A Complete Analysis of HA and NA Genes of Influenza A Viruses
Identifieur interne : 000B18 ( Pmc/Curation ); précédent : 000B17; suivant : 000B19A Complete Analysis of HA and NA Genes of Influenza A Viruses
Auteurs : Weifeng Shi [Irlande (pays)] ; Fumin Lei [République populaire de Chine] ; Chaodong Zhu [République populaire de Chine] ; Fabian Sievers [Irlande (pays)] ; Desmond G. Higgins [Irlande (pays)]Source :
- PLoS ONE [ 1932-6203 ] ; 2010.
Abstract
More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.
This paper describes an analysis and complete classification of all HA and NA gene sequences available in public databases using multivariate and phylogenetic methods.
We analyzed 18975 HA sequences and divided them into 280 subgroups according to multivariate and phylogenetic analyses. Similarly, we divided 11362 NA sequences into 202 subgroups. Compared to previous analyses, this work is more detailed and comprehensive, especially for the bigger datasets. Therefore, it can be used to show the full and complex phylogenetic diversity and provides a framework for studying the molecular evolution and epidemiology of type A influenza virus. For more than 85% of type A influenza HA and NA sequences into GenBank, they are categorized in one unambiguous and unique group. Therefore, our results are a kind of genetic and phylogenetic annotation for influenza HA and NA sequences. In addition, sequences of swine influenza viruses come from 56 HA and 45 NA subgroups. Most of these subgroups also include viruses from other hosts indicating cross species transmission of the viruses between pigs and other hosts. Furthermore, the phylogenetic diversity of swine influenza viruses from Eurasia is greater than that of North American strains and both of them are becoming more diverse. Apart from viruses from human, pigs, birds and horses, viruses from other species show very low phylogenetic diversity. This might indicate that viruses have not become established in these species. Based on current evidence, there is no simple pattern of inter-hemisphere transmission of avian influenza viruses and it appears to happen sporadically. However, for H6 subtype avian influenza viruses, such transmissions might have happened very frequently and multiple and bidirectional transmission events might exist.
Url:
DOI: 10.1371/journal.pone.0014454
PubMed: 21209922
PubMed Central: 3012125
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000B18
Links to Exploration step
PMC:3012125Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A Complete Analysis of HA and NA Genes of Influenza A Viruses</title><author><name sortKey="Shi, Weifeng" sort="Shi, Weifeng" uniqKey="Shi W" first="Weifeng" last="Shi">Weifeng Shi</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland</addr-line></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin</wicri:regionArea></affiliation></author><author><name sortKey="Lei, Fumin" sort="Lei, Fumin" uniqKey="Lei F" first="Fumin" last="Lei">Fumin Lei</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Zoology, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Zoology, Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Zhu, Chaodong" sort="Zhu, Chaodong" uniqKey="Zhu C" first="Chaodong" last="Zhu">Chaodong Zhu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Zoology, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Zoology, Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Sievers, Fabian" sort="Sievers, Fabian" uniqKey="Sievers F" first="Fabian" last="Sievers">Fabian Sievers</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland</addr-line></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin</wicri:regionArea></affiliation></author><author><name sortKey="Higgins, Desmond G" sort="Higgins, Desmond G" uniqKey="Higgins D" first="Desmond G." last="Higgins">Desmond G. Higgins</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland</addr-line></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21209922</idno><idno type="pmc">3012125</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012125</idno><idno type="RBID">PMC:3012125</idno><idno type="doi">10.1371/journal.pone.0014454</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000B18</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B18</idno><idno type="wicri:Area/Pmc/Curation">000B18</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000B18</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A Complete Analysis of HA and NA Genes of Influenza A Viruses</title><author><name sortKey="Shi, Weifeng" sort="Shi, Weifeng" uniqKey="Shi W" first="Weifeng" last="Shi">Weifeng Shi</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland</addr-line></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin</wicri:regionArea></affiliation></author><author><name sortKey="Lei, Fumin" sort="Lei, Fumin" uniqKey="Lei F" first="Fumin" last="Lei">Fumin Lei</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Zoology, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Zoology, Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Zhu, Chaodong" sort="Zhu, Chaodong" uniqKey="Zhu C" first="Chaodong" last="Zhu">Chaodong Zhu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Zoology, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Zoology, Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Sievers, Fabian" sort="Sievers, Fabian" uniqKey="Sievers F" first="Fabian" last="Sievers">Fabian Sievers</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland</addr-line></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin</wicri:regionArea></affiliation></author><author><name sortKey="Higgins, Desmond G" sort="Higgins, Desmond G" uniqKey="Higgins D" first="Desmond G." last="Higgins">Desmond G. Higgins</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland</addr-line></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.</p></sec><sec><title>Methodology/Principal Findings</title><p>This paper describes an analysis and complete classification of all HA and NA gene sequences available in public databases using multivariate and phylogenetic methods.</p></sec><sec><title>Conclusions/Significance</title><p>We analyzed 18975 HA sequences and divided them into 280 subgroups according to multivariate and phylogenetic analyses. Similarly, we divided 11362 NA sequences into 202 subgroups. Compared to previous analyses, this work is more detailed and comprehensive, especially for the bigger datasets. Therefore, it can be used to show the full and complex phylogenetic diversity and provides a framework for studying the molecular evolution and epidemiology of type A influenza virus. For more than 85% of type A influenza HA and NA sequences into GenBank, they are categorized in one unambiguous and unique group. Therefore, our results are a kind of genetic and phylogenetic annotation for influenza HA and NA sequences. In addition, sequences of swine influenza viruses come from 56 HA and 45 NA subgroups. Most of these subgroups also include viruses from other hosts indicating cross species transmission of the viruses between pigs and other hosts. Furthermore, the phylogenetic diversity of swine influenza viruses from Eurasia is greater than that of North American strains and both of them are becoming more diverse. Apart from viruses from human, pigs, birds and horses, viruses from other species show very low phylogenetic diversity. This might indicate that viruses have not become established in these species. Based on current evidence, there is no simple pattern of inter-hemisphere transmission of avian influenza viruses and it appears to happen sporadically. However, for H6 subtype avian influenza viruses, such transmissions might have happened very frequently and multiple and bidirectional transmission events might exist.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name></author><author><name sortKey="Bean, Wj" uniqKey="Bean W">WJ Bean</name></author><author><name sortKey="Gorman, Ot" uniqKey="Gorman O">OT Gorman</name></author><author><name sortKey="Chambers, Tm" uniqKey="Chambers T">TM Chambers</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fouchier, Ra" uniqKey="Fouchier R">RA Fouchier</name></author><author><name sortKey="Munster, V" uniqKey="Munster V">V Munster</name></author><author><name sortKey="Wallensten, A" uniqKey="Wallensten A">A Wallensten</name></author><author><name sortKey="Bestebroer, Tm" uniqKey="Bestebroer T">TM Bestebroer</name></author><author><name sortKey="Herfst, S" uniqKey="Herfst S">S Herfst</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alexander, Dj" uniqKey="Alexander D">DJ Alexander</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, Jm" uniqKey="Chen J">JM Chen</name></author><author><name sortKey="Ma, Hc" uniqKey="Ma H">HC Ma</name></author><author><name sortKey="Chen, Jw" uniqKey="Chen J">JW Chen</name></author><author><name sortKey="Sun, Yx" uniqKey="Sun Y">YX Sun</name></author><author><name sortKey="Li, Jm" uniqKey="Li J">JM Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, Jm" uniqKey="Chen J">JM Chen</name></author><author><name sortKey="Sun, Yx" uniqKey="Sun Y">YX Sun</name></author><author><name sortKey="Chen, Jw" uniqKey="Chen J">JW Chen</name></author><author><name sortKey="Liu, S" uniqKey="Liu S">S Liu</name></author><author><name sortKey="Yu, Jm" uniqKey="Yu J">JM Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, S" uniqKey="Liu S">S Liu</name></author><author><name sortKey="Ji, K" uniqKey="Ji K">K Ji</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Tai, D" uniqKey="Tai D">D Tai</name></author><author><name sortKey="Jiang, W" uniqKey="Jiang W">W Jiang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, Hc" uniqKey="Ma H">HC Ma</name></author><author><name sortKey="Chen, Jm" uniqKey="Chen J">JM Chen</name></author><author><name sortKey="Chen, Jw" uniqKey="Chen J">JW Chen</name></author><author><name sortKey="Sun, Yx" uniqKey="Sun Y">YX Sun</name></author><author><name sortKey="Li, Jm" uniqKey="Li J">JM Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bao, Y" uniqKey="Bao Y">Y Bao</name></author><author><name sortKey="Bolotov, P" uniqKey="Bolotov P">P Bolotov</name></author><author><name sortKey="Dernovoy, D" uniqKey="Dernovoy D">D Dernovoy</name></author><author><name sortKey="Kiryutin, B" uniqKey="Kiryutin B">B Kiryutin</name></author><author><name sortKey="Zaslavsky, L" uniqKey="Zaslavsky L">L Zaslavsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ito, T" uniqKey="Ito T">T Ito</name></author><author><name sortKey="Couceiro, Jn" uniqKey="Couceiro J">JN Couceiro</name></author><author><name sortKey="Kelm, S" uniqKey="Kelm S">S Kelm</name></author><author><name sortKey="Baum, Lg" uniqKey="Baum L">LG Baum</name></author><author><name sortKey="Krauss, S" uniqKey="Krauss S">S Krauss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Suzuki, Y" uniqKey="Suzuki Y">Y Suzuki</name></author><author><name sortKey="Ito, T" uniqKey="Ito T">T Ito</name></author><author><name sortKey="Suzuki, T" uniqKey="Suzuki T">T Suzuki</name></author><author><name sortKey="Holland, Re" uniqKey="Holland R">RE Holland</name></author><author><name sortKey="Chambers, Tm" uniqKey="Chambers T">TM Chambers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shi, Wf" uniqKey="Shi W">WF Shi</name></author><author><name sortKey="Gibbs, Mj" uniqKey="Gibbs M">MJ Gibbs</name></author><author><name sortKey="Zhang, Yz" uniqKey="Zhang Y">YZ Zhang</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Zhao, Xm" uniqKey="Zhao X">XM Zhao</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Peiris, Js" uniqKey="Peiris J">JS Peiris</name></author><author><name sortKey="Poon, Ll" uniqKey="Poon L">LL Poon</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y Guan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Keawcharoen, J" uniqKey="Keawcharoen J">J Keawcharoen</name></author><author><name sortKey="Oraveerakul, K" uniqKey="Oraveerakul K">K Oraveerakul</name></author><author><name sortKey="Kuiken, T" uniqKey="Kuiken T">T Kuiken</name></author><author><name sortKey="Fouchier, Ra" uniqKey="Fouchier R">RA Fouchier</name></author><author><name sortKey="Amonsin, A" uniqKey="Amonsin A">A Amonsin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Songserm, T" uniqKey="Songserm T">T Songserm</name></author><author><name sortKey="Amonsin, A" uniqKey="Amonsin A">A Amonsin</name></author><author><name sortKey="Jam On, R" uniqKey="Jam On R">R Jam-on</name></author><author><name sortKey="Sae Heng, N" uniqKey="Sae Heng N">N Sae-Heng</name></author><author><name sortKey="Meemak, N" uniqKey="Meemak N">N Meemak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leschnik, M" uniqKey="Leschnik M">M Leschnik</name></author><author><name sortKey="Weikel, J" uniqKey="Weikel J">J Weikel</name></author><author><name sortKey="Mostl, K" uniqKey="Mostl K">K Möstl</name></author><author><name sortKey="Revilla Fernandez, S" uniqKey="Revilla Fernandez S">S Revilla-Fernández</name></author><author><name sortKey="Wodak, E" uniqKey="Wodak E">E Wodak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Songserm, T" uniqKey="Songserm T">T Songserm</name></author><author><name sortKey="Amonsin, A" uniqKey="Amonsin A">A Amonsin</name></author><author><name sortKey="Jam On, R" uniqKey="Jam On R">R Jam-on</name></author><author><name sortKey="Sae Heng, N" uniqKey="Sae Heng N">N Sae-Heng</name></author><author><name sortKey="Pariyothorn, N" uniqKey="Pariyothorn N">N Pariyothorn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qi, X" uniqKey="Qi X">X Qi</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Rider, P" uniqKey="Rider P">P Rider</name></author><author><name sortKey="Fan, W" uniqKey="Fan W">W Fan</name></author><author><name sortKey="Gu, H" uniqKey="Gu H">H Gu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, J" uniqKey="Zhou J">J Zhou</name></author><author><name sortKey="Sun, W" uniqKey="Sun W">W Sun</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Guo, J" uniqKey="Guo J">J Guo</name></author><author><name sortKey="Yin, W" uniqKey="Yin W">W Yin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krauss, S" uniqKey="Krauss S">S Krauss</name></author><author><name sortKey="Obert, Ca" uniqKey="Obert C">CA Obert</name></author><author><name sortKey="Franks, J" uniqKey="Franks J">J Franks</name></author><author><name sortKey="Walker, D" uniqKey="Walker D">D Walker</name></author><author><name sortKey="Jones, K" uniqKey="Jones K">K Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pearce, Jm" uniqKey="Pearce J">JM Pearce</name></author><author><name sortKey="Ramey, Am" uniqKey="Ramey A">AM Ramey</name></author><author><name sortKey="Ip, Hs" uniqKey="Ip H">HS Ip</name></author><author><name sortKey="Gill, Re" uniqKey="Gill R">RE Gill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Makarova, Nv" uniqKey="Makarova N">NV Makarova</name></author><author><name sortKey="Kaverin, Nv" uniqKey="Kaverin N">NV Kaverin</name></author><author><name sortKey="Krauss, S" uniqKey="Krauss S">S Krauss</name></author><author><name sortKey="Senne, D" uniqKey="Senne D">D Senne</name></author><author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hatchette, Tf" uniqKey="Hatchette T">TF Hatchette</name></author><author><name sortKey="Walker, D" uniqKey="Walker D">D Walker</name></author><author><name sortKey="Johnson, C" uniqKey="Johnson C">C Johnson</name></author><author><name sortKey="Baker, A" uniqKey="Baker A">A Baker</name></author><author><name sortKey="Pryor, Sp" uniqKey="Pryor S">SP Pryor</name></author><author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Dh" uniqKey="Lee D">DH Lee</name></author><author><name sortKey="Lee, Hj" uniqKey="Lee H">HJ Lee</name></author><author><name sortKey="Lee, Yn" uniqKey="Lee Y">YN Lee</name></author><author><name sortKey="Park, Jk" uniqKey="Park J">JK Park</name></author><author><name sortKey="Lim, Th" uniqKey="Lim T">TH Lim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olsen, B" uniqKey="Olsen B">B Olsen</name></author><author><name sortKey="Munster, Vj" uniqKey="Munster V">VJ Munster</name></author><author><name sortKey="Wallensten, A" uniqKey="Wallensten A">A Wallensten</name></author><author><name sortKey="Waldenstrom, J" uniqKey="Waldenstrom J">J Waldenstrom</name></author><author><name sortKey="Osterhaus, Adme" uniqKey="Osterhaus A">ADME Osterhaus</name></author><author><name sortKey="Fouchier, Ram" uniqKey="Fouchier R">RAM Fouchier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Normile, D" uniqKey="Normile D">D Normile</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gaidet, N" uniqKey="Gaidet N">N Gaidet</name></author><author><name sortKey="Cappelle, J" uniqKey="Cappelle J">J Cappelle</name></author><author><name sortKey="Takekawa, Jy" uniqKey="Takekawa J">JY Takekawa</name></author><author><name sortKey="Prosser, Dj" uniqKey="Prosser D">DJ Prosser</name></author><author><name sortKey="Iverson, Sa" uniqKey="Iverson S">SA Iverson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liang, L" uniqKey="Liang L">L Liang</name></author><author><name sortKey="Xu, B" uniqKey="Xu B">B Xu</name></author><author><name sortKey="Chen, Y" uniqKey="Chen Y">Y Chen</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Cao, W" uniqKey="Cao W">W Cao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Normile, D" uniqKey="Normile D">D Normile</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Feare, Cj" uniqKey="Feare C">CJ Feare</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Takekawa, Jy" uniqKey="Takekawa J">JY Takekawa</name></author><author><name sortKey="Prosser, Dj" uniqKey="Prosser D">DJ Prosser</name></author><author><name sortKey="Newman, Sh" uniqKey="Newman S">SH Newman</name></author><author><name sortKey="Muzaffar, Sb" uniqKey="Muzaffar S">SB Muzaffar</name></author><author><name sortKey="Hill, Nj" uniqKey="Hill N">NJ Hill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gower, Jc" uniqKey="Gower J">JC Gower</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Higgins, Dg" uniqKey="Higgins D">DG Higgins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kuiken, C" uniqKey="Kuiken C">C Kuiken</name></author><author><name sortKey="Hraber, P" uniqKey="Hraber P">P Hraber</name></author><author><name sortKey="Thurmond, J" uniqKey="Thurmond J">J Thurmond</name></author><author><name sortKey="Yusim, K" uniqKey="Yusim K">K Yusim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Torgerson, Ws" uniqKey="Torgerson W">WS Torgerson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, Dj" uniqKey="Smith D">DJ Smith</name></author><author><name sortKey="Lapedes, As" uniqKey="Lapedes A">AS Lapedes</name></author><author><name sortKey="De Jong, Jc" uniqKey="De Jong J">JC de Jong</name></author><author><name sortKey="Bestebroer, Tm" uniqKey="Bestebroer T">TM Bestebroer</name></author><author><name sortKey="Rimmelzwaan, Gf" uniqKey="Rimmelzwaan G">GF Rimmelzwaan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tzeng, J" uniqKey="Tzeng J">J Tzeng</name></author><author><name sortKey="Lu, Hh" uniqKey="Lu H">HH Lu</name></author><author><name sortKey="Li, Wh" uniqKey="Li W">WH Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Edgar, Rc" uniqKey="Edgar R">RC Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hall, Ta" uniqKey="Hall T">TA Hall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kimura, M" uniqKey="Kimura M">M Kimura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Felsenstein, J" uniqKey="Felsenstein J">J Felsenstein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Belongie, S" uniqKey="Belongie S">S Belongie</name></author><author><name sortKey="Fowlkes, C" uniqKey="Fowlkes C">C Fowlkes</name></author><author><name sortKey="Chung, F" uniqKey="Chung F">F Chung</name></author><author><name sortKey="Malik, J" uniqKey="Malik J">J Malik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saitou, N" uniqKey="Saitou N">N Saitou</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Swofford, Dl" uniqKey="Swofford D">DL Swofford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hasegawa, M" uniqKey="Hasegawa M">M Hasegawa</name></author><author><name sortKey="Kishino, H" uniqKey="Kishino H">H Kishino</name></author><author><name sortKey="Yano, T" uniqKey="Yano T">T Yano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guindon, S" uniqKey="Guindon S">S Guindon</name></author><author><name sortKey="Gascuel, O" uniqKey="Gascuel O">O Gascuel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Z" uniqKey="Yang Z">Z Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name></author><author><name sortKey="Richter, Dc" uniqKey="Richter D">DC Richter</name></author><author><name sortKey="Rausch, C" uniqKey="Rausch C">C Rausch</name></author><author><name sortKey="Dezulian, T" uniqKey="Dezulian T">T Dezulian</name></author><author><name sortKey="Franz, M" uniqKey="Franz M">M Franz</name></author><author><name sortKey="Rupp, R" uniqKey="Rupp R">R Rupp</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pensaert, M" uniqKey="Pensaert M">M Pensaert</name></author><author><name sortKey="Ottis, K" uniqKey="Ottis K">K Ottis</name></author><author><name sortKey="Vandeputte, J" uniqKey="Vandeputte J">J Vandeputte</name></author><author><name sortKey="Kaplan, Mm" uniqKey="Kaplan M">MM Kaplan</name></author><author><name sortKey="Bachmann, Pa" uniqKey="Bachmann P">PA Bachmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Scholtissek, C" uniqKey="Scholtissek C">C Scholtissek</name></author><author><name sortKey="Burger, H" uniqKey="Burger H">H Burger</name></author><author><name sortKey="Bachmann, Pa" uniqKey="Bachmann P">PA Bachmann</name></author><author><name sortKey="Hannoun, C" uniqKey="Hannoun C">C Hannoun</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, Gj" uniqKey="Smith G">GJ Smith</name></author><author><name sortKey="Bahl, J" uniqKey="Bahl J">J Bahl</name></author><author><name sortKey="Vijaykrishna, D" uniqKey="Vijaykrishna D">D Vijaykrishna</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Poon, Ll" uniqKey="Poon L">LL Poon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Crawford, Pc" uniqKey="Crawford P">PC Crawford</name></author><author><name sortKey="Dubovi, Ej" uniqKey="Dubovi E">EJ Dubovi</name></author><author><name sortKey="Castleman, Wl" uniqKey="Castleman W">WL Castleman</name></author><author><name sortKey="Stephenson, I" uniqKey="Stephenson I">I Stephenson</name></author><author><name sortKey="Gibbs, Ep" uniqKey="Gibbs E">EP Gibbs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gagnon, Ca" uniqKey="Gagnon C">CA Gagnon</name></author><author><name sortKey="Spearman, G" uniqKey="Spearman G">G Spearman</name></author><author><name sortKey="Hamel, A" uniqKey="Hamel A">A Hamel</name></author><author><name sortKey="Godson, Dl" uniqKey="Godson D">DL Godson</name></author><author><name sortKey="Fortin, A" uniqKey="Fortin A">A Fortin</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Belser, Ja" uniqKey="Belser J">JA Belser</name></author><author><name sortKey="Bridges, Cb" uniqKey="Bridges C">CB Bridges</name></author><author><name sortKey="Katz, Jm" uniqKey="Katz J">JM Katz</name></author><author><name sortKey="Tumpey, Tm" uniqKey="Tumpey T">TM Tumpey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koehler, Av" uniqKey="Koehler A">AV Koehler</name></author><author><name sortKey="Pearce, Jm" uniqKey="Pearce J">JM Pearce</name></author><author><name sortKey="Flint, Pl" uniqKey="Flint P">PL Flint</name></author><author><name sortKey="Franson, Jc" uniqKey="Franson J">JC Franson</name></author><author><name sortKey="Ip, Hs" uniqKey="Ip H">HS Ip</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, Nn" uniqKey="Zhou N">NN Zhou</name></author><author><name sortKey="Shortridge, Kf" uniqKey="Shortridge K">KF Shortridge</name></author><author><name sortKey="Claas, Ec" uniqKey="Claas E">EC Claas</name></author><author><name sortKey="Krauss, Sl" uniqKey="Krauss S">SL Krauss</name></author><author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cheng, Mc" uniqKey="Cheng M">MC Cheng</name></author><author><name sortKey="Lee, Ms" uniqKey="Lee M">MS Lee</name></author><author><name sortKey="Ho, Yh" uniqKey="Ho Y">YH Ho</name></author><author><name sortKey="Chyi, Wl" uniqKey="Chyi W">WL Chyi</name></author><author><name sortKey="Wang, Ch" uniqKey="Wang C">CH Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cheng, Mc" uniqKey="Cheng M">MC Cheng</name></author><author><name sortKey="Soda, K" uniqKey="Soda K">K Soda</name></author><author><name sortKey="Lee, Ms" uniqKey="Lee M">MS Lee</name></author><author><name sortKey="Lee, Sh" uniqKey="Lee S">SH Lee</name></author><author><name sortKey="Sakoda, Y" uniqKey="Sakoda Y">Y Sakoda</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Okamatsu, M" uniqKey="Okamatsu M">M Okamatsu</name></author><author><name sortKey="Saito, T" uniqKey="Saito T">T Saito</name></author><author><name sortKey="Yamamoto, Y" uniqKey="Yamamoto Y">Y Yamamoto</name></author><author><name sortKey="Mase, M" uniqKey="Mase M">M Mase</name></author><author><name sortKey="Tsuduku, S" uniqKey="Tsuduku S">S Tsuduku</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, C" uniqKey="Li C">C Li</name></author><author><name sortKey="Yu, K" uniqKey="Yu K">K Yu</name></author><author><name sortKey="Tian, G" uniqKey="Tian G">G Tian</name></author><author><name sortKey="Yu, D" uniqKey="Yu D">D Yu</name></author><author><name sortKey="Liu, L" uniqKey="Liu L">L Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pereda, Aj" uniqKey="Pereda A">AJ Pereda</name></author><author><name sortKey="Uhart, M" uniqKey="Uhart M">M Uhart</name></author><author><name sortKey="Perez, Aa" uniqKey="Perez A">AA Perez</name></author><author><name sortKey="Zaccagnini, Me" uniqKey="Zaccagnini M">ME Zaccagnini</name></author><author><name sortKey="La Sala, L" uniqKey="La Sala L">L La Sala</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kida, H" uniqKey="Kida H">H Kida</name></author><author><name sortKey="Ito, T" uniqKey="Ito T">T Ito</name></author><author><name sortKey="Yasuda, J" uniqKey="Yasuda J">J Yasuda</name></author><author><name sortKey="Shimizu, Y" uniqKey="Shimizu Y">Y Shimizu</name></author><author><name sortKey="Itakura, C" uniqKey="Itakura C">C Itakura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, W" uniqKey="Ma W">W Ma</name></author><author><name sortKey="Lager, Km" uniqKey="Lager K">KM Lager</name></author><author><name sortKey="Vincent, Al" uniqKey="Vincent A">AL Vincent</name></author><author><name sortKey="Janke, Bh" uniqKey="Janke B">BH Janke</name></author><author><name sortKey="Gramer, Mr" uniqKey="Gramer M">MR Gramer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Scholtissek, C" uniqKey="Scholtissek C">C Scholtissek</name></author><author><name sortKey="Burgerh" uniqKey="Burgerh">BurgerH</name></author><author><name sortKey="Kistner, O" uniqKey="Kistner O">O Kistner</name></author><author><name sortKey="Shortridgekf" uniqKey="Shortridgekf">ShortridgeKF</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daly, Jm" uniqKey="Daly J">JM Daly</name></author><author><name sortKey="Macrae, S" uniqKey="Macrae S">S MacRae</name></author><author><name sortKey="Newton, Jr" uniqKey="Newton J">JR Newton</name></author><author><name sortKey="Wattrang, E" uniqKey="Wattrang E">E Wattrang</name></author><author><name sortKey="Elton, Dm" uniqKey="Elton D">DM Elton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thanawongnuwech, R" uniqKey="Thanawongnuwech R">R Thanawongnuwech</name></author><author><name sortKey="Amonsin, A" uniqKey="Amonsin A">A Amonsin</name></author><author><name sortKey="Tantilertcharoen, R" uniqKey="Tantilertcharoen R">R Tantilertcharoen</name></author><author><name sortKey="Damrongwatanapokin, S" uniqKey="Damrongwatanapokin S">S Damrongwatanapokin</name></author><author><name sortKey="Theamboonlers, A" uniqKey="Theamboonlers A">A Theamboonlers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peterson, At" uniqKey="Peterson A">AT Peterson</name></author><author><name sortKey="Benz, Bw" uniqKey="Benz B">BW Benz</name></author><author><name sortKey="Papes, M" uniqKey="Papes M">M Papes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pearce, Jm" uniqKey="Pearce J">JM Pearce</name></author><author><name sortKey="Ramey, Am" uniqKey="Ramey A">AM Ramey</name></author><author><name sortKey="Flint, Pl" uniqKey="Flint P">PL Flint</name></author><author><name sortKey="Koehler, Av" uniqKey="Koehler A">AV Koehler</name></author><author><name sortKey="Fleskes, Jp" uniqKey="Fleskes J">JP Fleskes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brown, Jd" uniqKey="Brown J">JD Brown</name></author><author><name sortKey="Stallknecht, De" uniqKey="Stallknecht D">DE Stallknecht</name></author><author><name sortKey="Swayne, De" uniqKey="Swayne D">DE Swayne</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Keawcharoen, J" uniqKey="Keawcharoen J">J Keawcharoen</name></author><author><name sortKey="Van Riel, D" uniqKey="Van Riel D">D van Riel</name></author><author><name sortKey="Van Amerongen, G" uniqKey="Van Amerongen G">G van Amerongen</name></author><author><name sortKey="Bestebroer, T" uniqKey="Bestebroer T">T Bestebroer</name></author><author><name sortKey="Beyer, We" uniqKey="Beyer W">WE Beyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Procter, Jb" uniqKey="Procter J">JB Procter</name></author><author><name sortKey="Thompson, J" uniqKey="Thompson J">J Thompson</name></author><author><name sortKey="Letunic, I" uniqKey="Letunic I">I Letunic</name></author><author><name sortKey="Creevey, C" uniqKey="Creevey C">C Creevey</name></author><author><name sortKey="Jossinet, F" uniqKey="Jossinet F">F Jossinet</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21209922</article-id><article-id pub-id-type="pmc">3012125</article-id><article-id pub-id-type="publisher-id">10-PONE-RA-20607R2</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0014454</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Evolutionary Biology/Microbial Evolution and Genomics</subject><subject>Microbiology/Microbial Evolution and Genomics</subject><subject>Virology/Emerging Viral Diseases</subject><subject>Public Health and Epidemiology/Epidemiology</subject><subject>Public Health and Epidemiology/Infectious Diseases</subject></subj-group></article-categories><title-group><article-title>A Complete Analysis of HA and NA Genes of Influenza A Viruses</article-title><alt-title alt-title-type="running-head">Complete Analysis of Influenza</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Shi</surname><given-names>Weifeng</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lei</surname><given-names>Fumin</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhu</surname><given-names>Chaodong</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sievers</surname><given-names>Fabian</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Higgins</surname><given-names>Desmond G.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Institute of Zoology, Chinese Academy of Sciences, Beijing, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Brown</surname><given-names>Justin</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">University of Georgia, United States of America</aff><author-notes><corresp id="cor1">* E-mail: <email>weifeng.shi@ucd.ie</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: WS FL CZ DGH. Performed the experiments: WS CZ. Analyzed the data: WS FL. Wrote the paper: WS FS DGH.</p></fn></author-notes><pub-date pub-type="collection"><year>2010</year></pub-date><pub-date pub-type="epub"><day>29</day><month>12</month><year>2010</year></pub-date><volume>5</volume><issue>12</issue><elocation-id>e14454</elocation-id><history><date date-type="received"><day>29</day><month>6</month><year>2010</year></date><date date-type="accepted"><day>29</day><month>11</month><year>2010</year></date></history><permissions><copyright-statement>Shi et al.</copyright-statement><copyright-year>2010</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p></license></permissions><abstract><sec><title>Background</title><p>More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.</p></sec><sec><title>Methodology/Principal Findings</title><p>This paper describes an analysis and complete classification of all HA and NA gene sequences available in public databases using multivariate and phylogenetic methods.</p></sec><sec><title>Conclusions/Significance</title><p>We analyzed 18975 HA sequences and divided them into 280 subgroups according to multivariate and phylogenetic analyses. Similarly, we divided 11362 NA sequences into 202 subgroups. Compared to previous analyses, this work is more detailed and comprehensive, especially for the bigger datasets. Therefore, it can be used to show the full and complex phylogenetic diversity and provides a framework for studying the molecular evolution and epidemiology of type A influenza virus. For more than 85% of type A influenza HA and NA sequences into GenBank, they are categorized in one unambiguous and unique group. Therefore, our results are a kind of genetic and phylogenetic annotation for influenza HA and NA sequences. In addition, sequences of swine influenza viruses come from 56 HA and 45 NA subgroups. Most of these subgroups also include viruses from other hosts indicating cross species transmission of the viruses between pigs and other hosts. Furthermore, the phylogenetic diversity of swine influenza viruses from Eurasia is greater than that of North American strains and both of them are becoming more diverse. Apart from viruses from human, pigs, birds and horses, viruses from other species show very low phylogenetic diversity. This might indicate that viruses have not become established in these species. Based on current evidence, there is no simple pattern of inter-hemisphere transmission of avian influenza viruses and it appears to happen sporadically. However, for H6 subtype avian influenza viruses, such transmissions might have happened very frequently and multiple and bidirectional transmission events might exist.</p></sec></abstract><counts><page-count count="15"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/H2N2V1/Data/Pmc/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000B18 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 000B18 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= H2N2V1
|flux= Pmc
|étape= Curation
|type= RBID
|clé= PMC:3012125
|texte= A Complete Analysis of HA and NA Genes of Influenza A Viruses
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:21209922" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a H2N2V1
| This area was generated with Dilib version V0.6.33. |  |