A reverse transcription polymerase chain reaction (RT-PCR) procedure is described for the detecti... more A reverse transcription polymerase chain reaction (RT-PCR) procedure is described for the detection of marine caliciviruses including vesicular exanthema of swine virus (VESV), San Miguel sea lion virus (SMSV), bovine Tillamook virus (BCV Bos-1) and caliciviruses (CV) isolated from dolphin (Cetacean CV), gorilla (Primate CV) and rattlesnake (Reptile CV) using primers (1F and 1R) designed from the capsid-coding region of
The genome sequences of three duck hepatitis virus type 1 (DHV-1) strains were determined. Compar... more The genome sequences of three duck hepatitis virus type 1 (DHV-1) strains were determined. Comparative sequence analyses showed that they possessed a typical picornavirus genome organization apart from the unique possession of three in-tandem 2A genes. The 2A1 protein of DHV-1 is an aphthovirus-like 2A protein; the 2A2 protein is not related to any known picornavirus protein; the 2A3 protein is a human parechovirus-like 2A protein. Several other features were found to be unique to the DHV-1 genome when compared with other picornaviruses: (i) the 3' UTR of DHV-1 was composed of 314 nt, the largest among the picornaviruses; (ii) pair-wise amino acid sequence identities between polyprotein of DHV-1 and other picornaviruses are all less than 30%. The pair-wise amino acid sequence identities in the 3D region of DHV-1 with LV and HPeV-1 is only 38.6 and 36.6%, respectively, and less than 30% with all other picornaviruses; (iii) the DHV-1 capsid polypeptide VP0 is not proteolytically cleaved into VP4 and VP2; and (iv) phylogenetic and evolutionary analysis of DHV-1 reveals a new picornavirus clade. It is therefore proposed that DHV-1 should be assigned to a new genus in the Picornaviridae.
Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subjec... more Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as “coxsackieviruses”, “polioviruses” and “echoviruses”, which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series...
In recent years, foot-and-mouth disease virus (FMDV) serotype O, topotype Middle East-South Asia ... more In recent years, foot-and-mouth disease virus (FMDV) serotype O, topotype Middle East-South Asia (ME-SA), lineage Ind-2001d has spread from the Indian subcontinent to the Middle East, North Africa, and Southeast Asia. In the current report, we describe the first detection of this lineage in Vietnam in May, 2015 in Đắk Nông province. Three subsequent outbreaks caused by genetically related viruses occurred between May-October, 2015 after which the virus was not detected in clinical outbreaks for at least 15 subsequent months. The observed outbreaks affected (in chronological order): cattle in Đắk Nông province, pigs in Đắk Lắk province and Đắk Nông province, and cattle in Ninh Thuận province. The clinical syndromes associated with these outbreaks were consistent with typical FMD in the affected species. Overall attack rate on affected premises was 0.85 in pigs and 0.93 in cattle over the course of the outbreak. Amongst 378 pigs at risk on affected premises, 85 pigs died during the ou...
The deletion of residues 93-102 in non-structure protein 3A of foot-and-mouth disease virus (FMDV... more The deletion of residues 93-102 in non-structure protein 3A of foot-and-mouth disease virus (FMDV) is associated with the inability of FMDV to grow in bovine cells and attenuated virulence in cattle.Whereas, a previously reported FMDV strain O/HKN/21/70 harboring 93-102 deletion in 3A protein grew equally well in bovine and swine cells. This suggests that changes inFMDV genome sequence, in addition to 93-102 deletion in 3A, may also affectthe viral growth phenotype in bovine cellsduring infection and replication.However, it is nuclear that changes in which region (inside or outside of 3A region) influences FMDV growth phenotype in bovine cells.In this study, to determine the region in FMDV genomeaffecting viral growth phenotype in bovine cells, we constructed chimeric FMDVs, rvGZSB-HKN3A and rvHN-HKN3A, by introducing the 3A coding region of O/HKN/21/70 into the context of O/SEA/Mya-98 strain O/GZSB/2011 and O Cathay topotype strain O/HN/CHA/93, respectively, since O/GZSB/2011 conta...
The current measures to control foot-and-mouth disease (FMD) include vaccination, movement contro... more The current measures to control foot-and-mouth disease (FMD) include vaccination, movement control and slaughter of infected or susceptible animals. One of the difficulties in controlling FMD by vaccination arises due to the substantial diversity found among the seven serotypes of FMD virus (FMDV) and the strains within these serotypes. Therefore, vaccination using a single vaccine strain may not fully cross-protect against all strains within that serotype, and therefore selection of appropriate vaccines requires serological comparison of the field virus and potential vaccine viruses using relationship coefficients (r 1 values). Limitations of this approach are that antigenic relationships among field viruses are not addressed, as comparisons are only with potential vaccine virus. Furthermore, inherent variation among vaccine sera may impair reproducibility of one-way relationship scores. Here, we used antigenic cartography to quantify and visualize the antigenic relationships among FMD serotype A viruses, aiming to improve the understanding of FMDV antigenic evolution and the scope and reliability of vaccine matching. Our results suggest that predicting antigenic difference using genetic sequence alone or by geographical location is not currently reliable. We found co-circulating lineages in one region that were genetically similar but antigenically distinct. Nevertheless, by comparing antigenic distances measured from the antigenic maps with the full capsid (P1) sequence, we identified a specific amino acid substitution associated with an antigenic mismatch among field viruses and a commonly used prototype vaccine strain, A22/IRQ/24/64.
A reverse transcription polymerase chain reaction (RT-PCR) procedure is described for the detecti... more A reverse transcription polymerase chain reaction (RT-PCR) procedure is described for the detection of marine caliciviruses including vesicular exanthema of swine virus (VESV), San Miguel sea lion virus (SMSV), bovine Tillamook virus (BCV Bos-1) and caliciviruses (CV) isolated from dolphin (Cetacean CV), gorilla (Primate CV) and rattlesnake (Reptile CV) using primers (1F and 1R) designed from the capsid-coding region of
The genome sequences of three duck hepatitis virus type 1 (DHV-1) strains were determined. Compar... more The genome sequences of three duck hepatitis virus type 1 (DHV-1) strains were determined. Comparative sequence analyses showed that they possessed a typical picornavirus genome organization apart from the unique possession of three in-tandem 2A genes. The 2A1 protein of DHV-1 is an aphthovirus-like 2A protein; the 2A2 protein is not related to any known picornavirus protein; the 2A3 protein is a human parechovirus-like 2A protein. Several other features were found to be unique to the DHV-1 genome when compared with other picornaviruses: (i) the 3' UTR of DHV-1 was composed of 314 nt, the largest among the picornaviruses; (ii) pair-wise amino acid sequence identities between polyprotein of DHV-1 and other picornaviruses are all less than 30%. The pair-wise amino acid sequence identities in the 3D region of DHV-1 with LV and HPeV-1 is only 38.6 and 36.6%, respectively, and less than 30% with all other picornaviruses; (iii) the DHV-1 capsid polypeptide VP0 is not proteolytically cleaved into VP4 and VP2; and (iv) phylogenetic and evolutionary analysis of DHV-1 reveals a new picornavirus clade. It is therefore proposed that DHV-1 should be assigned to a new genus in the Picornaviridae.
Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subjec... more Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as “coxsackieviruses”, “polioviruses” and “echoviruses”, which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series...
In recent years, foot-and-mouth disease virus (FMDV) serotype O, topotype Middle East-South Asia ... more In recent years, foot-and-mouth disease virus (FMDV) serotype O, topotype Middle East-South Asia (ME-SA), lineage Ind-2001d has spread from the Indian subcontinent to the Middle East, North Africa, and Southeast Asia. In the current report, we describe the first detection of this lineage in Vietnam in May, 2015 in Đắk Nông province. Three subsequent outbreaks caused by genetically related viruses occurred between May-October, 2015 after which the virus was not detected in clinical outbreaks for at least 15 subsequent months. The observed outbreaks affected (in chronological order): cattle in Đắk Nông province, pigs in Đắk Lắk province and Đắk Nông province, and cattle in Ninh Thuận province. The clinical syndromes associated with these outbreaks were consistent with typical FMD in the affected species. Overall attack rate on affected premises was 0.85 in pigs and 0.93 in cattle over the course of the outbreak. Amongst 378 pigs at risk on affected premises, 85 pigs died during the ou...
The deletion of residues 93-102 in non-structure protein 3A of foot-and-mouth disease virus (FMDV... more The deletion of residues 93-102 in non-structure protein 3A of foot-and-mouth disease virus (FMDV) is associated with the inability of FMDV to grow in bovine cells and attenuated virulence in cattle.Whereas, a previously reported FMDV strain O/HKN/21/70 harboring 93-102 deletion in 3A protein grew equally well in bovine and swine cells. This suggests that changes inFMDV genome sequence, in addition to 93-102 deletion in 3A, may also affectthe viral growth phenotype in bovine cellsduring infection and replication.However, it is nuclear that changes in which region (inside or outside of 3A region) influences FMDV growth phenotype in bovine cells.In this study, to determine the region in FMDV genomeaffecting viral growth phenotype in bovine cells, we constructed chimeric FMDVs, rvGZSB-HKN3A and rvHN-HKN3A, by introducing the 3A coding region of O/HKN/21/70 into the context of O/SEA/Mya-98 strain O/GZSB/2011 and O Cathay topotype strain O/HN/CHA/93, respectively, since O/GZSB/2011 conta...
The current measures to control foot-and-mouth disease (FMD) include vaccination, movement contro... more The current measures to control foot-and-mouth disease (FMD) include vaccination, movement control and slaughter of infected or susceptible animals. One of the difficulties in controlling FMD by vaccination arises due to the substantial diversity found among the seven serotypes of FMD virus (FMDV) and the strains within these serotypes. Therefore, vaccination using a single vaccine strain may not fully cross-protect against all strains within that serotype, and therefore selection of appropriate vaccines requires serological comparison of the field virus and potential vaccine viruses using relationship coefficients (r 1 values). Limitations of this approach are that antigenic relationships among field viruses are not addressed, as comparisons are only with potential vaccine virus. Furthermore, inherent variation among vaccine sera may impair reproducibility of one-way relationship scores. Here, we used antigenic cartography to quantify and visualize the antigenic relationships among FMD serotype A viruses, aiming to improve the understanding of FMDV antigenic evolution and the scope and reliability of vaccine matching. Our results suggest that predicting antigenic difference using genetic sequence alone or by geographical location is not currently reliable. We found co-circulating lineages in one region that were genetically similar but antigenically distinct. Nevertheless, by comparing antigenic distances measured from the antigenic maps with the full capsid (P1) sequence, we identified a specific amino acid substitution associated with an antigenic mismatch among field viruses and a commonly used prototype vaccine strain, A22/IRQ/24/64.
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