Bioinformatics and Molecular Analysis of the Evolutionary Relationship between Bovine Rhinitis A Viruses and Foot-And-Mouth Disease Virus
Identifieur interne : 000881 ( Main/Exploration ); précédent : 000880; suivant : 000882Bioinformatics and Molecular Analysis of the Evolutionary Relationship between Bovine Rhinitis A Viruses and Foot-And-Mouth Disease Virus
Auteurs : Devendra K. Rai [États-Unis] ; Paul Lawrence [États-Unis] ; Steve J. Pauszek [États-Unis] ; Maria E. Piccone [États-Unis] ; Nick J. Knowles [Royaume-Uni] ; Elizabeth Rieder [États-Unis]Source :
- Bioinformatics and Biology Insights [ 1177-9322 ] ; 2016.
Abstract
Bovine rhinitis viruses (BRVs) cause mild respiratory disease of cattle. In this study, a near full-length genome sequence of a virus named RS3X (formerly classified as bovine rhinovirus type 1), isolated from infected cattle from the UK in the 1960s, was obtained and analyzed. Compared to other closely related Aphthoviruses, major differences were detected in the leader protease (Lpro), P1, 2B, and 3A proteins. Phylogenetic analysis revealed that RS3X was a member of the species bovine rhinitis A virus (BRAV). Using different codon-based and branch-site selection models for Aphthoviruses, including BRAV RS3X and foot-and-mouth disease virus, we observed no clear evidence for genomic regions undergoing positive selection. However, within each of the BRV species, multiple sites under positive selection were detected. The results also suggest that the probability (determined by Recombination Detection Program) for recombination events between BRVs and other Aphthoviruses, including foot-and-mouth disease virus was not significant. In contrast, within BRVs, the probability of recombination increases. The data reported here provide genetic information to assist in the identification of diagnostic signatures and research tools for BRAV.
Url:
DOI: 10.4137/BBI.S37223
PubMed: 27081310
PubMed Central: 4822724
Affiliations:
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Rai</name><affiliation wicri:level="1"><nlm:aff id="af1-bbi-suppl.2-2015-043">Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, USA.</nlm:aff><country xml:lang="fr" wicri:curation="lc">États-Unis</country><wicri:regionArea>Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY</wicri:regionArea><wicri:noRegion>NY</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-bbi-suppl.2-2015-043">Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, USA.</nlm:aff><country xml:lang="fr" wicri:curation="lc">États-Unis</country><wicri:regionArea>Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT</wicri:regionArea><wicri:noRegion>CT</wicri:noRegion></affiliation></author><author><name sortKey="Lawrence, Paul" sort="Lawrence, Paul" uniqKey="Lawrence P" first="Paul" last="Lawrence">Paul Lawrence</name><affiliation wicri:level="1"><nlm:aff id="af1-bbi-suppl.2-2015-043">Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, USA.</nlm:aff><country xml:lang="fr" wicri:curation="lc">États-Unis</country><wicri:regionArea>Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY</wicri:regionArea><wicri:noRegion>NY</wicri:noRegion></affiliation></author><author><name sortKey="Pauszek, Steve J" sort="Pauszek, Steve J" uniqKey="Pauszek S" first="Steve J." last="Pauszek">Steve J. Pauszek</name><affiliation wicri:level="1"><nlm:aff id="af1-bbi-suppl.2-2015-043">Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, USA.</nlm:aff><country xml:lang="fr" wicri:curation="lc">États-Unis</country><wicri:regionArea>Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY</wicri:regionArea><wicri:noRegion>NY</wicri:noRegion></affiliation></author><author><name sortKey="Piccone, Maria E" sort="Piccone, Maria E" uniqKey="Piccone M" first="Maria E." last="Piccone">Maria E. Piccone</name><affiliation wicri:level="1"><nlm:aff id="af1-bbi-suppl.2-2015-043">Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, USA.</nlm:aff><country xml:lang="fr" wicri:curation="lc">États-Unis</country><wicri:regionArea>Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY</wicri:regionArea><wicri:noRegion>NY</wicri:noRegion></affiliation></author><author><name sortKey="Knowles, Nick J" sort="Knowles, Nick J" uniqKey="Knowles N" first="Nick J." last="Knowles">Nick J. Knowles</name><affiliation wicri:level="1"><nlm:aff id="af3-bbi-suppl.2-2015-043">The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, UK.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country><wicri:regionArea>The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey</wicri:regionArea><wicri:noRegion>Surrey</wicri:noRegion></affiliation></author><author><name sortKey="Rieder, Elizabeth" sort="Rieder, Elizabeth" uniqKey="Rieder E" first="Elizabeth" last="Rieder">Elizabeth Rieder</name><affiliation wicri:level="1"><nlm:aff id="af1-bbi-suppl.2-2015-043">Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, USA.</nlm:aff><country xml:lang="fr" wicri:curation="lc">États-Unis</country><wicri:regionArea>Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY</wicri:regionArea><wicri:noRegion>NY</wicri:noRegion></affiliation></author></analytic><series><title level="j">Bioinformatics and Biology Insights</title><idno type="eISSN">1177-9322</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Bovine rhinitis viruses (BRVs) cause mild respiratory disease of cattle. In this study, a near full-length genome sequence of a virus named RS3X (formerly classified as bovine rhinovirus type 1), isolated from infected cattle from the UK in the 1960s, was obtained and analyzed. Compared to other closely related Aphthoviruses, major differences were detected in the leader protease (L<sup>pro</sup>), P1, 2B, and 3A proteins. Phylogenetic analysis revealed that RS3X was a member of the species bovine rhinitis A virus (BRAV). Using different codon-based and branch-site selection models for Aphthoviruses, including BRAV RS3X and foot-and-mouth disease virus, we observed no clear evidence for genomic regions undergoing positive selection. However, within each of the BRV species, multiple sites under positive selection were detected. The results also suggest that the probability (determined by Recombination Detection Program) for recombination events between BRVs and other Aphthoviruses, including foot-and-mouth disease virus was not significant. In contrast, within BRVs, the probability of recombination increases. The data reported here provide genetic information to assist in the identification of diagnostic signatures and research tools for BRAV.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Snowder, Gd" uniqKey="Snowder G">GD Snowder</name></author><author><name sortKey="Van Vleck, Ld" uniqKey="Van Vleck L">LD Van Vleck</name></author><author><name sortKey="Cundiff, Lv" uniqKey="Cundiff L">LV Cundiff</name></author><author><name sortKey="Bennett, Gl" uniqKey="Bennett G">GL Bennett</name></author><author><name sortKey="Koohmaraie, M" uniqKey="Koohmaraie M">M Koohmaraie</name></author><author><name sortKey="Dikeman, Me" uniqKey="Dikeman M">ME Dikeman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ellis, Ja" uniqKey="Ellis J">JA Ellis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Glotov, Ag" uniqKey="Glotov A">AG Glotov</name></author><author><name 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Rai</name></noRegion><name sortKey="Lawrence, Paul" sort="Lawrence, Paul" uniqKey="Lawrence P" first="Paul" last="Lawrence">Paul Lawrence</name><name sortKey="Pauszek, Steve J" sort="Pauszek, Steve J" uniqKey="Pauszek S" first="Steve J." last="Pauszek">Steve J. Pauszek</name><name sortKey="Piccone, Maria E" sort="Piccone, Maria E" uniqKey="Piccone M" first="Maria E." last="Piccone">Maria E. Piccone</name><name sortKey="Rai, Devendra K" sort="Rai, Devendra K" uniqKey="Rai D" first="Devendra K." last="Rai">Devendra K. Rai</name><name sortKey="Rieder, Elizabeth" sort="Rieder, Elizabeth" uniqKey="Rieder E" first="Elizabeth" last="Rieder">Elizabeth Rieder</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Knowles, Nick J" sort="Knowles, Nick J" uniqKey="Knowles N" first="Nick J." last="Knowles">Nick J. Knowles</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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