Expert review of gastroenterology & hepatology, 2017
We investigated the real-world effectiveness of interferon-free regimens for the treatment of pat... more We investigated the real-world effectiveness of interferon-free regimens for the treatment of patients with compensated cirrhosis infected with hepatitis C virus (HCV). Using the Irish national HCV treatment registry, the effectiveness and safety of interferon-free regimens for HCV-infected patients treated between April 2015 and August 2016, was determined. A SVR12 was achieved in 86% of subjects treated with sofosbuvir/ledipasvir ± ribavirin (SOF/LDV±RBV), 93% treated with paritaprevir, ombitasvir and ritonavir combined with dasabuvir ± ribavirin (3D±RBV) and 89% treated with sofosbuvir/daclatasvir ± ribavirin (SOF/DCV±RBV). The discontinuation rate was 5% and the on-treatment mortality rate was 1%. The availability of interferon-free regimens represents a significant breakthrough for the treatment of HCV infection. Treatments options, with high SVR12 rates, are now available for patients with compensated cirrhosis who were unsuitable for treatment with interferon-based regimens. ...
ObjectiveThis study investigated seroprevalence of SARS-CoV-2-specific IgG antibodies, using the ... more ObjectiveThis study investigated seroprevalence of SARS-CoV-2-specific IgG antibodies, using the Abbott antinucleocapsid IgG chemiluminescent microparticle immunoassay (CMIA) assay, in five prespecified healthcare worker (HCW) subgroups following the first wave of the COVID-19 pandemic.SettingAn 800-bed tertiary-level teaching hospital in the south of Ireland.ParticipantsSerum was collected for anti-SARS-CoV-2 nucleocapsid IgG using the Abbott ARCHITECT SARS-CoV-2 IgG CMIA qualitative assay, as per the manufacturer’s specifications.The groups were as follows: (1) HCWs who had real-time PCR (RT-PCR) confirmed COVID-19 infection (>1-month postpositive RT-PCR); (2) HCWs identified as close contacts of persons with COVID-19 infection and who subsequently developed symptoms (virus not detected by RT-PCR on oropharyngeal/nasopharyngeal swab); (3) HCWs identified as close contacts of COVID-19 cases and who remained asymptomatic (not screened by RT-PCR); (4) HCWs not included in the afor...
<p>All trees have been rooted using the nearest detectable ancestor to the insertion event,... more <p>All trees have been rooted using the nearest detectable ancestor to the insertion event, GQ985348 [red square, 17]. The sample specific isolation of each sequence is defined by the color legend. (A) The L1b sequence subset was split into two groups, A (black squares) and B (open squares), which were defined by the constituent HVR1 amino acid motifs. (B) Colored nodes identify those sequences coding for HVR1 motifs that have previously been associated with IgG-bound virions [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167089#pone.0167089.ref007" target="_blank">7</a>]. A single IgG-associated motif from group A was isolated from sample 1 (red circle). An additional IgG-associated motif for group B was isolated from sample 6 (grey circle), four years after the motif was first detected in whole patient serum. A phylogenetically diverse branch of L1b group A sequences not subject to detectable IgG binding is indicated by red branches. (C) Group A sequences not subject to IgG-targeting exhibited the greatest sequence diversity. Nevertheless, this subpopulation collapsed post-sample 5. The genetic distance is shown as a bracketed scale bar. Bootstrap values >80 of 1000 resamplings are shown. Genetic distance is given by the scale bar.</p
<p><b>A.</b> The multiple sequence alignment (MSA) of the E2 glycoprotein. HCVp... more <p><b>A.</b> The multiple sequence alignment (MSA) of the E2 glycoprotein. HCVpp1b-1-3 is a reference sequence; HCVpp1b-1-1, HCVpp1a-1-3 and HCVppH77 were the infectious pseudoparticles. AF011751 is an H77 strain. aa marked with *: targeted by patient derived VF-Fabs. The colour code of the epitopes represent the position of the epitope in 3D structure of E2 glycoprotein (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t004" target="_blank">Table 4</a>); aa in dotted box: linear epitope targeted by AP33 mouse MAb [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.ref035" target="_blank">35</a>]; aa in red box: residues on E2 interact with AR3C HuMAb [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.ref013" target="_blank">13</a>]; aa marked with ‡: residues important for CD81 binding [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.ref013" target="_blank">13</a>]. <b>B.</b> The 3D model of HCV-E1E2 glycoprotein shown in white cartoon with flexible non-modelled E2 N-termini (384–412) labelled with spheres. Sequence <sub>428</sub>NCNDSLNTGFLAALFYTHRF<sub>447</sub> is highlighted in yellow, <sub>539</sub>LLNNTRPPRGNWF<sub>550</sub> in red and <sub>599</sub>SGPWLTPRCM<sub>608</sub> in blue (Pepscan Presto; Lelystad, Netherlands)</p
<p>VF-Fab were purified from antibody-virus complex. VF-Fab1a-1-1, VF-Fab1a-1-2, VF-Fab 1a-... more <p>VF-Fab were purified from antibody-virus complex. VF-Fab1a-1-1, VF-Fab1a-1-2, VF-Fab 1a-1-3 were purified from a patient infected with HCV genotype 1a. VF-Fab1b-1-2, VF-Fab1b-1-3 and VF-Fab1b-10-1 were purified from a patients infected with genotype 1b whose common source of infection was HCV infected anti D immunoglobulin [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.ref025" target="_blank">25</a>]. VF-Fab1b-5-1 were purified from a blood transfusion patient infected with genotype 1b. VF-Fab3a-1-1 was purified from a patient infected with HCV genotype 3a (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t001" target="_blank">Table 1</a>). HCVpp incorporating E1E2 derived from genotype 1a (HCVpp1a-1-3, HCVppH77), 1b (HCVpp1b-1-2 and HCVpp1b-1-3) were pre-incubated with different concentrations (0.006 to 0.4 mg/ml) of purified VF-Fabs prior to infection of Huh7 cells. No envelope control was used to normalise the data. The neutralising activity of the VF-Fab is expressed as percentage of inhibition of the infectious titres. VF-Fab1b-5-1 bottom values were constraint to zero for that data set only. Each experiment was repeated three times. IC<sub>50</sub> for each VF-Fab is detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t003" target="_blank">Table 3</a>. Error bars indicate standard deviation.</p
The humoral immune system responds to chronic hepatitis C virus (HCV) infection by producing neut... more The humoral immune system responds to chronic hepatitis C virus (HCV) infection by producing neutralising antibodies (nAb). In this study we generated three HCV pseudoparticles in which E1E2 glycoprotein sequence was targeted by the host humoral immune system. We used patient derived virus free Fabs (VF-Fabs) obtained from HCV genotype 1a (n = 3), genotype 1b (n = 7) and genotype 3a (n = 1) for neutralisation of HCVpp produced in this study both individually and in combination. Based on the available anti-HCV monoclonal nAb mapping information we selected amino acid region 384-619 for conformational epitope mapping. Amongst our notable findings, we observed significant reduction in HCVpp infectivity (p<0.05) when challenged with a combination of inter genotype and subtype VF-Fabs. We also identified five binding motifs targeted by patient derived VF-Fab upon peptide mapping, of which two shared the residues with previously reported epitopes. One epitope lies within an immunodomin...
<p>HCVpp1a-1-3, HCVpp1b-1-2, HCVpp1b-1-3 and control HCVppH77 were tested for neutralisatio... more <p>HCVpp1a-1-3, HCVpp1b-1-2, HCVpp1b-1-3 and control HCVppH77 were tested for neutralisation using the average Log IC<sub>50</sub> (mg/ml) for the VF-Fab in combinations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t005" target="_blank">Table 5</a>). The data is obtained from three independent experiments. Data for all the HCVpp were grouped together for statistical analysis. Significance was tested using one-way ANOVA with Dunnett t test (p<0.05–0.001, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t005" target="_blank">Table 5</a>). Each VF-Fab combination was compared against individual VF-Fab at the concentration used in combination experiments.</p
<p>Top panel: Co-evolving pairs are identified as nonsynonymous-nonsynonymous, synonymous-s... more <p>Top panel: Co-evolving pairs are identified as nonsynonymous-nonsynonymous, synonymous-synonymous or a combination of one site mutating nonsynonymously and one site mutating synonymously. Bottom panel: The combined odds of a mutation co-varying with a mutation at a second site are given by the colored scale bar. Co-varying pairs represented by grey bars have combined odds <0.6 which indicates that, for a given sequence set, one of the two sites has a greater observed mutational flexibility than that observed at the second site. Raw data counts, individual odds and combined odds are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167089#pone.0167089.s005" target="_blank">S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167089#pone.0167089.s006" target="_blank">S5</a> Tables for reference.</p
Expert review of gastroenterology & hepatology, 2017
We investigated the real-world effectiveness of interferon-free regimens for the treatment of pat... more We investigated the real-world effectiveness of interferon-free regimens for the treatment of patients with compensated cirrhosis infected with hepatitis C virus (HCV). Using the Irish national HCV treatment registry, the effectiveness and safety of interferon-free regimens for HCV-infected patients treated between April 2015 and August 2016, was determined. A SVR12 was achieved in 86% of subjects treated with sofosbuvir/ledipasvir ± ribavirin (SOF/LDV±RBV), 93% treated with paritaprevir, ombitasvir and ritonavir combined with dasabuvir ± ribavirin (3D±RBV) and 89% treated with sofosbuvir/daclatasvir ± ribavirin (SOF/DCV±RBV). The discontinuation rate was 5% and the on-treatment mortality rate was 1%. The availability of interferon-free regimens represents a significant breakthrough for the treatment of HCV infection. Treatments options, with high SVR12 rates, are now available for patients with compensated cirrhosis who were unsuitable for treatment with interferon-based regimens. ...
ObjectiveThis study investigated seroprevalence of SARS-CoV-2-specific IgG antibodies, using the ... more ObjectiveThis study investigated seroprevalence of SARS-CoV-2-specific IgG antibodies, using the Abbott antinucleocapsid IgG chemiluminescent microparticle immunoassay (CMIA) assay, in five prespecified healthcare worker (HCW) subgroups following the first wave of the COVID-19 pandemic.SettingAn 800-bed tertiary-level teaching hospital in the south of Ireland.ParticipantsSerum was collected for anti-SARS-CoV-2 nucleocapsid IgG using the Abbott ARCHITECT SARS-CoV-2 IgG CMIA qualitative assay, as per the manufacturer’s specifications.The groups were as follows: (1) HCWs who had real-time PCR (RT-PCR) confirmed COVID-19 infection (>1-month postpositive RT-PCR); (2) HCWs identified as close contacts of persons with COVID-19 infection and who subsequently developed symptoms (virus not detected by RT-PCR on oropharyngeal/nasopharyngeal swab); (3) HCWs identified as close contacts of COVID-19 cases and who remained asymptomatic (not screened by RT-PCR); (4) HCWs not included in the afor...
<p>All trees have been rooted using the nearest detectable ancestor to the insertion event,... more <p>All trees have been rooted using the nearest detectable ancestor to the insertion event, GQ985348 [red square, 17]. The sample specific isolation of each sequence is defined by the color legend. (A) The L1b sequence subset was split into two groups, A (black squares) and B (open squares), which were defined by the constituent HVR1 amino acid motifs. (B) Colored nodes identify those sequences coding for HVR1 motifs that have previously been associated with IgG-bound virions [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167089#pone.0167089.ref007" target="_blank">7</a>]. A single IgG-associated motif from group A was isolated from sample 1 (red circle). An additional IgG-associated motif for group B was isolated from sample 6 (grey circle), four years after the motif was first detected in whole patient serum. A phylogenetically diverse branch of L1b group A sequences not subject to detectable IgG binding is indicated by red branches. (C) Group A sequences not subject to IgG-targeting exhibited the greatest sequence diversity. Nevertheless, this subpopulation collapsed post-sample 5. The genetic distance is shown as a bracketed scale bar. Bootstrap values >80 of 1000 resamplings are shown. Genetic distance is given by the scale bar.</p
<p><b>A.</b> The multiple sequence alignment (MSA) of the E2 glycoprotein. HCVp... more <p><b>A.</b> The multiple sequence alignment (MSA) of the E2 glycoprotein. HCVpp1b-1-3 is a reference sequence; HCVpp1b-1-1, HCVpp1a-1-3 and HCVppH77 were the infectious pseudoparticles. AF011751 is an H77 strain. aa marked with *: targeted by patient derived VF-Fabs. The colour code of the epitopes represent the position of the epitope in 3D structure of E2 glycoprotein (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t004" target="_blank">Table 4</a>); aa in dotted box: linear epitope targeted by AP33 mouse MAb [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.ref035" target="_blank">35</a>]; aa in red box: residues on E2 interact with AR3C HuMAb [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.ref013" target="_blank">13</a>]; aa marked with ‡: residues important for CD81 binding [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.ref013" target="_blank">13</a>]. <b>B.</b> The 3D model of HCV-E1E2 glycoprotein shown in white cartoon with flexible non-modelled E2 N-termini (384–412) labelled with spheres. Sequence <sub>428</sub>NCNDSLNTGFLAALFYTHRF<sub>447</sub> is highlighted in yellow, <sub>539</sub>LLNNTRPPRGNWF<sub>550</sub> in red and <sub>599</sub>SGPWLTPRCM<sub>608</sub> in blue (Pepscan Presto; Lelystad, Netherlands)</p
<p>VF-Fab were purified from antibody-virus complex. VF-Fab1a-1-1, VF-Fab1a-1-2, VF-Fab 1a-... more <p>VF-Fab were purified from antibody-virus complex. VF-Fab1a-1-1, VF-Fab1a-1-2, VF-Fab 1a-1-3 were purified from a patient infected with HCV genotype 1a. VF-Fab1b-1-2, VF-Fab1b-1-3 and VF-Fab1b-10-1 were purified from a patients infected with genotype 1b whose common source of infection was HCV infected anti D immunoglobulin [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.ref025" target="_blank">25</a>]. VF-Fab1b-5-1 were purified from a blood transfusion patient infected with genotype 1b. VF-Fab3a-1-1 was purified from a patient infected with HCV genotype 3a (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t001" target="_blank">Table 1</a>). HCVpp incorporating E1E2 derived from genotype 1a (HCVpp1a-1-3, HCVppH77), 1b (HCVpp1b-1-2 and HCVpp1b-1-3) were pre-incubated with different concentrations (0.006 to 0.4 mg/ml) of purified VF-Fabs prior to infection of Huh7 cells. No envelope control was used to normalise the data. The neutralising activity of the VF-Fab is expressed as percentage of inhibition of the infectious titres. VF-Fab1b-5-1 bottom values were constraint to zero for that data set only. Each experiment was repeated three times. IC<sub>50</sub> for each VF-Fab is detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t003" target="_blank">Table 3</a>. Error bars indicate standard deviation.</p
The humoral immune system responds to chronic hepatitis C virus (HCV) infection by producing neut... more The humoral immune system responds to chronic hepatitis C virus (HCV) infection by producing neutralising antibodies (nAb). In this study we generated three HCV pseudoparticles in which E1E2 glycoprotein sequence was targeted by the host humoral immune system. We used patient derived virus free Fabs (VF-Fabs) obtained from HCV genotype 1a (n = 3), genotype 1b (n = 7) and genotype 3a (n = 1) for neutralisation of HCVpp produced in this study both individually and in combination. Based on the available anti-HCV monoclonal nAb mapping information we selected amino acid region 384-619 for conformational epitope mapping. Amongst our notable findings, we observed significant reduction in HCVpp infectivity (p<0.05) when challenged with a combination of inter genotype and subtype VF-Fabs. We also identified five binding motifs targeted by patient derived VF-Fab upon peptide mapping, of which two shared the residues with previously reported epitopes. One epitope lies within an immunodomin...
<p>HCVpp1a-1-3, HCVpp1b-1-2, HCVpp1b-1-3 and control HCVppH77 were tested for neutralisatio... more <p>HCVpp1a-1-3, HCVpp1b-1-2, HCVpp1b-1-3 and control HCVppH77 were tested for neutralisation using the average Log IC<sub>50</sub> (mg/ml) for the VF-Fab in combinations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t005" target="_blank">Table 5</a>). The data is obtained from three independent experiments. Data for all the HCVpp were grouped together for statistical analysis. Significance was tested using one-way ANOVA with Dunnett t test (p<0.05–0.001, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175349#pone.0175349.t005" target="_blank">Table 5</a>). Each VF-Fab combination was compared against individual VF-Fab at the concentration used in combination experiments.</p
<p>Top panel: Co-evolving pairs are identified as nonsynonymous-nonsynonymous, synonymous-s... more <p>Top panel: Co-evolving pairs are identified as nonsynonymous-nonsynonymous, synonymous-synonymous or a combination of one site mutating nonsynonymously and one site mutating synonymously. Bottom panel: The combined odds of a mutation co-varying with a mutation at a second site are given by the colored scale bar. Co-varying pairs represented by grey bars have combined odds <0.6 which indicates that, for a given sequence set, one of the two sites has a greater observed mutational flexibility than that observed at the second site. Raw data counts, individual odds and combined odds are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167089#pone.0167089.s005" target="_blank">S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167089#pone.0167089.s006" target="_blank">S5</a> Tables for reference.</p
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