A Complete Analysis of HA and NA Genes of Influenza A Viruses
Identifieur interne : 000F09 ( Main/Exploration ); précédent : 000F08; suivant : 000F10A 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
Affiliations:
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Higgins</name><affiliation wicri:level="4"><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><orgName type="university">University College Dublin</orgName><placeName><settlement type="city">Dublin</settlement><region type="région" nuts="2">Leinster</region></placeName></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" 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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><affiliations><list><country><li>Irlande (pays)</li><li>République populaire de Chine</li></country><region><li>Leinster</li></region><settlement><li>Dublin</li><li>Pékin</li></settlement><orgName><li>University College Dublin</li></orgName></list><tree><country name="Irlande (pays)"><region name="Leinster"><name sortKey="Shi, Weifeng" sort="Shi, Weifeng" uniqKey="Shi W" first="Weifeng" last="Shi">Weifeng Shi</name></region><name sortKey="Higgins, Desmond G" sort="Higgins, Desmond G" uniqKey="Higgins D" first="Desmond G." last="Higgins">Desmond G. Higgins</name><name sortKey="Sievers, Fabian" sort="Sievers, Fabian" uniqKey="Sievers F" first="Fabian" last="Sievers">Fabian Sievers</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Lei, Fumin" sort="Lei, Fumin" uniqKey="Lei F" first="Fumin" last="Lei">Fumin Lei</name></noRegion><name sortKey="Zhu, Chaodong" sort="Zhu, Chaodong" uniqKey="Zhu C" first="Chaodong" last="Zhu">Chaodong Zhu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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