic effect on neutralizing one, two, three, four, five or more live SARS beta coronaviruses; exhibits effector function; is protective in one or more relevant animal models of infection; and can be produced in sufficient quantities for large-scale production.
In certain embodiments, the composition comprises two or more different antibodies or antigen binding fragments according to the present disclosure. In certain embodiments, the first antibody or antigen-binding fragment and the second antibody or antigen-binding fragment may be A) both an antibody or antigen-binding fragment of S3A3, an antibody or antigen-binding fragment having sufficient CDR, VH, and/or VH identity to S3A3 to confer similar specific binding, or a fragment thereof, such as comprising: i) a VH sequence as in SEQ ID NO: 23 and a VL sequence as in SEQ ID NO: 27, ii) CDRs as described in SEQ ID NOs: 23 and 27, according to any numbering system disclosed herein, or iii) a VH sequence as in SEQ ID NO: 23 and 27, according to any numbering system disclosed herein, or iv) a VH sequence as in SEQ ID NO: 23 and 27, according to any numbering system disclosed herein. 24 to 26 (H1 to H3) and 28 to 30 (L1 to L3); B) an antibody or antigen-binding fragment of S3A19, an antibody or fragment thereof having sufficient CDR, VH, and/or VH identity to S3A19 to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 31, 35, 36 or 43 and a VL sequence as SEQ ID NO: 37, iii) a CDR as set forth in any one of SEQ ID NOs: 31, 35, 36, or 43 and SEQ ID NO: 37, according to any numbering system disclosed herein, or as set forth in SEQ ID NO: C) an antibody or antigen-binding fragment of S3I2, an antibody or fragment thereof having sufficient CDR, VH, and/or VH identity to S3I2 to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, or 190 and a VL sequence as any one of SEQ ID NOs: 87 or 194, ii) a CDR as described in any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, or 190, and any one of SEQ ID NOs: 87 or 193, according to any numbering system disclosed herein, or iii) a VH sequence as described in SEQ ID NOs: 83, 179, 181, 183, 185, 188, or 190, and a VL sequence as described in SEQ ID NOs: 87 or 194, 84 (H1), 85 (H2), and 86 or 186 (H3), and 88 or 194 (L1), 89 (L2), and 90 (L3); D) are antibodies or antigen-binding fragments of S3O13, antibodies or fragments thereof having sufficient CDR, VH, and/or VH identity with S3O13 to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and a VL sequence as any one of SEQ ID NOs: 97, 225, 228, or 231, ii) a VL sequence as in SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and the CDRs described in any of SEQ ID NOs: 97, 225, 228, or 231, according to any numbering system disclosed herein, or iii) as described in SEQ ID NO: 94, 198, or 208 (H1), 95 (H2), and 96, 199, 202, or 205 (H3), and 98, 226, 229, or 232 (L1), 39 (L2), and 99 (L3); E) are antibodies or antigen-binding fragments of S3L17, antibodies or fragments thereof having sufficient CDR, VH, and/or VH identity to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence as any one of SEQ ID NOs: 105, 254, 257, or 260, ii) a VL sequence as in SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and the CDRs described in any of SEQ ID NOs: 105, 254, 257, or 260, according to any numbering system disclosed herein, or iii) as described in SEQ ID NO: 103 (H1), 85 (H2), and 104, 236, or 239 (H3), and the CDRs described in 106 or 255 (L1), 107 (L2), and 108 or 258 (H3); F) are antibodies or antigen-binding fragments of S2V29 (or both S2V29a or S2V29b), antibodies or fragments thereof having sufficient CDR, VH, and/or VH identity with S2V29 to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NO: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VH sequence as SEQ ID NO: 115, 121, 157, 272, 277, 279, 282, 286, or 290, ii) any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, according to any numbering system disclosed herein, or iii) any one of SEQ ID NOs: 112 (H1), 113 (H2), 114 (H3), 115 (H4), 116 (H5), 117 (H6), 118 (H7), 119 (H8), 120 (H9), 121 (H10), 122 (H111), 123 (H124), 125 (H25 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270 (H2), and 114, 139, 143, 147, 151, or 155 (H3) and 116, 273, or 283 (L1), 117, 274, or 287 (L2), and 118, 122, 158, 275, 280, 284, 288, or 192 (L3); G) is an antibody or antigen-binding fragment according to A), B), C), D), E), or F) and a different antibody or antigen-binding fragment according to A), B), C), D), E), or F).
In certain embodiments, the composition comprises two or more different antibodies or antigen-binding fragments according to the present disclosure. In certain embodiments, the first antibody or antigen-binding fragment may be A) an antibody or antigen-binding fragment of S3A3, an antibody or fragment thereof having sufficient CDR, VH, and/or VH identity to S3A3 to confer similar specific binding, such as comprising: i) a VH sequence as in SEQ ID NO: 23 and a VL sequence as in SEQ ID NO: 27, ii) CDRs as described in SEQ ID NOs: 23 and 27, according to any numbering system disclosed herein, or iii) CDRs as described in SEQ ID NOs: 24 to 26 (H1 to H3) and 28 to 30 (L1 to L3); B) Antibodies or antigen-binding fragments of S3A19, antibodies or fragments thereof having sufficient CDR, VH, and/or VH identity to S3A19 to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 31, 35, 36 or 43 and a VL sequence as SEQ ID NO: 37, iii) CDRs as described in any one of SEQ ID NOs: 31, 35, 36, or 43 and SEQ ID NO: 37, according to any numbering system disclosed herein, or CDRs as described in SEQ ID NOs: 32 to 34 (H1 to H3) and 37 to 40 (L1 to L3); C) Antibodies or antigen-binding fragments of S3I2, antibodies or fragments thereof having sufficient CDR, VH, and/or VH identity to S3I2 to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, or 190 and a VL sequence as any one of SEQ ID NOs: 87 or 194, ii) CDRs as described in any one of SEQ ID NOs: 83, 179, 181, 183, 185, 188, or 190, and any one of SEQ ID NOs: 87 or 193, according to any numbering system disclosed herein, or iii) a VL sequence as described in SEQ ID NOs: 84 (H1), 85 (H2), and 86 or 186 (H3) and 88 or 194 (L1), 89 (L2), and 90 (L3); D) an antibody or antigen-binding fragment of S3O13, an antibody or fragment thereof having sufficient CDR, VH, and/or VH identity to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and a VL sequence as any one of SEQ ID NOs: 97, 225, 228, or 231, ii) a VL sequence as in SEQ ID NOs: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and any one of SEQ ID NOs: 97, 225, 228, or 231, according to any numbering system disclosed herein, or iii) CDRs as described in SEQ ID NOs: 94, 198, or 208 (H1), 95 (H2), and 96, 199, 202, or 205 (H3), and 98, 226, 229, or 232 (L1), 39 (L2), and 99 (L3); E) Antibodies or antigen-binding fragments of S3L17, antibodies or fragments thereof having sufficient CDR, VH, and/or VH identity to S3L17 to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence as any one of SEQ ID NOs: 105, 254, 257, or 260, ii) CDRs as described in any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of SEQ ID NOs: 105, 254, 257, or 260, according to any numbering system disclosed herein, or iii) a VH sequence as described in any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence as any one of SEQ ID NOs: 105, 254, 257, or 260. 103 (H1), 85 (H2), and 104, 236, or 239 (H3), and the CDRs described in 106 or 255 (L1), 107 (L2), and 108 or 258 (H3); F) an antibody or antigen-binding fragment of S2V29 (or both S2V29a or S2V29b), an antibody or fragment thereof having sufficient CDR, VH, and/or VH identity to S2V29 to confer similar specific binding, such as comprising the following: i) a VH sequence as any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VH sequence as described in SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, ii) any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, according to any numbering system disclosed herein, or iii) any one of SEQ ID NOs: 112 (H1), 113 (H2), 114 (H3), 115 (H4), 116 (H5), 117 (H6), 118 (H7), 119 (H8), 120 (H9), 121 (H10), 122 (H111), 123 (H124), 125 (H25 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270 (H2), and 114, 139, 143, 147, 151, or 155 (H3) and 116, 273, or 283 (L1), 117, 274, or 287 (L2), and 118, 122, 158, 275, 280, 284, 288, or 192 (L3); and the second antibody or antigen-binding fragment may be sotorovimab, S2K146, S2X259, S2X324, S2X324-v3.1, or S309 or an antigen-binding fragment thereof, particularly having: a VH having the amino acid sequence of SEQ ID NO: 14 and having: a VH having the amino acid sequence of SEQ ID NO: 14 NO: 15, an antibody or antigen-binding fragment having a VH having an amino acid sequence of SEQ ID NO: 16 and a VL having an amino acid sequence of SEQ ID NO: 17, an antibody or antigen-binding fragment having a VH having an amino acid sequence of SEQ ID NO: 18 and a VL having an amino acid sequence of SEQ ID NO: 19, an antibody or antigen-binding fragment having a VH having an amino acid sequence of SEQ ID NO: 20 and a VL having an amino acid sequence of SEQ ID NO: 22, an antibody or antigen-binding fragment having a VH having an amino acid sequence of SEQ ID NO: 21 and a VL having an amino acid sequence of SEQ ID NO: 22, or a VH having an amino acid sequence of SEQ ID NO: 41 and a VL having an amino acid sequence of SEQ ID NO: 42, or an antibody or antigen-binding fragment having a VL with a CDR as found in any of the aforementioned VH and VL combinations according to any numbering system disclosed herein. In a specific embodiment, the second antibody or antigen-binding fragment thereof may be sotoviromab or S2K146.
In some embodiments, the composition may comprise or may comprise: an antibody or antigen-binding fragment comprising or consisting of: A) a first antibody or antigen-binding fragment, which may be an antibody or antigen-binding fragment of S3L17, an antibody or antigen-binding fragment having sufficient CDR, VH, and/or VH identity to S3L17 to confer similar specific binding, or a fragment thereof, such as comprising: i) a VH sequence as any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence as any one of SEQ ID NOs: 105, 254, 257, or 260, ii) a VL sequence as any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence as any one of SEQ ID NOs: 105, 254, 257, or 260; NO: 105, 254, 257, or 260, according to any numbering system disclosed herein, or iii) the CDRs described in SEQ ID NO: 103 (H1), 85 (H2), and 104, 236, or 239 (H3), and 106 or 255 (L1), 107 (L2), and 108 or 258 (H3); and B) a second antibody or antigen-binding fragment, which may be an antibody or antigen-binding fragment of S2V29 (or both S2V29a or S2V29b), an antibody or antigen-binding fragment having sufficient CDR, VH, and/or VH identity with S2V29 to confer similar specific binding, or a fragment thereof, such as comprising the following: i) the CDR of SEQ ID NO: 115, 121, 157, 272, 277, 279, 282, 286, or 290, ii) the CDRs depicted in any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, according to any numbering system disclosed herein, or iii) the CDRs depicted in any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, according to any numbering system disclosed herein, or 112 (H1), 113 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270 (H2), and 114, 139, 143, 147, 151, or 155 (H3), and 116, 273, or 283 (L1), 117, 274, or 287 (L2), and 118, 122, 158, 275, 280, 284, 288, or 192 (L3).
In some embodiments, a composition is provided comprising a first antibody or antigen-binding fragment and a second antibody or antigen-binding fragment (a multispecific (e.g., bispecific) antibody or antigen-binding fragment) or a combination therapy is provided comprising a first antibody or antigen-binding fragment and a second antibody or antigen-binding fragment, wherein the first antibody or antigen-binding fragment and the second antibody or antigen-binding fragment respectively comprise, or the multispecific antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3, and optionally VH and VL, are based on: (i) any S3A3 antibody and any S3A19 antibody; (ii) any S3A3 antibody and sotoviromab; (iii) any S3A3 antibody and S2K146; (iv) any S3A3 antibody and S2X259; (v) any S3A3 antibody and any S2X324 antibody; vi) any S3A3 antibody and S309; (vi) any S3A19 antibody and sotoviromab; (vii) any S3A19 antibody and S2K146; (viii) any S3A19 antibody and S2X259; (ix) any S3A19 antibody and any S2X324 antibody; (x) any S3A19 antibody and S309; (xi) any S3I2 antibody and any S3A3 antibody; (xii) any any S3I2 antibody and any S3A19 antibody; (xiii) any S3I2 antibody and sotoviromab; (xiv) any S3I2 antibody and S2K146; (xv) any S3I2 antibody and S2X259; (xvi) any S3I2 antibody and any S2X324 antibody; (xvii) any S3I2 antibody and S309; (xviii) any S3I2 antibody and any S3O13 antibody; (xviii) any S3I2 antibody and any S3O13 antibody; ix) any S3I2 antibody and any S3L17 antibody; (xx) any S3O13 antibody and any S3A3 antibody; (xxi) any S3O13 antibody and any S3A19 antibody; (xxii) any S3O13 antibody and sotoviromab; (xxiii) any S3O13 antibody and S2K146; (xxiv) any S3O13 antibody and S2X259; (xxv) any S3O13 antibody and any S2X324 antibody; (xxvi) any S3O13 antibody and S309; (xxvii) any S3O13 antibody and any S3L17 antibody; (xxviii) any S3L17 antibody and any S3A3 antibody; (xxix) any S3L17 antibody and any S3A19 antibody; (xxx) any S3L17 antibody and sotovir; (xxxi) any S3L17 antibody and S2K 146; (xxxii) any S3L17 antibody and S2X259; (xxxiii) any S3L17 antibody and any S2X324 antibody; (xxxiv) any S3L17 antibody and S309; (xxxv) any S2V29 antibody and any S3A3 antibody; (xxxvi) any S2V29 antibody and any S3A19 antibody; (xxxvii) any S2V29 antibody and sotovir Antibody; (xxxviii) any S2V29 antibody and S2K146; (xxxix) any S2V29 antibody and S2X259; (xl) any S2V29 antibody and any S2X324 antibody; (xli) any S2V29 antibody and S309; (lxlii) any S2V29 antibody and any S3L17 antibody; and (xliii) any S2V29 antibody and any S3O13 antibody.
In certain embodiments, the composition comprises a first vector and a second vector, the first vector comprising a first plasmid and the second vector comprising a second plasmid, wherein the first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH of an antibody or an antigen-binding fragment thereof, and the second plasmid comprises a polynucleotide encoding a cognate light chain, VL, or VL+CL of an antibody or an antigen-binding fragment thereof. In certain embodiments, the composition comprises a polynucleotide (e.g., mRNA) coupled to a suitable delivery vehicle or carrier. Exemplary vehicles or carriers for administration to human subjects include lipids or lipid-derived delivery vehicles, such as liposomes, solid lipid nanoparticles, oily suspensions, submicron lipid emulsions, lipid microbubbles, inverse lipid micelles, cochlear liposomes, lipid microtubules, lipid microcylinders, or lipid nanoparticles (LNPs) or nanoscale platforms (see, e.g., Li
et al. Wilery Interdiscip Rev. Nanomed Nanobiotechnol. 11(2):e1530 (2019)). The principles, reagents and techniques for designing appropriate mRNA and formulating mRNA-LNPs and delivering the mRNA-LNPs are described in, for example, Pardi
et al.(
J Control Release 217345-351(2015)); Thess
et al.(
Mol Ther 23: 1456-1464(2015));Thran
et al.(
EMBO Mol Med 9(10):1434-1448(2017);Kose
et al.(
Sci. Immunol.4eaaw6647 (2019); and Sabnis
et al.(
Mol. Ther. 26:1509-1519 (2018)), the techniques include capping, codon optimization, nucleoside modification, purification of mRNA, incorporation of mRNA into stable lipid nanoparticles (e.g., ionizable cationic lipids/phosphatidylcholine/cholesterol/PEG-lipids; ionizable lipids: distearyl PC: cholesterol: polyethylene glycol lipids), and subcutaneous, intramuscular, intradermal, intravenous, intraperitoneal, and intratracheal administration of the mRNA-LNP, and are incorporated herein by reference.
Methods and uses Also provided herein are methods for using the antibodies or antigen-binding fragments, nucleic acids, vectors, cells, or compositions disclosed herein for diagnosing severe acute respiratory syndrome beta coronavirus infection (e.g., in a human individual or in a sample obtained from a human individual). The diagnostic method (e.g., in vitro, ex vivo) may include contacting the antibody, antibody fragment (e.g., antigen-binding fragment) with the sample. Such a sample may be isolated from an individual, such as an isolated tissue sample taken from, for example, the nasal passages, sinus cavities, salivary glands, lungs, liver, pancreas, kidneys, ears, eyes, placenta, digestive tract, heart, ovaries, pituitary glands, adrenal glands, thyroid glands, brain, skin, or blood. The method of diagnosis may also include detecting antigen/antibody complexes, particularly after the antibody or antibody fragment has come into contact with the sample. Such a detection step can be performed on a bench, i.e. without any contact with the human or animal body. Embodiments of the detection method are well known to those of ordinary skill in the art and include, for example, ELISA (enzyme-linked immunosorbent assay), including direct, indirect and sandwich ELISA. Also provided herein is a method for treating an individual using the antibody or antigen-binding fragment disclosed herein, or a composition comprising the same, wherein the individual has, is believed to have, or is at risk of having an infection caused by a severe acute respiratory syndrome beta coronavirus. "Treatment" or "ameliorate" refers to the medical management of a disease, disorder or condition in a subject (e.g., a human or non-human mammal, such as a primate, horse, cat, dog, goat, mouse, or rat). Generally, an appropriate dose or treatment regimen comprising an antibody or composition of the present disclosure is administered in an amount sufficient to induce a therapeutic or prophylactic benefit. A therapeutic or prophylactic benefit includes improved clinical prognosis; reduction or alleviation of symptoms associated with the disease; reduction in the occurrence of symptoms; improved quality of life; longer disease-free state; reduction in disease severity, stabilization of disease state; delay or prevention of disease progression; remission; survival; prolonged survival; or any combination thereof. In some embodiments, the therapeutic or preventive benefit includes reducing or preventing hospitalization for SARS-CoV-2 infection (i.e., in a statistically significant manner). In some embodiments, the therapeutic or preventive benefit includes reducing the duration of hospitalization for SARS-CoV-2 infection (i.e., in a statistically significant manner). In some embodiments, the therapeutic or preventive benefit includes reducing or eliminating the need for respiratory interventions, such as intubation and/or the use of a ventilator. In some embodiments, the therapeutic or preventive benefit includes reversing advanced disease pathology and/or reducing mortality. The "therapeutically effective amount" or "effective amount" of the antibody, antigen binding fragment, polynucleotide, vector, host cell, or composition disclosed herein refers to the amount of the composition or molecule sufficient to produce a therapeutic effect, including improving clinical prognosis in a statistically significant manner; reducing or alleviating symptoms associated with the disease; reducing the occurrence of symptoms; improving quality of life; longer disease-free state; reducing disease severity, stabilizing disease state; delaying disease progression; remission; survival; or prolonging survival. When referring to the administration of an individual active ingredient alone, the therapeutically effective amount refers to the effect of that ingredient or a cell expressing that ingredient alone. When referring to a combination, whether administered sequentially, sequentially or simultaneously, a therapeutically effective amount refers to the combined amount of active ingredients that produce a therapeutic effect, or a combination of adjuvant active ingredients and cells expressing the active ingredients. The combination may include, for example, two different antibodies that specifically bind to SARS-CoV-2 antigens, which in certain embodiments may be the same or different SARS-CoV-2 antigens, and/or may include the same or different epitopes. Therefore, in certain embodiments, methods for treating SARS-CoV-2 infection in an individual are provided, wherein the methods comprise administering to the individual an effective amount of an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition disclosed herein. Individuals that can be treated by the present disclosure are typically humans and other primate individuals, such as monkeys and apes for veterinary medical purposes. Other model organisms, such as mice and rats, can also be treated according to the present disclosure. In any of the foregoing specific examples, the individual can be a human individual. The individual can be male or female, and can be of any appropriate age, including infants, teenagers, adolescents, adults, and elderly individuals. It is believed that many criteria will cause a high risk of severe symptoms or death associated with severe acute respiratory syndrome beta coronavirus infection. These include but are not limited to age, occupation, general health condition, previous health conditions, and lifestyle. In some specific embodiments, the individual treated according to the present disclosure includes one or more risk factors. In certain embodiments, the human subject treated according to the present disclosure is an infant, a child, a young person, a middle-aged person, or an elderly person. In certain embodiments, the human subject treated according to the present disclosure is less than 1 year old, or is 1 to 5 years old, or is between 5 and 125 years old (e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, or 125 years old, including any and all ages therein or therebetween). In certain embodiments, the human subject treated according to the present disclosure is 0 to 19 years old, 20 to 44 years old, 45 to 54 years old, 55 to 64 years old, 65 to 74 years old, 75 to 84 years old, or 85 years old, or older. Middle-aged people, and especially the elderly, are believed to be particularly at risk. In specific embodiments, the human subject is 45 to 54 years old, 55 to 64 years old, 65 to 74 years old, 75 to 84 years old, or 85 years old, or older. In some embodiments, the human subject is male. In some embodiments, the human subject is female. In certain embodiments, the human subject treated according to the present disclosure is a resident of a nursing home or long-term care facility, a hospice worker, a healthcare provider or healthcare worker, a first responder, a family member or other close contact of an individual diagnosed with or suspected of having severe acute respiratory syndrome beta coronavirus infection, an overweight or clinically obese person, a smoker or a former smoker, a person who has or has had chronic obstructive pulmonary disease (COPD), a person with asthma (e.g., moderate to severe asthma), a person with an autoimmune disease or condition (e.g., diabetes), and/or a person with an immune Individuals with impaired or depleted immune systems (e.g., due to AIDS/HIV infection, cancer (e.g., leukemia), lymphodepleting therapy (e.g., chemotherapy), bone marrow or organ transplants, or genetic immune conditions), chronic liver disease, cardiovascular disease, lung or heart defects, or those who work or spend a long time in close contact with others (e.g., in factories, transportation centers, hospital environments, etc.). In certain embodiments, the individual treated according to the present disclosure has received a severe acute respiratory syndrome beta coronavirus vaccine and the vaccine was determined to be ineffective, for example, by infection or symptoms after vaccination of the individual, by clinical diagnosis, or by scientific or regulatory guidelines. In certain embodiments, the treatment is administered as peri-exposure prophylaxis. In certain embodiments, the treatment is administered to individuals with mild to moderate disease, which may be in an outpatient setting. In certain embodiments, the treatment is administered to individuals with moderate to severe disease, such as those requiring hospitalization. Typical routes of administration of the presently disclosed compositions thus include, but are not limited to, oral, topical, transdermal, inhalation, parenteral, sublingual, buccal, rectal, vaginal, and intranasal. The term "parenteral" as used herein includes subcutaneous injections, intravenous, intramuscular, intrasternal injection or infusion techniques. In certain embodiments, administration comprises administration by a route selected from the group consisting of oral, intravenous, parenteral, intragastric, intrapleural, intrapulmonary, intrarectal, intradermal, intraperitoneal, intratumoral, subcutaneous, topical, transdermal, intracisternal, intrathecal, intranasal, and intramuscular. In certain embodiments, the method comprises orally administering an antibody, an antigen binding fragment, a polynucleotide, a vector, a host cell, or a composition to a subject. The pharmaceutical compositions according to certain embodiments of the present invention are formulated so that the active ingredients contained therein are bioavailable after the composition is administered to a patient. The composition to be administered to an individual or patient may be in the form of one or more dosage units, where, for example, a tablet may be a single dosage unit, and the container of the antibody or antigen binding agent described herein in the form of an aerosol may accommodate multiple dosage units. Actual methods for preparing such dosage forms are known or will be apparent to those of ordinary skill in the art; see, for example, Remington: The Science and Practice of Pharmacy, 20th Edition (Philadelphia College of Pharmacy and Science, 2000). The composition to be administered will in any case contain an effective amount of the antibody or antigen binding fragment, polynucleotide, vector, host cell, or composition disclosed herein for use in treating the disease or condition of interest according to the teachings herein. The composition may be in the form of a solid or liquid. In some embodiments, one or more carriers are microparticles, so that the composition is, for example, in the form of tablets or powders. One or more carriers may be liquids, and the composition is, for example, an oral oil, an injectable liquid, or an aerosol that can be used, for example, for inhalation administration. When oral administration is intended, the pharmaceutical composition is preferably in solid or liquid form, wherein semi-solid, semi-liquid, suspension, and gel forms are included in the forms considered as solid or liquid herein. As a solid composition for oral administration, the pharmaceutical composition can be formulated into powders, granules, compressed tablets, pills, capsules, chewable tablets, powder tablets, etc. Such solid compositions will generally contain one or more inert diluents or edible carriers. In addition, one or more of the following may be present: binders such as carboxymethylcellulose, ethylcellulose, microcrystalline cellulose, tragacanth gum or gelatin; formulators such as starch, lactose or dextrin; disintegrants such as alginic acid, sodium alginate, starch sodium hydroxyacetate (Primogel), corn starch, etc.; lubricants such as magnesium stearate or hydrogenated vegetable oil (Sterotex); glidants such as colloidal silicon dioxide; sweeteners such as sucrose or saccharin; flavorings such as mint, methyl salicylate or citrus flavoring; and coloring agents. When the composition is in the form of a capsule, such as a gelatin capsule, it may contain, in addition to the above types of materials, a liquid carrier such as polyethylene glycol or oil. The composition may be in the form of a liquid, such as an elixir, syrup, solution, emulsion or suspension. As two examples, the liquid may be used for oral administration or for delivery by injection. When intended for oral administration, in addition to the compounds of the present invention, the preferred composition also contains one or more of a sweetener, a preservative, a dye/colorant and a flavor enhancer. In a composition intended for administration by injection, one or more of surfactants, preservatives, wetting agents, dispersants, suspending agents, buffers, stabilizers and isotonic agents may be included. Liquid pharmaceutical compositions, whether in the form of solutions, suspensions or other similar forms, may include one or more of the following adjuvants: sterile diluents such as water for injection, saline solutions (preferably physiological saline), Ringer's solution, solution), isotonic sodium chloride, nonvolatile oils (such as synthetic mono- or di-glycerides that can serve as solvents or suspending media), polyethylene glycol, glycerol, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates; and agents for tonicity adjustment such as sodium chloride or dextrose. Parenteral preparations can be enclosed in ampoules made of glass or plastic, disposable syringes or multi-dose vials. Physiological saline is a preferred adjuvant. Injectable pharmaceutical compositions are preferably sterile. Liquid compositions intended for parenteral or oral administration should contain an amount of an antibody or antigen binding fragment as disclosed herein so that a suitable dosage is obtained. Generally speaking, this amount is at least 0.01% of the antibody or antigen binding fragment in the composition. When intended for oral administration, this amount may vary between 0.1% and about 70% of the weight of the composition. Certain oral pharmaceutical compositions contain between about 4% and about 75% of the antibody or antigen binding fragment. In certain specific embodiments, pharmaceutical compositions and formulations according to the present invention are prepared so that the parenteral dosage unit contains between 0.01 and 10% by weight of the antibody or antigen binding fragment before dilution. The composition may be intended for topical administration, in which case the carrier may suitably comprise a solution, emulsion, ointment or gel base. For example, the base may comprise one or more of: wax, lanolin, polyethylene glycol, beeswax, mineral oil, diluents such as water and alcohol, and emulsifiers and stabilizers. A thickening agent may be present in the composition for topical administration. If intended for transdermal administration, the composition may include a transdermal patch or an iontophoresis device. The pharmaceutical composition may be intended for rectal administration in the form of, for example, a suppository, which will melt in the rectum and release the drug. Compositions for rectal administration may contain an oily base as a suitable non-irritating formulation. Suitable bases include, but are not limited to, lanolin, cocoa butter, and polyethylene glycol. Compositions may include various materials that change the physical form of a solid or liquid dosage unit. For example, a composition may include a material that forms a coating shell around an active ingredient. The material forming the coating shell is generally inert and may be selected from, for example, sugar, wormwood, and other enteric coating agents. Alternatively, the active ingredient may be packaged in a gelatin capsule. Compositions in solid or liquid form may include agents that bind to the antibodies or antigen binding fragments disclosed herein and thereby assist in the delivery of compounds. Suitable agents that may function in this capacity include single or multiple antibodies, one or more proteins, or liposomes. The composition may consist essentially of dosage units that can be administered as an aerosol. The term aerosol is used to denote a variety of systems ranging from those systems of colloidal nature to systems consisting of pressurized packages. Delivery may be by liquefying or compressing a gas or by a suitable pump system for dispensing the active ingredient. Aerosols may be delivered in the form of a single-phase, two-phase, or three-phase system to deliver one or more active ingredients. The delivery of an aerosol includes necessary containers, activators, valves, sub-containers, etc., which together may form a set. A person of ordinary skill in the art may determine the preferred aerosol without undue experimentation. It should be understood that the compositions of the present disclosure also encompass carrier molecules (e.g., lipid nanoparticles, nanoscale delivery platforms, etc.) for polynucleotides as described herein. Pharmaceutical compositions can be prepared by methods well known in the art of pharmaceutical technology. For example, a composition intended for administration by injection can be prepared by combining a composition comprising an antibody, an antigen-binding fragment thereof, or an antibody conjugate as described herein and, as required, one or more of a salt, a buffer, and/or a stabilizer with sterile distilled water to form a solution. A surfactant may be added to promote the formation of a homogeneous solution or suspension. A surfactant is a compound that non-covalently interacts with a peptide composition to promote dissolution or homogeneous suspension of the antibody or its antigen-binding fragment in an aqueous delivery system. In general, appropriate dosages and treatment regimens provide one or more components in an amount sufficient to provide a therapeutic and/or preventive benefit, as described herein, including improved clinical outcomes (e.g., reduced frequency, duration, or severity of diarrhea or related dehydration, or inflammation, or longer disease-free and/or overall survival, or reduced severity of symptoms). For preventive uses, the dosage should be sufficient to Preventing disease, delaying the onset of, or reducing the severity of a disease or condition associated with the disease or condition. The prophylactic benefit of the compositions administered according to the methods described herein can be determined by conducting preclinical (including in vitro and in vivo animal studies) and clinical studies, and analyzing the data obtained therefrom by appropriate statistical, biological, and clinical methods and techniques, all of which are readily practiced by those having ordinary knowledge in the art. The compositions are administered in an effective amount (e.g., to treat SARS-CoV-2 infection), which will vary depending on a variety of factors, including the activity of the specific compound employed; the metabolic stability and duration of action of the compound; the age, weight, general health, sex, and diet of the individual; the mode of administration and time; excretion rate; drug combination; severity of the particular disease or condition; and the therapy the subject is undergoing. In certain embodiments, after administration of therapy according to the formulations and methods of the present disclosure, the test subject will exhibit from about 10% to up to about 99% reduction in one or more symptoms associated with the disease or condition being treated, as compared to a placebo-treated or other appropriate control subject. Generally speaking, the therapeutically effective daily dose of an antibody or antigen-binding fragment is about 0.001 mg/kg (i.e., 0.07 mg) to about 100 mg/kg (i.e., 7.0 g) (for a 70 kg mammal); preferably, the therapeutically effective dose is about 0.01 mg/kg (i.e., 0.7 mg) to about 50 mg/kg (i.e., 3.5 g) (for a 70 kg mammal); more preferably, the therapeutically effective dose is about 1 mg/kg (i.e., 70 mg) to about 25 mg/kg (i.e., 1.75 g) (for a 70 kg mammal). For the polynucleotides, vectors, host cells, and related compositions disclosed herein, the therapeutically effective dose may be different from the therapeutically effective dose of an antibody or antigen-binding fragment. A single intramuscular (IM) administration of an age- and/or weight-appropriate dose of a S2V29-v1.2 antibody or fragment thereof as described herein, particularly S2V29-v1.2-IgG1m17_Lamda or S2V29-v1.2-IgG1m17,1-LS antibody, may be sufficient to treat SARS-CoV-2 infection or have a prophylactic benefit of between three and six months or up to six months. In certain embodiments, the method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition to a subject 2, 3, 4, 5, 6, 7, 8, 9, 10 times, or more. In certain embodiments, the method comprises administering an antibody, an AF, or a composition to an individual multiple times, wherein the second or consecutive administration is performed about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 24, about 48, about 74, about 96 hours, or longer after the first or previous administration. In certain embodiments, the method comprises administering an antibody, an AF, a polynucleotide, a vector, a host cell, or a composition at least once before the individual is infected with severe acute respiratory syndrome beta coronavirus. Compositions comprising antibodies, AF, polynucleotides, vectors, host cells, or compositions disclosed herein may also be administered simultaneously with, before, or after the administration of one or more other therapeutic agents. Such combination therapy may include administration of a single pharmaceutical dosage formulation containing a compound of the invention and one or more additional active agents, as well as administration of a composition comprising an antibody or antigen-binding fragment of the present disclosure and each active agent in its own separate dosage formulation. For example, an antibody or antigen-binding fragment thereof as described herein and other active agents may be administered to a patient together in a single oral dosage formulation (such as a tablet or capsule), or each dose may be administered in a separate oral dosage formulation. Similarly, an antibody or antigen-binding fragment thereof as described herein and other active agents may be administered to a patient together in a single parenteral dosage formulation (such as a saline solution or other physiologically acceptable solution), or each dose may be administered in a separate parenteral dosage formulation. In the case of using independent dosage formulations, the composition comprising the antibody or antigen binding fragment and one or more additional active agents can be administered substantially simultaneously, i.e., concurrently, or separately staggered, i.e., sequentially and in any order; combination therapy should be understood to include all such regimens. In certain embodiments, combination therapy is provided, which comprises one or more anti-severe acute respiratory syndrome beta coronavirus antibodies (or one or more nucleic acids, host cells, vectors, or compositions) disclosed herein and one or more anti-inflammatory agents and/or one or more antiviral agents. In specific embodiments, one or more anti-inflammatory agents comprise corticosteroids, such as, for example, dexamethasone, prednisone, etc. In some embodiments, one or more anti-inflammatory agents include an interleukin antagonist, such as, for example, an antibody that binds to IL6 (such as siltuximab), or to IL-6R (such as tocilizumab), or to IL-1β, IL-7, IL-8, IL-9, IL-10, FGF, G-CSF, GM-CSF, IFN-γ, IP-10, MCP-1, MIP-1A, MIP1-B, PDGR, TNF-α, or VEGF. In some embodiments, an anti-inflammatory agent such as leronlimab, ruxolitinib, and/or anakinra is used. In some embodiments, one or more antiviral agents include nucleotide analogs or nucleotide analog prodrugs, such as, for example, remdesivir, sofosbuvir, acyclovir, and zidovudine. In certain embodiments, the antiviral agent includes lopinavir, ritonavir, favipiravir, or any combination thereof. Other anti-inflammatory agents used in the combination therapy of the present disclosure include non-steroidal anti-inflammatory drugs (NSAIDS). It should be understood that in such combination therapy, one or more antibodies (or one or more nucleic acids, host cells, vectors, or compositions) and one or more anti-inflammatory agents and/or one or more antiviral agents can be administered in any order and in any order, or administered together. In some embodiments, the antibodies (or one or more nucleic acids, host cells, vectors, or compositions) are administered to an individual who has previously received one or more anti-inflammatory agents and/or one or more antiviral agents. In some embodiments, the one or more anti-inflammatory agents and/or one or more antiviral agents are administered to an individual who has previously received the antibodies (or one or more nucleic acids, host cells, vectors, or compositions). In certain embodiments, combination therapies are provided that include two or more anti-severe acute respiratory syndrome beta coronavirus antibodies disclosed herein. The method may include administering a first antibody to an individual who has received a second antibody, or may include administering two or more antibodies together. For example, in a particular embodiment, a method is provided that includes administering to an individual (a) a first antibody or antigen-binding fragment when the individual has received a second antibody or antigen-binding fragment; (b) a second antibody or antigen-binding fragment when the individual has received a first antibody or antigen-binding fragment; or (c) a first antibody or antigen-binding fragment, and a second antibody or antigen-binding fragment. In a related aspect, uses of the antibodies, antigen-binding fragments, vectors, host cells, and compositions disclosed herein are provided. The present disclosure further provides a kit comprising one or more of any antibody, antigen binding fragment, polynucleotide, nucleic acid, vector, or other composition disclosed herein. The kit may further include one or more of a container (such as a test tube, vial, or syringe), an activator, a valve, a subcontainer, or instructions for use (such as administration to an individual). In certain embodiments, antibodies, antigen binding fragments, polynucleotides, vectors, host cells, or compositions are provided, which are used in methods for treating severe acute respiratory syndrome beta-coronavirus infection in an individual. In certain embodiments, antibodies, antigen binding fragments, or compositions are provided, which are used in methods for manufacturing or preparing a drug for treating severe acute respiratory syndrome beta-coronavirus infection in an individual. The present disclosure provides the following specific embodiments: Embodiment 1. An antibody, or an antigen-binding fragment thereof, comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein: (A) (i) the CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 24, or a functional variant thereof, wherein the functional variant comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: (iii) the CDRH3 comprises or consists of an amino acid sequence such as SEQ ID NO: 26, or a functional variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence such as SEQ ID NO: 28, or a functional variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence such as SEQ ID NO: 30, or a functional variant thereof, which comprises one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; NO: 29, or a functional variant thereof, the functional variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retained substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 30, or a functional variant thereof, the functional variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retained substitutions and/or substitutions of germline-encoded amino acids, (B) (i) the CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 32 or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of an amino acid sequence such as SEQ ID NO: 33, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) the CDRH3 comprises or consists of an amino acid sequence such as SEQ ID NO: 34, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence such as SEQ ID NO: (v) the CDRL2 comprises or consists of an amino acid sequence as described in SEQ ID NO: 39, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of an amino acid sequence as described in SEQ ID NO: 39, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; 40, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids, (C) (i) the CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 84, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 85, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) the CDRH3 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 86, or a sequence variant thereof NO: 86 or 186, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of the following: an amino acid sequence as in any one of SEQ ID NO: 88 or 194, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of the following: an amino acid sequence as in any one of SEQ ID NO: 86 or 186, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; 89, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 90, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (D) (i) the CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 94, 198, or 208, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 95, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) the CDRH3 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 96, 199, 202, or 205, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence as described in any one of SEQ ID NOs: 98, 226, 229, 232, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence as described in any one of SEQ ID NOs: 39, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 99, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (e) (i) the CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 103 or a sequence variant thereof, said sequence variant comprising one, two, or three amino acid substitutions, one or more of said substitutions being optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) said CDRH2 comprising or consisting of: an amino acid sequence such as SEQ ID NO: 85, or a sequence variant thereof, said sequence variant comprising one, two, or three amino acid substitutions, one or more of said substitutions being optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) said CDRH3 comprising or consisting of: an amino acid sequence such as SEQ ID NO: 104, 236, or 239, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence as in SEQ ID NO: 106 or 255, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence as in SEQ ID NO: 107, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of an amino acid sequence such as SEQ ID NO: 258, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; or (F) (i) the CDRH1 comprises or consists of an amino acid sequence such as SEQ ID NO: 112, or a sequence variant thereof, said sequence variant comprising one, two, or three amino acid substitutions, one or more of said substitutions being optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) said CDRH2 comprising or consisting of an amino acid sequence as in any one of SEQ ID NOs: 113, 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270, or a sequence variant thereof, said sequence variant comprising one, two, or three amino acid substitutions, one or more of said substitutions being optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) said CDRH3 comprising or consisting of an amino acid sequence as in any one of SEQ ID NOs: 114, 139, 143, 147, 151, or 155, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence as any one of SEQ ID NO: 116, 273, or 283, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence as any one of SEQ ID NO: 117, 274, or 287, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retained substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of the following: an amino acid sequence as described in any one of SEQ ID NOs: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retained substitutions and/or substitutions of germline-encoded amino acids, wherein the substitutions are optionally substitutions as described in Table 2 or Table 3, and wherein the antibody or antigen-binding fragment can bind to the surface glycoprotein of severe acute respiratory syndrome beta coronavirus. Specific embodiment 2. An antibody, or an antigen-binding fragment thereof, comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), wherein the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, and the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein the CDRH1, CDRH2, and CDRH3 and the CDRL1, CDRL2, and CDRL3 have the following amino acid sequences: (A) SEQ ID NOs: 24 to 26 and 28 to 30, respectively; (B) SEQ ID NOs: 32 to 34 and 38 to 40, respectively; (C) SEQ ID NOs: 84 to 86 or 84, 85 and 186 and 88 to 90 or 194, 89, and 90, respectively; (D) SEQ ID NOs: 94 to 96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202; or 208, 95, and 205, and 98, 39, and 99; 226, 39, and 99; or 229, 39, and 232; (E) are SEQ ID NOs: 103, 85, and 104; 103, 85, and 236; or 103, 85, and 239, and 106 to 108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258; and (F) are SEQ ID NOs: 112 to 114; 112, 126, and 114; 112, 129, and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112, 267, and 114; 112, 270, and 114; 112, 113, and 139 ; 112, 126, and 139; 112, 129, and 139; 112, 132, and 139; 112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112, 150, and 139; 112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112, 12 6, and 143; 112, 129, and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129, and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 147; 112, 154, and 147; 112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112, 129 and 151; 112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and 151; 112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 151; 112, 113, and 155; 1 12, 126, and 155; 112, 129, and 155; 112, 132, and 155; 112, 135, and 155; 112, 138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270 , and 155; and 116 to 118; 116, 274, and 118; 116, 287, and 118; 116, 117, and 122; 116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116, 287, and 275; 116, 117, and 280; 116, 2 74, and 280; 116, 287, and 280; 116, 117, and 284; 116, 274, and 284; 116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 116, 117, and 291; 116, 274, and 291; 116, 287, and 291 ; 273, 117, and 118; 273, 274, and 118; 273, 287, and 118; 273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and 275; 273, 287, and 275; 273, 117, and 280; 273, 27 4, and 280; 1273, 287, and 280; 273, 117, and 284; 273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273, 287, and 288; 273, 117, and 291; 273, 274, and 291; 273, 287, and 291 ; 283, 117, 118; 283, 274, and 118; 283, 287, and 118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 283, 117, and 158; 283, 274, and 275; 283, 287, and 275; 283, 117, and 280; 283, 274 , and 280; 283, 287, and 280; 283, 117, and 284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288; 283, 287, and 288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291. Specific embodiment 3. The antibody or antigen-binding fragment of specific embodiment 1 or 2, wherein the SARS beta coronavirus is a clade 1b SARS beta coronavirus. Embodiment 4. The antibody or antigen binding fragment of Embodiment 3, wherein the severe acute respiratory syndrome beta coronavirus is SARS-CoV-2 WT, SARS-CoV-2 BA.1, RATG13, PANG/GD, or PAND/GX. Embodiment 5. The antibody or antigen binding fragment of any one of Embodiments 1 to 4, wherein the antibody or antigen binding fragment is capable of binding to the surface glycoprotein when the surface glycoprotein is expressed on the cell surface of the host cell and/or contained on the virus particle. Embodiment 6. The antibody or antigen binding fragment of any one of Embodiments 1 to 5, which is capable of binding to the surface glycoprotein from two or more (e.g., two, three, four, five, or more) severe acute respiratory syndrome beta coronaviruses. Specific embodiment 7. An antibody or antigen binding fragment as described in any one of Specific Embodiments 1 to 6, which is capable of neutralizing an infection caused by one or more severe acute respiratory syndrome beta coronaviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in humans. Specific embodiment 8. An antibody or antigen binding fragment as described in any one of Specific Embodiments 1 to 7, which is capable of neutralizing an infection caused by two or more severe acute respiratory syndrome beta coronaviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in humans. Specific embodiment 9. The antibody or antigen-binding fragment of any one of embodiments 1 to 8, wherein the VH and VL each comprise or consist of an amino acid sequence that is at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence described below; or each comprise or consist of the amino acid sequence described below: (I) 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 19) SEQ ID NO: 185 and 87; 20) SEQ ID NO: 185 and 87; 21) SEQ ID NO: 185 and 193; 22) SEQ ID NO: 190 and 87; 23) SEQ ID NO: 190 and 193; 24) SEQ ID NO: 93 and 97; 25) SEQ ID NO: 93 and 225; 26) SEQ ID NO: 93 and 228; 27) SEQ ID NO: 93 and 231; 28) SEQ ID NO: 197 and 97; 29) SEQ ID NO: 197 and 225; 30) SEQ ID NO: 197 and 228; 31) SEQ ID NO: 197 and 231; 32) SEQ ID NO: 201 and 97; 33) SEQ ID NO: 201 and 225; 34) SEQ ID NO: 201 and 228; 35) SEQ ID NO: 201 and 231; 36) SEQ ID NO: 204 and 97; 37) SEQ ID NO: 204 and 225; 38) SEQ ID 49) SEQ ID NO: 212 and 225; 50) SEQ ID NO: 212 and 228; 51) SEQ ID NO: 212 and 231; 52) SEQ ID NO: 214 and 97; 53) SEQ ID NO: 214 and 97; 54) SEQ ID NO: 216 and 97; 55) SEQ ID NO: 216 and 97; 56) SEQ ID NO: 216 and 97; 57) SEQ ID NO: 216 and 97; 58) SEQ ID NO: 216 and 97; 59) SEQ ID NO: 216 and 97; 60) SEQ ID NO: 216 and 97; 61) SEQ ID NO: 216 and 97; 62) SEQ ID NO: 216 and 97; 63) SEQ ID NO: 216 and 97; 64) SEQ ID NO: 220 and 97; 65) SEQ ID NO: 220 and 225; 66) SEQ ID NO: 220 and 228; 67) SEQ ID NO: 220 and 231; 68) SEQ ID NO: 220 and 97; 69) SEQ ID NO: 220 and 231; 70) SEQ ID NO: 220 and 231; 71) SEQ ID NO: 220 and 231; 72) SEQ ID NO: 220 and 231; 73) SEQ ID NO: 220 and 231; 74) SEQ ID NO: 221 and 97; 75) SEQ ID NO: 221 and 231; 76) SEQ ID NO: 221 and 231; 77) SEQ ID NO: 221 and 231; 78) SEQ ID NO: 221 and 231; 79) SEQ ID NO: 222 and 97; 80) SEQ ID NO: 222 and 231; 81) SEQ ID NO: 222 and 97; 82) SEQ ID NO: 222 and 231; 83) SEQ ID NO: 222 and 231; 84) SEQ ID NO: 223 54) SEQ ID NO: 102 and 257; 75) SEQ ID NO: 102 and 260; 76) SEQ ID NO: 235 and 105; 77) SEQ ID NO: 235 and 254; 78) SEQ ID NO: 235 and 257; 79) SEQ ID NO: 235 and 260; 80) SEQ ID NO: 238 and 105; 81) SEQ ID NO: 238 and 254; 82) SEQ ID NO: 92) SEQ ID NO: 245 and 105; 93) SEQ ID NO: 245 and 254; 94) SEQ ID NO: 245 and 257; 95) SEQ ID NO: 245 and 260; 96) SEQ ID NO: 247 and 105; 97) SEQ ID NO: 247 and 105; 98) SEQ ID NO: 247 and 105; 99) SEQ ID NO: 248 and 254; 100) SEQ ID NO: 248 and 257; 101) SEQ ID NO: 248 and 254; 102) SEQ ID NO: 248 and 254; 103) SEQ ID NO: 248 and 254; 104) SEQ ID NO: 248 and 257; 105) SEQ ID NO: 248 and 254; 106) SEQ ID NO: 248 and 257; 107) SEQ ID NO: 248 and 254; 108) SEQ ID NO: 248 and 254; 109) SEQ ID NO: 248 and 257 SEQ ID NOs: 247 and 254; 98) SEQ ID NOs: 247 and 257; 99) SEQ ID NOs: 247 and 260; 100) SEQ ID NOs: 249 and 105; 101) SEQ ID NOs: 249 and 254; 102) SEQ ID NOs: 249 and 257; 103) SEQ ID NOs: 249 and 260; 104) SEQ ID NOs: 251 and 105; 105) SEQ ID NOs: 251 and 254; 106) SEQ ID NOs: 251 and 257; 107) SEQ ID NOs: 251 and 260; 108) SEQ ID NOs: 111 and 115; 109) SEQ ID NOs: 111 and 121; 110) SEQ ID NOs: 111 and 157; 111) SEQ ID NO: 111 and 272; 112) SEQ ID NO: 111 and 277; 113) SEQ ID NO: 111 and 279; 114) SEQ ID NO: 111 and 282; 115) SEQ ID NO: 111 and 286; 116) SEQ ID NO: 111 and 290; 117) SEQ ID NO: 125 and 115; 118) SEQ ID NO: 125 and 121; 119) SEQ ID NO: 125 and 157; 120) SEQ ID NO: 125 and 272; 121) SEQ ID NO: 125 and 277; 122) SEQ ID NO: 125 and 279; 123) SEQ ID NO: 125 and 282; 124) SEQ ID NO: 134) SEQ ID NO: 131 and 115; 135) SEQ ID NO: 131 and 157; 136) SEQ ID NO: 131 and 272; 137) SEQ ID NO: 131 and 279; 138) SEQ ID NO: 132 and 279; 139) SEQ ID NO: 133 and 115; 140) SEQ ID NO: 134 and 115; 141) SEQ ID NO: 134 and 115; 142) SEQ ID NO: 134 and 115; 143) SEQ ID NO: 134 and 115; 144) SEQ ID NO: 134 and 115; 145) SEQ ID NO: 134 and 115; 146) SEQ ID NO: 134 and 115 147) SEQ ID NO: 134 and 279; 148) SEQ ID NO: 134 and 282; 149) SEQ ID NO: 134 and 286; 150) SEQ ID NO: 134 and 290; 151) SEQ ID NO: 134 and 115; 152) SEQ ID NO: 134 and 121; 153) SEQ ID NO: 134 and 121; 154) SEQ ID NO: 134 and 157; 155) SEQ ID NO: 134 and 272; 156) SEQ ID NO: 134 and 277; 157) SEQ ID NO: 134 and 279; 158) SEQ ID NO: 134 and 282; 159) SEQ ID NO: 134 and 286; 160) SEQ ID NO: 134 and 290; 161) SEQ ID NO: 134 and 291; 154) SEQ ID NO: 137 and 272; 155) SEQ ID NO: 137 and 277; 156) SEQ ID NO: 137 and 279; 157) SEQ ID NO: 137 and 282; 158) SEQ ID NO: 137 and 286; 159) SEQ ID NO: 137 and 290; 160) SEQ ID NO: 141 and 115; 161) SEQ ID NO: 141 and 121; 162) SEQ ID NO: 141 and 157; 162) SEQ ID NO: 141 and 272; 162) SEQ ID NO: 141 and 277; 163) SEQ ID NO: 141 and 279; 164) SEQ ID NO: 141 and 282; 165) SEQ ID NO: 141 and 286; 166) SEQ ID NO: 141 and 290; 167) SEQ ID NO: 145 and 115; 168) SEQ ID NO: 145 and 121; 169) SEQ ID NO: 145 and 157; 170) SEQ ID NO: 145 and 272; 171) SEQ ID NO: 145 and 277; 172) SEQ ID NO: 145 and 279; 173) SEQ ID NO: 145 and 282; 174) SEQ ID NO: 145 and 282; 175) SEQ ID NO: 145 and 286; 176) SEQ ID NO: 177) SEQ ID NO: 149 and 115; 178) SEQ ID NO: 149 and 121; 179) SEQ ID NO: 149 and 157; 180) SEQ ID NO: 149 and 272; 181) SEQ ID NO: 149 and 277; 182) SEQ ID NO: 149 and 279; and 183) SEQ ID NO: 149 and 282; 184) SEQ ID NO: 149 and 286; 185) SEQ ID NO: 149 and 290; 186) SEQ ID NO: 153 and 115; 187) SEQ ID NO: 153 and 121; 188) SEQ ID NO: 153 and 157; 189) SEQ ID NO: 153 and 272; 190) SEQ ID 194) SEQ ID NO: 153 and 290; 195) SEQ ID NO: 264 and 115; 196) SEQ ID NO: 264 and 121; 197) SEQ ID NO: 264 and 157; 198) SEQ ID NO: 264 and 272; 199) SEQ ID NO: 264 and 277; 200) SEQ ID NO: 264 and 279; 201) SEQ ID NO: 264 and 282; 202) SEQ ID NO: 264 and 286; 203) SEQ ID NO: 264 and 290; 204) SEQ 205) SEQ ID NO: 266 and 121; 206) SEQ ID NO: 266 and 157; 207) SEQ ID NO: 266 and 272; 208) SEQ ID NO: 266 and 277; 209) SEQ ID NO: 266 and 279; 210) SEQ ID NO: 266 and 282; 211) SEQ ID NO: 266 and 286; 212) SEQ ID NO: 266 and 290; 213) SEQ ID NO: 269 and 115; 214) SEQ ID NO: 269 and 121; 215) SEQ ID NO: 269 and 157; 216) SEQ ID NO: 269 and 157; 217) SEQ ID NO: 269 and 272; 218) SEQ ID NOs: 269 and 277; 219) SEQ ID NOs: 269 and 279; 219) SEQ ID NOs: 269 and 282; 220) SEQ ID NOs: 269 and 286; or 221) SEQ ID NOs: 269 and 290, or (II) any other combination of the same antibody types as described in Tables 2 and 3. Specific embodiment 10. The antibody or antigen-binding fragment of any one of embodiments 1 to 9, wherein the VH and the VL respectively comprise or consist of the amino acid sequences described below: 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NO: 179 and 193; 15) SEQ ID NO: 181 and 87; 16) SEQ ID NO: 181 and 193; 17) SEQ ID NO: 183 and 87; 18) SEQ ID NO: 183 and 193; 18) SEQ ID NO: 185 and 87; 19) SEQ ID NO: 185 and 193; 20) SEQ ID NO: 188 and 87; 21) SEQ ID NO: 188 and 193; 22) SEQ ID NO: 190 and 87; 23) SEQ ID NO: 190 and 193; 24) SEQ ID NO: 93 and 97; 25) SEQ ID NO: 93 and 225; 26) SEQ ID NO: 93 and 228; 27) SEQ ID NO: 93 and 231; 28) SEQ ID NO: 41) SEQ ID NO: 207 and 225; 42) SEQ ID NO: 207 and 228; 43) SEQ ID NO: 54) SEQ ID NO: 214 and 228; 55) SEQ ID NO: 214 and 231; 56) SEQ ID NO: 216 and 97; 57) SEQ ID NO: 216 and 225; 58) SEQ ID NO: 69) SEQ ID NO: 222 and 225; 70) SEQ ID NO: 222 and 228; 71) SEQ ID NO: 222 and 231; 72) SEQ ID NO: 102 and 105; 73) SEQ ID NO: 106 and 107; 74) SEQ ID NO: 108 and 109; 75) SEQ ID NO: 112 and 113; 76) SEQ ID NO: 114 and 115; 77) SEQ ID NO: 115 and 116; 78) SEQ ID NO: 116 and 228; 79) SEQ ID NO: 216 and 231; 80) SEQ ID NO: 218 and 97; 81) SEQ ID NO: 218 and 225; 82) SEQ ID NO: 218 and 228; 83) SEQ ID NO: 218 and 231; 84) SEQ ID NO: 220 and 97; 85) SEQ ID NO: 220 and 225; 86) SEQ ID NO: 220 and 228; 87) SEQ ID NO: 220 and 231; 88) SEQ ID NO: 222 and 97; 7) SEQ ID NO: 235 and 260; 80) SEQ ID NO: 238 and 105; 81) SEQ ID NO: 238 and 254; 82) SEQ ID NO: 238 and 257; 83) SEQ ID NO: 238 and 260; 84) SEQ ID NO: 241 and 105; 85) SEQ ID NO: 241 and 254; 86) SEQ ID NO: 241 and 257; 87) SEQ ID NO: 97) SEQ ID NO: 247 and 254; 98) SEQ ID NO: 247 and 257; 99) SEQ ID NO: 247 and 260; 100) SEQ ID NO: 249 and 105; 101) SEQ ID NO: 10) SEQ ID NO: 111 and 121; 110) SEQ ID NO: 111 and 157; 111) SEQ ID NO: 111 and 272; 112) SEQ ID NO: 111 and 277; 113) SEQ ID NO: 111 and 279; 114) SEQ ID NO: 111 and 282; 115) SEQ ID NO: 111 and 282; 125) SEQ ID NO: 125 and 290; 126) SEQ ID NO: 128 and 115; 127) SEQ ID NO: 128 and 121; 128) SEQ ID NO: 128 and 157; 129) SEQ ID NO: 129 and 272; 130) SEQ ID NO: 129 and 277; 131) SEQ ID NO: 129 and 279; 132) SEQ ID NO: 129 and 282; 133) SEQ ID NO: 129 and 286; 134) SEQ ID NO: 129 and 290; 135) SEQ ID NO: 128 and 115; 136) SEQ ID NO: 128 and 121; 137) SEQ ID NO: 128 and 157; 138) SEQ ID NO: 128 and 157; 139) SEQ ID NO: 129 and 272; 140) SEQ ID NO: 129 and 277; 141) SEQ ID NO: 129 and 279; 142) SEQ ID NO: 129 and 282; 143) SEQ ID NO: 129 and 286; 144) SEQ ID NO: 129 and 290; 145) SEQ ID NO: 129 and 291; 146) SEQ ID NO: 12 136) SEQ ID NO: 131 and 272; 137) SEQ ID NO: 131 and 277; 138) SEQ ID NO: 131 and 279; 139) SEQ ID NO: 131 and 282; 140) SEQ ID NO: 131 and 286; 141) SEQ ID NO: 131 and 290; 142) SEQ ID NO: 134 and 115; 143) SEQ ID NO: 134 and 121; 144) SEQ ID NO: 134 and 157; 145) SEQ ID NO: 134 and 272; 146) SEQ ID NO: 134 and 277; 147) SEQ ID NO: 134 and 279; 148) SEQ ID NO: 134 and 282; 149) SEQ ID NO: 134 and 286; 150) SEQ ID NO: 134 and 290; 151) SEQ ID NO: 137 and 115; 152) SEQ ID NO: 137 and 121; 153) SEQ ID NO: 137 and 157; 154) SEQ ID NO: 137 and 272; 155) SEQ ID NO: 156) SEQ ID NO: 137 and 279; 157) SEQ ID NO: 137 and 282; 158) SEQ ID NO: 137 and 286; 159) SEQ ID NO: 137 and 290; 160) SEQ ID NO: 141 and 115; 161) SEQ ID NO: 141 and 121; 162) SEQ ID NO: 141 and 157; 162) SEQ ID NO: 141 and 272; 162) SEQ ID NO: 141 and 277; 163) SEQ ID NO: 141 and 279; 164) SEQ ID NO: 141 and 282; 165) SEQ ID NO: 141 and 286; 166) SEQ ID NO: 141 290; 167) SEQ ID NO: 141 176) SEQ ID NO: 145 and 290; 177) SEQ ID NO: 149 and 115; 178) SEQ ID NO: 149 and 121; 179) SEQ ID NO: 149 and 157; 170) SEQ ID NO: 149 and 272; 171) SEQ ID NO: 149 and 277; 172) SEQ ID NO: 149 and 279; 173) SEQ ID NO: 149 and 282; 174) SEQ ID NO: 149 and 282; 175) SEQ ID NO: 149 and 286; 176) SEQ ID NO: 149 and 290; 177) SEQ ID NO: 149 and 115; 178) SEQ ID NO: 149 and 121; 179) SEQ ID NO: 149 and 157; 180) SEQ ID NO: 149 and 272; 181) SEQ ID NO: 149 and 277; 190) SEQ ID NO: 153 and 277; 191) SEQ ID NO: 153 and 279; 192) SEQ ID NO: 153 and 282; 193) SEQ ID NO: 153 and 286; 194) SEQ ID NO: 153 and 290; 195) SEQ ID NO: 153 and 115; 187) SEQ ID NO: 153 and 121; 188) SEQ ID NO: 153 and 157; 189) SEQ ID NO: 153 and 272; 190) SEQ ID NO: 153 and 277; 191) SEQ ID NO: 153 and 279; 192) SEQ ID NO: 153 and 282; 193) SEQ ID NO: 153 and 286; 194) SEQ ID NO: 153 and 290; 195) SEQ ID NO: 264 and 115; 196) SEQ ID NO: 264 and 121; 197) SEQ ID NO: 264 and 157; 198) SEQ ID NO: 264 and 272; 199) SEQ ID NO: 264 and 277; 200) SEQ ID NO: 264 and 279; 201) SEQ ID NO: 264 and 282; 202) SEQ ID NO: 264 and 286; 203) SEQ ID NO: 264 and 290; 204) SEQ ID NO: 266 and 115; 205) SEQ ID NO: 266 and 121; 206) SEQ ID NO: 266 and 157; 207) SEQ ID NO: 266 and 272; 208) SEQ ID NO: 269 and 272; 218) SEQ ID NO: 269 and 277; 219) SEQ ID NO: 269 and 279; 220) SEQ ID NO: 269 and 282; 221) SEQ ID NO: 269 and 286; 222) SEQ ID NO: 269 and 290; 223) SEQ ID NO: 269 and 115; 224) SEQ ID NO: 269 and 121; 225) SEQ ID NO: 269 and 157; 226) SEQ ID NO: 269 and 157; 227) SEQ ID NO: 269 and 272; 228) SEQ ID NO: 269 and 277; 229) SEQ ID NO: 269 and 279; 230) SEQ ID NO: 269 and 282; 231) SEQ ID NO: 269 and 286; or 232) SEQ ID NO: 269 and 286 NO: 269 and 290. Specific embodiment 11. The antibody or antigen-binding fragment of any one of embodiments 1 to 10, wherein: i) the VH and the VL comprise or consist of an amino acid sequence having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with the amino acid sequence depicted in SEQ ID NO: 111 and 157, respectively, or comprise or consist of the amino acids depicted in SEQ ID NO: 111 and 157, respectively. ii) the VH and the VL comprise the amino acid sequences described in SEQ ID NOs: 111 and 157, respectively, or consist of the amino acids described in SEQ ID NOs: 111 and 157; iii) the VH of i) or ii) comprises CDRH1, CDRH2, and CDRH3, and the VL of i) or ii) comprises CDRL1, CDRL2, and CDRL3, which have amino acid sequences determined by any VH and VL numbering scheme; iii) the VH comprises CDRH1, CDRH2, and CDRH3, and the VL comprises CDRL1, CDRL2, and CDRL3, which have amino acid sequences as described in SEQ ID NOs: 112 to 114, 116, 117, and 158, respectively; iv) the antibody or antigen-binding fragment comprises any one of i) to iv) and a polypeptide having a polypeptide as described in SEQ ID NO: 44 to 80 and a light chain constant region having a sequence such as SEQ ID NO: 292; v) the antibody or antigen-binding fragment comprises a heavy chain having a sequence such as SEQ ID NO: 293 and a light chain having a sequence such as SEQ ID NO: 294; or vi) the antibody or antigen-binding fragment comprises a heavy chain having a sequence such as SEQ ID NO: 295 and a light chain having a sequence such as SEQ ID NO: 296. Embodiment 12. The antibody or antigen-binding fragment of any one of Embodiments 1 to 11, wherein: (i) recognizes epitopes in the spike proteins of two or more, three or more, four or more, or five or more severe acute respiratory syndrome beta coronaviruses; (ii) is capable of blocking the interaction between the spike proteins of two or more, three or more, four or more, or five or more severe acute respiratory syndrome beta coronaviruses and one or more cell surface receptors corresponding thereto, wherein, as required, The cell surface receptor comprises human ACE2; (iii) recognizes an epitope retained in the spike protein of two or more, three or more, four or more, or five or more severe acute respiratory syndrome beta coronaviruses; (iv) is cross-reactive against two or more, three or more, four or more, or five or more severe acute respiratory syndrome beta coronaviruses, optionally including one or more clade 1b severe acute respiratory syndrome beta coronaviruses; or (v) any combination of (i) to (iv). Specific embodiment 13. The antibody or antigen-binding fragment of any one of embodiments 1 to 12, which is of IgG, IgA, IgM, IgE, or IgD isotype. Embodiment 14. The antibody or antigen-binding fragment of Embodiment 13, which is selected from the IgG isotype of IgG1, IgG2, IgG3, and IgG4, and preferably is the IgG1 isotype. Embodiment 15. The antibody or antigen-binding fragment of any one of Embodiments 1 to 14, which is human, humanized, or chimeric. Embodiment 16. The antibody or antigen-binding fragment of any one of Embodiments 1 to 15, wherein the antibody or the antigen-binding fragment comprises a human antibody, a monoclonal antibody, a purified antibody, a single-chain antibody, Fab, Fab', F(ab')2, Fv, scFv, or scFab. Embodiment 17. The antibody or antigen-binding fragment of Embodiment 16, wherein the scFv comprises more than one VH domain and more than one VL domain. Embodiment 18. The antibody or antigen-binding fragment of any one of Embodiments 1 to 17, wherein the antibody or antigen-binding fragment is a multispecific antibody or antigen-binding fragment. Embodiment 19. The antibody or antigen-binding fragment of Embodiment 18, wherein the antibody or antigen-binding fragment is a bispecific antibody or antigen-binding fragment. Embodiment 20. The antibody or antigen-binding fragment of embodiment 19, comprising: a first VH and a first VL; and a second VH and a second VL, wherein the first VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with the amino acid sequence described in SEQ ID NO: 23 and 27, respectively; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with the amino acid sequence described in SEQ ID NO: The amino acid sequence of NO. has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 83, 179, 181, 183, 185, 188, or 190 and any one of 87 or 193; iv) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and any one of 97, 225, 228, or 231; v) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of 105, 254, 257, or 260; or vi) with the following SEQ ID NO. The amino acid sequence described has at least 85% (i.e. 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with an amino acid sequence: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of 115, 121, 157, 272, 277, 279, 282, 286, or 290; and wherein the second VH and VL comprise i) respectively with SEQ ID NO: 23 and 27 have at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequences described in the following SEQ ID NOs.; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequences described in the following SEQ ID NOs.: 31, 35, 36, or 43, respectively, and 37; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequences described in the following SEQ ID NOs. NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 83, 179, 181, 183, 185, 188, or 190 and any one of 87 or 193; iv) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and any one of 97, 225, 228, or 231; v) with the following SEQ ID NO. The amino acid sequence has at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity with any one of 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of 105, 254, 257, or 260; or vi) with the following SEQ ID NO. has an amino acid sequence with at least 85% (i.e. 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity: any one of 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively; wherein the first VH and the second VL are different from the second VH and VL, and wherein the first VH and the first VL together form a first antigen-binding site, and wherein the second VH and the second VL together form a second antigen-binding site. Embodiment 21. The antibody or antigen-binding fragment of any one of Embodiments 1 to 20, wherein the antibody or antigen-binding fragment comprises an Fc polypeptide or a fragment thereof. Embodiment 22. The antibody or antigen-binding fragment of embodiment 21, wherein the Fc polypeptide or fragment thereof comprises: (i) a mutation that enhances binding to FcRn, as compared to a reference Fc polypeptide not comprising the mutation; (ii) a mutation that enhances binding to FcγR, as compared to a reference Fc polypeptide not comprising the mutation; (iii) a mutation that enhances binding to human FcγRIIa and/or reduces binding to human FcγRIIb, as compared to a reference Fc polypeptide not comprising the mutation; and/or (iv) a mutation that enhances binding to human C1q, as compared to a reference Fc polypeptide not comprising the mutation. Embodiment 23. The antibody or antigen-binding fragment of embodiment 22, wherein the Fc polypeptide comprises the substitution mutations M428L/N434S, M428L/N434A, G236A/A330L/I332E/M428L/N434S, or G236A/A330L/I332E/M428L/N434A, wherein, optionally, the antibody or antigen-binding fragment is of IgG1 isotype and comprises or consists of an Fc polypeptide or a fragment thereof, the Fc polypeptide or a fragment thereof comprising or consisting of: 44 to 80 having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity, optionally other than naturally occurring variants thereof; or the Fc polypeptide or fragment thereof comprises or consists of the amino acid sequence set forth in SEQ ID NOs: 52 to 80. Specific embodiment 24. An isolated polynucleotide encoding the antibody or antigen-binding fragment of any one of Specific embodiments 1 to 23. Specific embodiment 25. The polynucleotide of Specific embodiment 24, wherein the polynucleotide comprises or consists of: and SEQ ID NO: 81, 82, 91, 92, 100, 101, 109, 110, 119, 120, 123, 127, 130, 133, 136, 140, 144, 148, 152, 156, 159, 180, 182, 184, 187, 189, 191, 192, 195, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 224, 227, 230, 233 , 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, 261, 262, 263, 265, 268, 271, 276, 278, 281, 285, or 289. A nucleic acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence of one or more of Specific Embodiment 24 or Specific Embodiment 25. Specific Embodiment 26. A polynucleotide as in Specific Embodiment 24 or Specific Embodiment 25, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises a messaging RNA (mRNA). Embodiment 27. The polynucleotide of any one of Embodiments 24 to 26, which is codon-optimized for expression in a host cell. Embodiment 28. A recombinant vector comprising the polynucleotide of any one of Embodiments 24 to 27. Embodiment 29. A host cell comprising the polynucleotide of any one of Embodiments 24 to 27 and/or the vector of Embodiment 28, wherein the polynucleotide is heterologous to the host cell. Embodiment 30. A human B cell comprising the polynucleotide of any one of Embodiments 24 to 27 and/or the vector of Embodiment 28, wherein the polynucleotide is heterologous to the human B cell and/or wherein the human B cell is immortalized. Embodiment 31. A composition comprising: (i) an antibody or antigen-binding fragment as described in any one of Embodiments 1 to 23; (ii) a polynucleotide as described in any one of Embodiments 24 to 27; (iii) a recombinant vector as described in Embodiment 28; (iv) a host cell as described in Embodiment 29; and/or (v) a human B cell as described in Embodiment 30, and a pharmaceutically acceptable excipient, carrier, or diluent. Embodiment 32. The composition of embodiment 31, comprising two or more antibodies or antigen-binding fragments, wherein the first antibody or antigen-binding fragment and the second antibody or antigen-binding fragment respectively comprise, or the multispecific antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3, and optionally VH and VL, which are according to: (i) any S3A (ii) any S3A3 antibody and sotorovimab; (iii) any S3A3 antibody and S2K146; (iv) any S3A3 antibody and S2X259; (v) any S3A3 antibody and any S2X324 antibody; (vi) any S3A3 antibody and S309; (vii) any S3A19 antibody and sotorovimab; vii) any S3A19 antibody and S2K146; (viii) any S3A19 antibody and S2X259; (ix) any S3A19 antibody and any S2X324 antibody; (x) any S3A19 antibody and S309; (xi) any S3I2 antibody and any S3A3 antibody; (xii) any S3I2 antibody and any S3A19 antibody; (xiii) any S3I2 antibody and Sotovemab; (xiv) any S3I2 antibody and S2K146; (xv) any S3I2 antibody and S2X259; (xvi) any S3I2 antibody and any S2X324 antibody; (xvii) any S3I2 antibody and S309; (xviii) any S3I2 antibody and any S3O13 antibody; (xix) any S3I2 antibody and any S3L17 antibody; (xx) any S (xxi) any S3O13 antibody and any S3A3 antibody; (xxii) any S3O13 antibody and sotoviromab; (xxiii) any S3O13 antibody and S2K146; (xxiv) any S3O13 antibody and S2X259; (xxv) any S3O13 antibody and any S2X324 antibody; (xxvi) any S3O1 3 antibody and S309; (xxvii) any S3O13 antibody and any S3L17 antibody; (xxviii) any S3L17 antibody and any S3A3 antibody; (xxix) any S3L17 antibody and any S3A19 antibody; (xxx) any S3L17 antibody and sotoviromab; (xxxi) any S3L17 antibody and S2K146; (xxxii) any S3L17 antibody and S2X259; (xxxiii) any S3L17 antibody and any S2X324 antibody; (xxxiv) any S3L17 antibody and S309; (xxxv) any S2V29 antibody and any S3A3 antibody; (xxxvi) any S2V29 antibody and any S3A19 antibody; (xxxvii) any S2V29 antibody and sotoviromab; (xxxviii) any S 2V29 antibody and S2K146; (xxxix) any S2V29 antibody and S2X259; (xl) any S2V29 antibody and any S2X324 antibody; (xli) any S2V29 antibody and S309; (lxlii) any S2V29 antibody and any S3L17 antibody; and (xliii) any S2V29 antibody and any S3O13 antibody, or any antigen-binding fragment thereof. Specific embodiment 33. The composition of specific embodiment 31, wherein the first antibody or antigen-binding fragment comprises S3L17 antibody or antigen-binding fragment and the second antibody or antigen-binding fragment comprises S2V29 antibody. Embodiment 34. A composition as in embodiment 33, wherein the first antibody or antigen-binding fragment comprises the following CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences: such as SEQ ID NO: 103, 85, and, 104; 103, 85, and 236; or 103, 85, and 239, and 106 to 108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258, and the second antibody or antigen-binding fragment comprises the following CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences: such as SEQ ID NO: 112 to 114; 112, 126, and 114; 112, 129 and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112, 267, and 114; 112, 270, and 114; 112, 113, and 139; 112, 126, and 139; 112, 129 and 139; 112, 132, and 139; 112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112, 150, and 139; 112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112, 126, and 143; 112, 129, and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129, and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 1 47; 112, 154, and 147; 112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112, 129, and 151; 112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and 151; 112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 15 1; 112, 113, and 155; 112, 126, and 155; 112, 129, and 155; 112, 132, and 155; 112, 135, and 155; 112, 138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270, and 155; and 116 to 118; 116, 274, and 118; 116, 287, and 118; 1 16, 117, and 122; 116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116, 287, and 275; 116, 117, and 280; 116, 274, and 280; 116, 287, and 280; 116, 117, and 284; 116, 274, and 284; 116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 16, 117, and 291; 116, 274, and 291; 116, 287, and 291; 273, 117, and 118; 273, 274, and 118; 273, 287, and 118; 273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and 275; 273, 287, and 275; 273, 117, and 280; 273, 274, and 280; 1273, 287, and 280; 273, 117, and 284; 273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273, 287, and 288; 273, 117, and 291; 273, 274, and 291; 273, 287, and 291; 283, 117, 118; 283, 274, and 118; 283, 287, and 118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 2 83, 117, and 158; 283, 274, and 275; 283, 287, and 275; 283, 117, and 280; 283, 274, and 280; 283, 287, and 280; 283, 117, and 284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288; 283, 287, and 288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291. Specific Example 35. The composition of embodiment 33, wherein the first antibody or antigen-binding fragment comprises a heavy chain variable domain (VH) and a light chain variable domain (VL), the heavy chain variable domain comprises CDRH1, CDRH2, and CDRH3, the light chain variable domain comprises CDRL1, CDRL2, and CDRL3, wherein: (i) the CDRH1 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 103 or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of the substitutions being optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) the CDRH2 comprises or consists of the following: an amino acid sequence such as SEQ ID NO: 85, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) the CDRH3 comprises or consists of the following: an amino acid sequence as any one of SEQ ID NO: 104, 236, or 239, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of the following: an amino acid sequence as any one of SEQ ID NO: 106 or 255, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence such as SEQ ID NO: 107, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) the CDRL3 comprises or consists of an amino acid sequence such as SEQ ID NO: 108 or 258, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of the substitutions being optionally retention substitutions and/or substitutions of germline-encoded amino acids, and wherein the second antibody or antigen-binding fragment comprises a heavy chain variable domain (VH) and a light chain variable domain (VL), the heavy chain variable domain comprising CDRH1, CDRH2, and CDRH3, the light chain variable domain comprising CDRL1, CDRL2, and CDRL3, wherein: (i) the CDRH1 comprises or consists of: as shown in SEQ ID NO: 112, or a sequence variant thereof, said sequence variant comprising one, two, or three amino acid substitutions, one or more of said substitutions being optionally retention substitutions and/or substitutions of germline-encoded amino acids; (ii) said CDRH2 comprising or consisting of an amino acid sequence as in any one of SEQ ID NOs: 113, 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270, or a sequence variant thereof, said sequence variant comprising one, two, or three amino acid substitutions, one or more of said substitutions being optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iii) said CDRH3 comprising or consisting of an amino acid sequence as in any one of SEQ ID NOs: 114, 139, 143, 147, 151, or 155, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (iv) the CDRL1 comprises or consists of an amino acid sequence as any one of SEQ ID NO: 116, 273, or 283, or a sequence variant thereof, the sequence variant comprising one, two, or three amino acid substitutions, one or more of which are optionally retention substitutions and/or substitutions of germline-encoded amino acids; (v) the CDRL2 comprises or consists of an amino acid sequence as any one of SEQ ID NO: or (vi) the CDRL3 comprises or consists of an amino acid sequence of any one of SEQ ID NOs: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof, said sequence variant comprising one, two, or three amino acid substitutions, one or more of said substitutions being optionally retaining substitutions and/or substitutions of germline-encoded amino acids; and/or (vi) said CDRL3 comprises or consists of an amino acid sequence of any one of SEQ ID NOs: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof, said sequence variant comprising one, two, or three amino acid substitutions, one or more of said substitutions being optionally retaining substitutions and/or substitutions of germline-encoded amino acids. Embodiment 36. The composition of embodiment 33, wherein the first antibody or antigen-binding fragment comprises a VH sequence as described in any one of SEQ ID NOs: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence as described in any one of SEQ ID NOs: 105, 254, 257, or 260, and wherein the second antibody or antigen-binding fragment comprises a VH sequence as described in any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence as described in any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290. Embodiment 37. A composition comprising a polynucleotide as in any one of embodiments 24 to 27 encapsulated in a carrier molecule, wherein the carrier molecule optionally comprises a lipid, a lipid-derived delivery vehicle, such as a liposome, a solid lipid nanoparticle, an oily suspension, a submicron lipid emulsion, a lipid microbubble, a reverse lipid micelle, an otic liposome, a lipid microtubule, a lipid microcolumn, a lipid nanoparticle (LNP), or a nanoscale platform. Embodiment 38. A method for treating severe acute respiratory syndrome beta coronavirus infection (e.g., infection caused by SARS-CoV-2) in a subject, the method comprising administering to the subject an effective amount of (i) an antibody or antigen-binding fragment as described in any one of Embodiments 1 to 23; (ii) a polynucleotide as described in any one of Embodiments 24 to 27; (iii) a recombinant vector as described in Embodiment 28; (iv) a host cell as described in Embodiment 29; and/or (v) a human B cell as described in Embodiment 30, and/or (vi) a composition as described in any one of Embodiments 31 to 37. Embodiment 39. An antibody or antigen-binding fragment of any one of Embodiments 1 to 23, a polynucleotide of any one of Embodiments 24 to 27, a recombinant vector of Embodiment 28, a host cell of Embodiment 29, a human B cell of Embodiment 30, and/or a composition of any one of Embodiments 31 to 37, for use in a method of treating severe acute respiratory syndrome beta coronavirus infection (e.g., infection caused by SARS-CoV-2) in an individual. Embodiment 40. An antibody or antigen-binding fragment of any one of Embodiments 1 to 23, a polynucleotide of any one of Embodiments 24 to 27, a recombinant vector of Embodiment 28, a host cell of Embodiment 29, a human B cell of Embodiment 30, and/or a composition of any one of Embodiments 31 to 37 for the preparation of a medicament for treating a severe acute respiratory syndrome beta coronavirus infection (e.g., an infection caused by SARS-CoV-2) in a subject. Embodiment 41. An antibody or antigen-binding fragment of any one of Embodiments 1 to 23 or 39 to 40, wherein the antibody or antigen-binding fragment binds to two or more severe acute respiratory syndrome beta coronavirus S proteins as measured using bio-thin layer interferometry. Embodiment 42. A kit comprising a liquid composition and instructions for use thereof in treating SARS-CoV-2 infection in an individual, wherein the liquid composition comprises the antibody or antigen-binding fragment of any one of Embodiments 1 to 23 or 39 to 40. Embodiment 43. The kit of Embodiment 42, wherein the instructions for use are for the method of Embodiment 38 or the use of any one of Embodiments 39 to 40. Embodiment 44. A method for in vitro diagnosis of severe acute respiratory syndrome beta coronavirus infection (e.g., infection caused by SARS-CoV-2), the method comprising: (i) contacting a sample from an individual with an antibody or antigen-binding fragment as described in any one of Embodiments 1 to 23; and (ii) detecting a complex comprising an antigen and the antibody, or comprising an antigen and the antigen-binding fragment. Embodiment 45. A method for producing an antibody or antigen-binding fragment as described in any one of Embodiments 1 to 23 or Embodiments 39 to 40, wherein the method comprises culturing a host cell expressing the antibody or antigen-binding fragment under conditions and for a time sufficient to produce the antibody or antigen-binding fragment. Embodiment 46. The method for producing an antibody or an antigen-binding fragment of Embodiment 45, wherein the host cell comprises the recombinant vector of Embodiment 28. Embodiment 47. The method for producing an antibody or an antigen-binding fragment of Embodiment 46, wherein the host cell is a mammalian cell. *Table 2 indicates CDRH1, CDRH2 and CDRH3d (IMGT definition) in bold in order in each corresponding VH sequence; and indicates CDRL1, CDRL2, CDRL3 in order in bold in each corresponding VL sequence.