Bioinformatics and Molecular Analysis of the Evolutionary Relationship between Bovine Rhinitis A Viruses and Foot-And-Mouth Disease Virus
Identifieur interne : 000042 ( Pmc/Curation ); précédent : 000041; suivant : 000043Bioinformatics 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
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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></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></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></affiliation></author><author><name sortKey="Pauszek, Steve J" sort="Pauszek, Steve J" uniqKey="Pauszek S" first="Steve J." last="Pauszek">Steve J. 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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></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></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></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></affiliation></author><author><name sortKey="Piccone, Maria E" sort="Piccone, Maria E" uniqKey="Piccone M" first="Maria E." last="Piccone">Maria E. 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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></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></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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<front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinform Biol Insights</journal-id><journal-id journal-id-type="iso-abbrev">Bioinform Biol Insights</journal-id><journal-id journal-id-type="publisher-id">Bioinformatics and Biology Insights</journal-id><journal-title-group><journal-title>Bioinformatics and Biology Insights</journal-title></journal-title-group><issn pub-type="epub">1177-9322</issn><publisher><publisher-name>Libertas Academica</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27081310</article-id><article-id pub-id-type="pmc">4822724</article-id><article-id pub-id-type="doi">10.4137/BBI.S37223</article-id><article-id pub-id-type="publisher-id">bbi-suppl.2-2015-043</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Research</subject></subj-group></article-categories><title-group><article-title>Bioinformatics and Molecular Analysis of the Evolutionary Relationship between Bovine Rhinitis A Viruses and Foot-And-Mouth Disease Virus</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Rai</surname><given-names>Devendra K.</given-names></name><xref ref-type="aff" rid="af1-bbi-suppl.2-2015-043">1</xref><xref ref-type="aff" rid="af2-bbi-suppl.2-2015-043">2</xref></contrib><contrib contrib-type="author"><name><surname>Lawrence</surname><given-names>Paul</given-names></name><xref ref-type="aff" rid="af1-bbi-suppl.2-2015-043">1</xref></contrib><contrib contrib-type="author"><name><surname>Pauszek</surname><given-names>Steve J.</given-names></name><xref ref-type="aff" rid="af1-bbi-suppl.2-2015-043">1</xref></contrib><contrib contrib-type="author"><name><surname>Piccone</surname><given-names>Maria E.</given-names></name><xref ref-type="aff" rid="af1-bbi-suppl.2-2015-043">1</xref></contrib><contrib contrib-type="author"><name><surname>Knowles</surname><given-names>Nick J.</given-names></name><xref ref-type="aff" rid="af3-bbi-suppl.2-2015-043">3</xref></contrib><contrib contrib-type="author"><name><surname>Rieder</surname><given-names>Elizabeth</given-names></name><xref ref-type="aff" rid="af1-bbi-suppl.2-2015-043">1</xref><xref ref-type="corresp" rid="c1-bbi-suppl.2-2015-043"></xref></contrib></contrib-group><aff id="af1-bbi-suppl.2-2015-043"><label>1</label>Agricultural Research Service, US Department of Agriculture, Plum Island Animal Disease Center, Greenport, NY, USA.</aff><aff id="af2-bbi-suppl.2-2015-043"><label>2</label>Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, USA.</aff><aff id="af3-bbi-suppl.2-2015-043"><label>3</label>The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, UK.</aff><author-notes><corresp id="c1-bbi-suppl.2-2015-043">CORRESPONDENCE: <email>Elizabeth.Rieder@ars.usda.gov</email></corresp></author-notes><pub-date pub-type="collection"><year>2015</year></pub-date><pub-date pub-type="epub"><day>04</day><month>4</month><year>2016</year></pub-date><volume>9</volume><issue>Suppl 2</issue><fpage>43</fpage><lpage>58</lpage><history><date date-type="received"><day>03</day><month>11</month><year>2015</year></date><date date-type="rev-recd"><day>21</day><month>12</month><year>2015</year></date><date date-type="accepted"><day>26</day><month>12</month><year>2015</year></date></history><permissions><copyright-statement>© 2015 the author(s), publisher and licensee Libertas Academica Ltd.</copyright-statement><copyright-year>2015</copyright-year><license license-type="open-access"><license-p>This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License.</license-p></license></permissions><abstract><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></abstract><kwd-group><kwd>BRAV RS3X</kwd><kwd>sequence</kwd><kwd>phylogeny</kwd><kwd>evolution</kwd><kwd>bioinformatics</kwd></kwd-group></article-meta></front><floats-group><fig id="f1-bbi-suppl.2-2015-043" position="float"><label>Figure 1</label><caption><p>(<bold>A</bold>) Alignment of polyprotein of Aphthoviruses: FMDV A<sub>24</sub> Cruzeiro strain was used as a template for alignment and feature annotation and marked as FMDV A<sub>24</sub> Cruz. BRAV RS3X (GeneBank: KT948520), BRBV EC-11 (GeneBank: EU236594) and ERAV (GeneBank: DQ272578) were aligned to FMDV A<sub>24</sub> Cruz (GeneBank: AY 593768). Marks the start of a protein sequence (N-terminus of), and the text following it identifies the protein. Yellow highlights suggest functionally critical (active site residue). (·) denotes a conserved residue in comparison to FMDV A<sub>24</sub> Cruz. (−) denotes a gap introduced in the alignment. Cyan highlights indicate functionally important residues of a protein other than active site residues. Green highlights denote the RGD cell surface receptor. (<bold>B</bold>) Alignment of polyprotein of BRVs: Color code of highlighting and feature marking is the same as (<bold>A</bold>). Text at the beginning of each line is the sequence identifier for the given virus strain. For example, BRAV RS3X indicates BRAV RS3X sequence. The GeneBank accession numbers of the sequences used in the alignment are KT948520, KP236128, KP236129, JN936206, KP264974, EU236594, KP236130, KP264975, and KP264980 for BRAV RS 3X, BRAV Sd-1, BRAV 140032-1, BRAV H-1, BRAV BSRI4, BRBV EC-11, BRBV 140032-2, BRAV BSRI3, and BRAV BSRI1, respectively.</p></caption><graphic xlink:href="bbi-suppl.2-2015-043f1"></graphic><graphic xlink:href="bbi-suppl.2-2015-043f1a"></graphic><graphic xlink:href="bbi-suppl.2-2015-043f1b"></graphic><graphic xlink:href="bbi-suppl.2-2015-043f1c"></graphic></fig><fig id="f2-bbi-suppl.2-2015-043" position="float"><label>Figure 2</label><caption><p>(<bold>A</bold>) Prediction of the transmembrane domain in: (i) FMDV A<sub>24</sub> Cruz 2B and (ii) BRAV RS3X 2B. Color codes for different features are explained adjacent to each image. (<bold>B</bold>) Modeled structures of VP1 structural proteins of (i) FMDV A<sub>24</sub> Cruz and BRAV RS3X are colored cyan, the G–H loop is marked with a yellow oval, and the RGD tripeptide is marked with cyan text. N- and C-terminus of the proteins in the structure are marked. (ii) The prediction of the 2B viroporin of: FMDV A<sub>24</sub> Cruz (purple) and BRAV RS3X (cyan) were superimposed on HCV p7. N- and C-terminus of the proteins in the structure are marked. Structure-based sequence alignments are positioned to the left of each image. All structures are rendered in cartoon representation using UCSF-Chimera ver 1.10</p></caption><graphic xlink:href="bbi-suppl.2-2015-043f2"></graphic><graphic xlink:href="bbi-suppl.2-2015-043f2a"></graphic></fig><fig id="f3-bbi-suppl.2-2015-043" position="float"><label>Figure 3</label><caption><p>Neighbor-joining phylogeny trees of the P1 structural protein region (<bold>A</bold>) and 3D<sup>pol</sup> non-structural protein (<bold>B</bold>) of family <italic>Picornaviridae</italic> including BRAV RS3X. Neighbor-joining phylogeny trees involving BRAV RS3X and all known members of <italic>Picornaviridae</italic> were constructed with the JTT model for amino acid substitution (pairwise deletions only) for (<bold>A</bold>) P1 structural proteins and (<bold>B</bold>) 3D<sup>pol</sup> non-structural protein. As shown, 1,000 bootstraps with only those of 70% and above are displayed. Scale of resolution is indicated at the bottom of each figure.</p><p><bold>Note:</bold> “ ” indicate proposed new species and genera in <italic>Picornaviridae</italic>.</p></caption><graphic xlink:href="bbi-suppl.2-2015-043f3"></graphic><graphic xlink:href="bbi-suppl.2-2015-043f3a"></graphic></fig><table-wrap id="t1-bbi-suppl.2-2015-043" position="float"><label>Table 1</label><caption><p>Distribution of positively or negatively selected sites among Aphthoviruses.</p></caption><table frame="box" rules="rows"><thead><tr><th rowspan="2" valign="top" align="left" colspan="1">ANALYSIS</th><th colspan="4" valign="top" align="left" rowspan="1">NEGATIVE SITES</th><th colspan="4" valign="top" align="left" rowspan="1">POSITIVE SITES</th></tr><tr><th valign="top" align="left" rowspan="1" colspan="1">NO.</th><th valign="top" align="left" rowspan="1" colspan="1">CODON SITE</th><th valign="top" align="left" rowspan="1" colspan="1">AVG. dN/dS</th><th valign="top" align="left" rowspan="1" colspan="1"><italic>P</italic>-VALUE</th><th valign="top" align="left" rowspan="1" colspan="1">NO.</th><th valign="top" align="left" rowspan="1" colspan="1">CODON SITE</th><th valign="top" align="left" rowspan="1" colspan="1">AVG. dN/dS</th><th valign="top" align="left" rowspan="1" colspan="1"><italic>P</italic>-VALUE</th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">SLAC</td><td valign="top" align="left" rowspan="1" colspan="1">363</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">7.65015e-05</td><td valign="top" align="left" rowspan="1" colspan="1">0.004–0.05</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">$0.05</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">FEL</td><td valign="top" align="left" rowspan="1" colspan="1">425</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">0.001946</td><td valign="top" align="left" rowspan="1" colspan="1">0.002–0.05</td><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">489, 832, 1958</td><td valign="top" align="left" rowspan="1" colspan="1">Infinite</td><td valign="top" align="left" rowspan="1" colspan="1">0.038–0.045</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">IFEL</td><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">1119, 2001, 2439</td><td valign="top" align="left" rowspan="1" colspan="1">0.0003</td><td valign="top" align="left" rowspan="1" colspan="1">0.002–0.05</td><td valign="top" align="left" rowspan="1" colspan="1">14</td><td valign="top" align="left" rowspan="1" colspan="1">393, 431, 465, 993, 1123, 1471, 1742, 1880, 1901, 1914, 1920, 2055, 2059, 2331</td><td valign="top" align="left" rowspan="1" colspan="1">Infinite</td><td valign="top" align="left" rowspan="1" colspan="1">0.008–0.05</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">MEME</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">49, 735, 884, 2054, 2331, 2394</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">0.015–0.048</td></tr></tbody></table></table-wrap><table-wrap id="t2-bbi-suppl.2-2015-043" position="float"><label>Table 2</label><caption><p>Distribution of positively or negatively selected sites among Bovine rhinitis viruses.</p></caption><table frame="box" rules="rows"><thead><tr><th rowspan="2" valign="top" align="left" colspan="1">ANALYSIS</th><th colspan="4" valign="top" align="left" rowspan="1">NEGATIVE SITES</th><th colspan="3" valign="top" align="left" rowspan="1">POSITIVE SITES</th></tr><tr><th valign="top" align="left" rowspan="1" colspan="1">NO.</th><th valign="top" align="left" rowspan="1" colspan="1">AVG. dN/dS</th><th valign="top" align="left" rowspan="1" colspan="1"><italic>P</italic>-VALUE</th><th valign="top" align="left" rowspan="1" colspan="1">NO.</th><th valign="top" align="left" rowspan="1" colspan="1">CODON SITE</th><th valign="top" align="left" rowspan="1" colspan="1">AVG. dN/dS</th><th valign="top" align="left" rowspan="1" colspan="1"><italic>P</italic>-VALUE</th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">SLAC</td><td valign="top" align="left" rowspan="1" colspan="1">511</td><td valign="top" align="left" rowspan="1" colspan="1">0.116349</td><td valign="top" align="left" rowspan="1" colspan="1">0.005–0.05</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">≥0.05</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">FEL</td><td valign="top" align="left" rowspan="1" colspan="1">1143</td><td valign="top" align="left" rowspan="1" colspan="1">0.016</td><td valign="top" align="left" rowspan="1" colspan="1">≥0.05</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">680</td><td valign="top" align="left" rowspan="1" colspan="1">Infinite</td><td valign="top" align="left" rowspan="1" colspan="1">0.034</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">IFEL</td><td valign="top" align="left" rowspan="1" colspan="1">843</td><td valign="top" align="left" rowspan="1" colspan="1">0.00539</td><td valign="top" align="left" rowspan="1" colspan="1">0.002–0.05</td><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">139, 614, 617, 680, 811, 1806</td><td valign="top" align="left" rowspan="1" colspan="1">Infinite</td><td valign="top" align="left" rowspan="1" colspan="1">0.008–0.05</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">MEME</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">22</td><td valign="top" align="left" rowspan="1" colspan="1">3, 5, 95, 448, 617, 630, 667, 684, 733, 789, 798, 811, 961, 985, 1008, 1010, 1249, 1412, 1479, 1490, 1745, 1901</td><td valign="top" align="left" rowspan="1" colspan="1">N.A.</td><td valign="top" align="left" rowspan="1" colspan="1">0.001–0.05</td></tr></tbody></table></table-wrap><table-wrap id="t3-bbi-suppl.2-2015-043" position="float"><label>Table 3</label><caption><p>Detection of potential recombination events between BRAV RS3X and closely related Aphthoviruses using ORF only.</p></caption><table frame="box" rules="rows"><thead><tr><th rowspan="2" valign="top" align="left" colspan="1">RENO.</th><th colspan="7" valign="top" align="left" rowspan="1">BREAKPOINT POSITIONS IN RECOMBINANT SEQUENCE</th><th colspan="7" valign="top" align="left" rowspan="1">DETECTION METHOD</th></tr><tr><th valign="top" align="left" rowspan="1" colspan="1">BEGIN</th><th valign="top" align="left" rowspan="1" colspan="1">END</th><th valign="top" align="left" rowspan="1" colspan="1">RECOMBINANT SEQ (S)</th><th valign="top" align="left" rowspan="1" colspan="1">MINOR PARENT SEQ (S)</th><th valign="top" align="left" rowspan="1" colspan="1">MAJOR PARENT SEQ (S)</th><th valign="top" align="left" rowspan="1" colspan="1">RDP</th><th valign="top" align="left" rowspan="1" colspan="1">GENE-CONV</th><th valign="top" align="left" rowspan="1" colspan="1">BOOTSCAN</th><th valign="top" align="left" rowspan="1" colspan="1">MAXCHI</th><th valign="top" align="left" rowspan="1" colspan="1">CHIMAERA</th><th valign="top" align="left" rowspan="1" colspan="1">SISSCAN</th><th valign="top" align="left" rowspan="1" colspan="1">PHYLPRO</th><th valign="top" align="left" rowspan="1" colspan="1">LARD</th><th valign="top" align="left" rowspan="1" colspan="1">3SEQ</th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">3127</td><td valign="top" align="left" rowspan="1" colspan="1">3371</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV</td><td valign="top" align="left" rowspan="1" colspan="1">ERAV</td><td valign="top" align="left" rowspan="1" colspan="1">FMDV A<sub>24</sub></td><td valign="top" align="left" rowspan="1" colspan="1">2.07E-03</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">6360</td><td valign="top" align="left" rowspan="1" colspan="1">6564</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV RS3X</td><td valign="top" align="left" rowspan="1" colspan="1">Unknown FMDV A<sub>24</sub></td><td valign="top" align="left" rowspan="1" colspan="1">BRBV EC11</td><td valign="top" align="left" rowspan="1" colspan="1">2.47E-03</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">1.76E-02</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">4.17E-02</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">5750<xref ref-type="table-fn" rid="tfn1-bbi-suppl.2-2015-043">*</xref></td><td valign="top" align="left" rowspan="1" colspan="1">5824</td><td valign="top" align="left" rowspan="1" colspan="1">FMDV A</td><td valign="top" align="left" rowspan="1" colspan="1">ERAV</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV RS3X</td><td valign="top" align="left" rowspan="1" colspan="1">1.81E-02</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1">2238</td><td valign="top" align="left" rowspan="1" colspan="1">2322</td><td valign="top" align="left" rowspan="1" colspan="1">FMDV A<sub>24</sub></td><td valign="top" align="left" rowspan="1" colspan="1">ERAV</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV RS3X</td><td valign="top" align="left" rowspan="1" colspan="1">2.21E-02</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1">965</td><td valign="top" align="left" rowspan="1" colspan="1">1122</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV RS3X</td><td valign="top" align="left" rowspan="1" colspan="1">FMDV A<sub>24</sub></td><td valign="top" align="left" rowspan="1" colspan="1">Unknown BRBV EC11</td><td valign="top" align="left" rowspan="1" colspan="1">2.67E-02</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">6640</td><td valign="top" align="left" rowspan="1" colspan="1">54</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV RS3X</td><td valign="top" align="left" rowspan="1" colspan="1">FMDV A<sub>24</sub></td><td valign="top" align="left" rowspan="1" colspan="1">Unknown BRBV EC11</td><td valign="top" align="left" rowspan="1" colspan="1">0.044604</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr></tbody></table><table-wrap-foot><fn><p><bold>Notes:</bold></p></fn><fn id="tfn1-bbi-suppl.2-2015-043"><label>*</label><p>The actual breakpoint position is undetermined (it was most likely overprinted by a subsequent recombination event). Minor Parent = Parent contributing the smaller fraction of sequence. Major Parent = Parent contributing the larger fraction of sequence. Unknown = Only one parent and a recombinant need be in the alignment for a recombination event to be detectable. The sequence listed as unknown was used to infer the existence of a missing parental sequence. NS = No significant. <italic>P</italic>-value was recorded for this recombination event using this method.</p></fn></table-wrap-foot></table-wrap><table-wrap id="t4-bbi-suppl.2-2015-043" position="float"><label>Table 4</label><caption><p>Detection of potential recombination events among bovine rhinitis viruses using ORF only.</p></caption><table frame="box" rules="rows"><thead><tr><th rowspan="2" valign="top" align="left" colspan="1">RENO.</th><th colspan="5" valign="top" align="left" rowspan="1">BREAKPOINT POSITIONS IN RECOMBINANT SEQUENCE</th><th colspan="9" valign="top" align="left" rowspan="1">DETECTION METHOD</th></tr><tr><th valign="top" align="left" rowspan="1" colspan="1">BEGIN</th><th valign="top" align="left" rowspan="1" colspan="1">END</th><th valign="top" align="left" rowspan="1" colspan="1">RECOMBINANT SEQ (S)</th><th valign="top" align="left" rowspan="1" colspan="1">MINOR PARENT SEQ (S)</th><th valign="top" align="left" rowspan="1" colspan="1">MAJOR PARENT SEQ (S)</th><th valign="top" align="left" rowspan="1" colspan="1">RDP</th><th valign="top" align="left" rowspan="1" colspan="1">GENECONV</th><th valign="top" align="left" rowspan="1" colspan="1">BOOTSCAN</th><th valign="top" align="left" rowspan="1" colspan="1">MAXCHI</th><th valign="top" align="left" rowspan="1" colspan="1">CHIMAERA</th><th valign="top" align="left" rowspan="1" colspan="1">SISSCAN</th><th valign="top" align="left" rowspan="1" colspan="1">PHYLPRO</th><th valign="top" align="left" rowspan="1" colspan="1">LARD</th><th valign="top" align="left" rowspan="1" colspan="1">3SEQ</th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">270</td><td valign="top" align="left" rowspan="1" colspan="1">2930</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV BSRI4</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV 140032-1</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV SD-1</td><td valign="top" align="left" rowspan="1" colspan="1">1.19E-48</td><td valign="top" align="left" rowspan="1" colspan="1">6.66E-39</td><td valign="top" align="left" rowspan="1" colspan="1">6.22E-58</td><td valign="top" align="left" rowspan="1" colspan="1">4.26E-38</td><td valign="top" align="left" rowspan="1" colspan="1">8.94E-33</td><td valign="top" align="left" rowspan="1" colspan="1">9.16E-51</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">2.32E-74</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">6422</td><td valign="top" align="left" rowspan="1" colspan="1">2963</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV BSRI1</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV 140032-2</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV EC-11</td><td valign="top" align="left" rowspan="1" colspan="1">4.09E-28</td><td valign="top" align="left" rowspan="1" colspan="1">1.36E-38</td><td valign="top" align="left" rowspan="1" colspan="1">1.63E-35</td><td valign="top" align="left" rowspan="1" colspan="1">1.15E-09</td><td valign="top" align="left" rowspan="1" colspan="1">2.19E-15</td><td valign="top" align="left" rowspan="1" colspan="1">2.86E-32</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">1.35E-11</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">2962</td><td valign="top" align="left" rowspan="1" colspan="1">704</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV RS3X</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV_Sd-1</td><td valign="top" align="left" rowspan="1" colspan="1">BRAV 140032-1 BRAV H-1</td><td valign="top" align="left" rowspan="1" colspan="1">5.11E-15</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">6.50E-09</td><td valign="top" align="left" rowspan="1" colspan="1">4.18E-14</td><td valign="top" align="left" rowspan="1" colspan="1">9.34E-17</td><td valign="top" align="left" rowspan="1" colspan="1">1.33E-36</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1">542</td><td valign="top" align="left" rowspan="1" colspan="1">6289</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV 140032-2</td><td valign="top" align="left" rowspan="1" colspan="1">Unknown BRBV BSRI3</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV EC-11</td><td valign="top" align="left" rowspan="1" colspan="1">1.32E-14</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">3.62E-14</td><td valign="top" align="left" rowspan="1" colspan="1">3.30E-11</td><td valign="top" align="left" rowspan="1" colspan="1">1.48E-05</td><td valign="top" align="left" rowspan="1" colspan="1">9.78E-05</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1">3415</td><td valign="top" align="left" rowspan="1" colspan="1">2963<xref ref-type="table-fn" rid="tfn2-bbi-suppl.2-2015-043">*</xref></td><td valign="top" align="left" rowspan="1" colspan="1">BRBV BSRI1</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV EC-11</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV 140032-2</td><td valign="top" align="left" rowspan="1" colspan="1">3.68E-09</td><td valign="top" align="left" rowspan="1" colspan="1">3.23E-04</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">3.60E-09</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">3.33E-06</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">3.30E-05</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">3069</td><td valign="top" align="left" rowspan="1" colspan="1">2899</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV BSRI3</td><td valign="top" align="left" rowspan="1" colspan="1">Unknown BRAV SD-1 Unknown BRAV 140032-1</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV_140032-2</td><td valign="top" align="left" rowspan="1" colspan="1">3.16E-07</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">2.18E-07</td><td valign="top" align="left" rowspan="1" colspan="1">1.19E-03</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">7</td><td valign="top" align="left" rowspan="1" colspan="1">138</td><td valign="top" align="left" rowspan="1" colspan="1">6407</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV BSRI1</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV_BSRI3</td><td valign="top" align="left" rowspan="1" colspan="1">BRBV_EC-11</td><td valign="top" align="left" rowspan="1" colspan="1">3.24E-02</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td><td valign="top" align="left" rowspan="1" colspan="1">NS</td></tr></tbody></table><table-wrap-foot><fn><p><bold>Notes:</bold></p></fn><fn id="tfn2-bbi-suppl.2-2015-043"><label>*</label><p>The actual breakpoint position is undetermined (it was most likely overprinted by a subsequent recombination event). Minor Parent = Parent contributing the smaller fraction of sequence. Major Parent = Parent contributing the larger fraction of sequence. Unknown = Only one parent and a recombinant need be in the alignment for a recombination event to be detectable. The sequence listed as unknown was used to infer the existence of a missing parental sequence. NS = No significant. <italic>P</italic>-value was recorded for this recombination event using this method. Sequence id is in the original sequence not in the alignment or in relation to any parent.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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