Comparative Co-Evolution Analysis Between the HA and NA Genes of Influenza A Virus
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Auteurs : Jinhwa Jang [Corée du Sud] ; Se-Eun Bae [Corée du Sud]Source :
- Virology : Research and Treatment [ 1178-122X ] ; 2018.
Abstract
Influenza A virus subtypes are determined based on envelope proteins encoded by the hemagglutinin (HA) gene and the neuraminidase (NA) gene, which are involved in attachment to the host, pathogenicity, and progeny production. Here, we evaluated such differences through co-evolution analysis between the HA and NA genes based on subtype and host. Event-based cophylogeny analysis revealed that humans had higher cospeciation values than avian. In particular, the yearly ML phylogenetic trees for the H1N1 and H3N2 subtypes in humans displayed similar topologies between the two genes in humans. Substitution analysis was verifying the strong positive correlation between the two genes in the H1N1 and H3N2 subtypes in humans compared with those in avian and swine. These results provided a proof of principle for the further development of vaccines according to hosts and subtypes against Influenza A virus.
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DOI: 10.1177/1178122X18788328
PubMed: 30038490
PubMed Central: 6053862
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative Co-Evolution Analysis Between the HA and NA Genes of Influenza A Virus</title><author><name sortKey="Jang, Jinhwa" sort="Jang, Jinhwa" uniqKey="Jang J" first="Jinhwa" last="Jang">Jinhwa Jang</name><affiliation wicri:level="1"><nlm:aff id="aff1-1178122X18788328">Center for Applied Scientific Computing, Division of Supercomputing, Korea Institute ofScience and Technology Information, Daejeon, Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Center for Applied Scientific Computing, Division of Supercomputing, Korea Institute ofScience and Technology Information, Daejeon</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2-1178122X18788328">Laboratory of Computational Biology & Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Laboratory of Computational Biology & Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Bae, Se Eun" sort="Bae, Se Eun" uniqKey="Bae S" first="Se-Eun" last="Bae">Se-Eun Bae</name><affiliation wicri:level="1"><nlm:aff id="aff3-1178122X18788328">Bioinformatics Laboratory, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Bioinformatics Laboratory, Samsung Genome Institute, Samsung Medical Center, Seoul</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">30038490</idno><idno type="pmc">6053862</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053862</idno><idno type="RBID">PMC:6053862</idno><idno type="doi">10.1177/1178122X18788328</idno><date when="2018">2018</date><idno type="wicri:Area/Pmc/Corpus">000C41</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000C41</idno><idno type="wicri:Area/Pmc/Curation">000C41</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000C41</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative Co-Evolution Analysis Between the HA and NA Genes of Influenza A Virus</title><author><name sortKey="Jang, Jinhwa" sort="Jang, Jinhwa" uniqKey="Jang J" first="Jinhwa" last="Jang">Jinhwa Jang</name><affiliation wicri:level="1"><nlm:aff id="aff1-1178122X18788328">Center for Applied Scientific Computing, Division of Supercomputing, Korea Institute ofScience and Technology Information, Daejeon, Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Center for Applied Scientific Computing, Division of Supercomputing, Korea Institute ofScience and Technology Information, Daejeon</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2-1178122X18788328">Laboratory of Computational Biology & Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Laboratory of Computational Biology & Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Bae, Se Eun" sort="Bae, Se Eun" uniqKey="Bae S" first="Se-Eun" last="Bae">Se-Eun Bae</name><affiliation wicri:level="1"><nlm:aff id="aff3-1178122X18788328">Bioinformatics Laboratory, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Bioinformatics Laboratory, Samsung Genome Institute, Samsung Medical Center, Seoul</wicri:regionArea></affiliation></author></analytic><series><title level="j">Virology : Research and Treatment</title><idno type="eISSN">1178-122X</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Influenza A virus subtypes are determined based on envelope proteins encoded by the hemagglutinin (HA) gene and the neuraminidase (NA) gene, which are involved in attachment to the host, pathogenicity, and progeny production. Here, we evaluated such differences through co-evolution analysis between the HA and NA genes based on subtype and host. Event-based cophylogeny analysis revealed that humans had higher cospeciation values than avian. In particular, the yearly ML phylogenetic trees for the H1N1 and H3N2 subtypes in humans displayed similar topologies between the two genes in humans. Substitution analysis was verifying the strong positive correlation between the two genes in the H1N1 and H3N2 subtypes in humans compared with those in avian and swine. These results provided a proof of principle for the further development of vaccines according to hosts and subtypes against Influenza A virus.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Couch, Rb" uniqKey="Couch R">RB. Couch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kilbournf, Ed" uniqKey="Kilbournf E">ED. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Virology (Auckl)</journal-id><journal-id journal-id-type="iso-abbrev">Virology (Auckl)</journal-id><journal-id journal-id-type="publisher-id">VRT</journal-id><journal-id journal-id-type="hwp">spvrt</journal-id><journal-title-group><journal-title>Virology : Research and Treatment</journal-title></journal-title-group><issn pub-type="epub">1178-122X</issn><publisher><publisher-name>SAGE Publications</publisher-name><publisher-loc>Sage UK: London, England</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">30038490</article-id><article-id pub-id-type="pmc">6053862</article-id><article-id pub-id-type="doi">10.1177/1178122X18788328</article-id><article-id pub-id-type="publisher-id">10.1177_1178122X18788328</article-id><article-id pub-id-type="publisher-manuscript">VRT-0044061</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Research</subject></subj-group></article-categories><title-group><article-title>Comparative Co-Evolution Analysis Between the HA and NA Genes of Influenza A Virus</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Jang</surname><given-names>Jinhwa</given-names></name><xref ref-type="aff" rid="aff1-1178122X18788328">1</xref><xref ref-type="aff" rid="aff2-1178122X18788328">2</xref></contrib><contrib contrib-type="author"><name><surname>Bae</surname><given-names>Se-Eun</given-names></name><xref ref-type="aff" rid="aff3-1178122X18788328">3</xref><xref ref-type="corresp" rid="corresp1-1178122X18788328"></xref></contrib></contrib-group><aff id="aff1-1178122X18788328"><label>1</label>Center for Applied Scientific Computing, Division of Supercomputing, Korea Institute ofScience and Technology Information, Daejeon, Republic of Korea</aff><aff id="aff2-1178122X18788328"><label>2</label>Laboratory of Computational Biology & Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea</aff><aff id="aff3-1178122X18788328"><label>3</label>Bioinformatics Laboratory, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea</aff><author-notes><corresp id="corresp1-1178122X18788328">Dr Se-Eun Bae, Bioinformatics Laboratory, Samsung Genome Institute, Samsung Hospital, 81 Irwon-ro, Gangnam-gu. Seoul 06351, Republic of Korea. Email: <email>seeun.bae@sbri.co.kr</email></corresp></author-notes><pub-date pub-type="epub"><day>19</day><month>7</month><year>2018</year></pub-date><pub-date pub-type="collection"><year>2018</year></pub-date><volume>9</volume><elocation-id>1178122X18788328</elocation-id><history><date date-type="received"><day>12</day><month>12</month><year>2017</year></date><date date-type="accepted"><day>21</day><month>6</month><year>2018</year></date></history><permissions><copyright-statement>© The Author(s) 2018</copyright-statement><copyright-year>2018</copyright-year><copyright-holder content-type="sage">SAGE Publications Ltd unless otherwise noted. Manuscript content on this site is licensed under Creative Commons Licenses</copyright-holder><license license-type="creative-commons" xlink:href="http://www.creativecommons.org/licenses/by-nc/4.0/"><license-p>This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (<ext-link ext-link-type="uri" xlink:href="http://www.creativecommons.org/licenses/by-nc/4.0/">http://www.creativecommons.org/licenses/by-nc/4.0/</ext-link>) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (<ext-link ext-link-type="uri" xlink:href="https://us.sagepub.com/en-us/nam/open-access-at-sage">https://us.sagepub.com/en-us/nam/open-access-at-sage</ext-link>).</license-p></license></permissions><abstract><p>Influenza A virus subtypes are determined based on envelope proteins encoded by the hemagglutinin (HA) gene and the neuraminidase (NA) gene, which are involved in attachment to the host, pathogenicity, and progeny production. Here, we evaluated such differences through co-evolution analysis between the HA and NA genes based on subtype and host. Event-based cophylogeny analysis revealed that humans had higher cospeciation values than avian. In particular, the yearly ML phylogenetic trees for the H1N1 and H3N2 subtypes in humans displayed similar topologies between the two genes in humans. Substitution analysis was verifying the strong positive correlation between the two genes in the H1N1 and H3N2 subtypes in humans compared with those in avian and swine. These results provided a proof of principle for the further development of vaccines according to hosts and subtypes against Influenza A virus.</p></abstract><kwd-group><kwd>Co-evolution</kwd><kwd>influenza A virus</kwd><kwd>hemagglutinin</kwd><kwd>neuraminidase</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>January-December 2018</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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