Panorama Phylogenetic Diversity and Distribution of Type A Influenza Virus
Identifieur interne : 000A87 ( Pmc/Curation ); précédent : 000A86; suivant : 000A88Panorama Phylogenetic Diversity and Distribution of Type A Influenza Virus
Auteurs : Shuo Liu [République populaire de Chine] ; Kang Ji [République populaire de Chine] ; Jiming Chen [République populaire de Chine] ; Di Tai [République populaire de Chine] ; Wenming Jiang [République populaire de Chine] ; Guangyu Hou [République populaire de Chine] ; Jie Chen [République populaire de Chine] ; Jinping Li [République populaire de Chine] ; Baoxu Huang [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2009.
Abstract
Type A influenza virus is one of important pathogens of various animals, including humans, pigs, horses, marine mammals and birds. Currently, the viral type has been classified into 16 hemagglutinin and 9 neuraminidase subtypes, but the phylogenetic diversity and distribution within the viral type largely remain unclear from the whole view.
The panorama phylogenetic trees of influenza A viruses were calculated with representative sequences selected from approximately 23000 candidates available in GenBank using web servers in NCBI and the software MEGA 4.0. Lineages and sublineages were classified according to genetic distances, topology of the phylogenetic trees and distributions of the viruses in hosts, regions and time.
Here, two panorama phylogenetic trees of type A influenza virus covering all the 16 hemagglutinin subtypes and 9 neuraminidase subtypes, respectively, were generated. The trees provided us whole views and some novel information to recognize influenza A viruses including that some subtypes of avian influenza viruses are more complicated than Eurasian and North American lineages as we thought in the past. They also provide us a framework to generalize the history and explore the future of the viral circulation and evolution in different kinds of hosts. In addition, a simple and comprehensive nomenclature system for the dozens of lineages and sublineages identified within the viral type was proposed, which if universally accepted, will facilitate communications on the viral evolution, ecology and epidemiology.
Url:
DOI: 10.1371/journal.pone.0005022
PubMed: 19325912
PubMed Central: 2658884
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Type A influenza virus is one of important pathogens of various animals, including humans, pigs, horses, marine mammals and birds. Currently, the viral type has been classified into 16 hemagglutinin and 9 neuraminidase subtypes, but the phylogenetic diversity and distribution within the viral type largely remain unclear from the whole view.</p>
</sec>
<sec><title>Methodology/Principal Findings</title>
<p>The panorama phylogenetic trees of influenza A viruses were calculated with representative sequences selected from approximately 23000 candidates available in GenBank using web servers in NCBI and the software MEGA 4.0. Lineages and sublineages were classified according to genetic distances, topology of the phylogenetic trees and distributions of the viruses in hosts, regions and time.</p>
</sec>
<sec><title>Conclusions/Significance</title>
<p>Here, two panorama phylogenetic trees of type A influenza virus covering all the 16 hemagglutinin subtypes and 9 neuraminidase subtypes, respectively, were generated. The trees provided us whole views and some novel information to recognize influenza A viruses including that some subtypes of avian influenza viruses are more complicated than Eurasian and North American lineages as we thought in the past. They also provide us a framework to generalize the history and explore the future of the viral circulation and evolution in different kinds of hosts. In addition, a simple and comprehensive nomenclature system for the dozens of lineages and sublineages identified within the viral type was proposed, which if universally accepted, will facilitate communications on the viral evolution, ecology and epidemiology.</p>
</sec>
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</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">19325912</article-id>
<article-id pub-id-type="pmc">2658884</article-id>
<article-id pub-id-type="publisher-id">08-PONE-RA-06366R1</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0005022</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/Bioinformatics</subject>
<subject>Virology/Virus Evolution and Symbiosis</subject>
<subject>Infectious Diseases/Viral Infections</subject>
</subj-group>
</article-categories>
<title-group><article-title>Panorama Phylogenetic Diversity and Distribution of Type A Influenza Virus</article-title>
<alt-title alt-title-type="running-head">Panorama of Influenza A Virus</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Liu</surname>
<given-names>Shuo</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author" equal-contrib="yes"><name><surname>Ji</surname>
<given-names>Kang</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Jiming</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>Tai</surname>
<given-names>Di</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jiang</surname>
<given-names>Wenming</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hou</surname>
<given-names>Guangyu</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Jie</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Jinping</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Huang</surname>
<given-names>Baoxu</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 Laboratory of Animal Epidemiological Surveillance, China Animal Health & Epidemiology Center, Qingdao, China</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>College of Veterinary Sciences, University of Northeastern China, Harbin, China</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Field</surname>
<given-names>Dawn</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">NERC Centre for Ecology and Hydrology, United Kingdom</aff>
<author-notes><corresp id="cor1">* E-mail: <email>jmchen66@yahoo.cn</email>
</corresp>
<fn fn-type="con"><p>Conceived and designed the experiments: JC. Performed the experiments: SL KJ JC DT. Analyzed the data: SL KJ JC DT WJ GH JC JL BH. Wrote the paper: JC.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2009</year>
</pub-date>
<pub-date pub-type="epub"><day>27</day>
<month>3</month>
<year>2009</year>
</pub-date>
<volume>4</volume>
<issue>3</issue>
<elocation-id>e5022</elocation-id>
<history><date date-type="received"><day>11</day>
<month>9</month>
<year>2008</year>
</date>
<date date-type="accepted"><day>18</day>
<month>2</month>
<year>2009</year>
</date>
</history>
<permissions><copyright-statement>Liu et al.</copyright-statement>
<copyright-year>2009</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>Type A influenza virus is one of important pathogens of various animals, including humans, pigs, horses, marine mammals and birds. Currently, the viral type has been classified into 16 hemagglutinin and 9 neuraminidase subtypes, but the phylogenetic diversity and distribution within the viral type largely remain unclear from the whole view.</p>
</sec>
<sec><title>Methodology/Principal Findings</title>
<p>The panorama phylogenetic trees of influenza A viruses were calculated with representative sequences selected from approximately 23000 candidates available in GenBank using web servers in NCBI and the software MEGA 4.0. Lineages and sublineages were classified according to genetic distances, topology of the phylogenetic trees and distributions of the viruses in hosts, regions and time.</p>
</sec>
<sec><title>Conclusions/Significance</title>
<p>Here, two panorama phylogenetic trees of type A influenza virus covering all the 16 hemagglutinin subtypes and 9 neuraminidase subtypes, respectively, were generated. The trees provided us whole views and some novel information to recognize influenza A viruses including that some subtypes of avian influenza viruses are more complicated than Eurasian and North American lineages as we thought in the past. They also provide us a framework to generalize the history and explore the future of the viral circulation and evolution in different kinds of hosts. In addition, a simple and comprehensive nomenclature system for the dozens of lineages and sublineages identified within the viral type was proposed, which if universally accepted, will facilitate communications on the viral evolution, ecology and epidemiology.</p>
</sec>
</abstract>
<counts><page-count count="20"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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