Panorama phylogenetic diversity and distribution of type A influenza viruses based on their six internal gene sequences
Identifieur interne : 000410 ( Ncbi/Merge ); précédent : 000409; suivant : 000411Panorama phylogenetic diversity and distribution of type A influenza viruses based on their six internal gene sequences
Auteurs : Ji-Ming Chen [République populaire de Chine] ; Ying-Xue Sun [République populaire de Chine] ; Ji-Wang Chen [États-Unis] ; Shuo Liu [République populaire de Chine] ; Jian-Min Yu [République populaire de Chine] ; Chao-Jian Shen [République populaire de Chine] ; Xiang-Dong Sun [République populaire de Chine] ; Dong Peng [République populaire de Chine]Source :
- Virology Journal [ 1743-422X ] ; 2009.
Abstract
Type A influenza viruses are important pathogens of humans, birds, pigs, horses and some marine mammals. The viruses have evolved into multiple complicated subtypes, lineages and sublineages. Recently, the phylogenetic diversity of type A influenza viruses from a whole view has been described based on the viral external HA and NA gene sequences, but remains unclear in terms of their six internal genes (PB2, PB1, PA, NP, MP and NS).
In this report, 2798 representative sequences of the six viral internal genes were selected from GenBank using the web servers in NCBI Influenza Virus Resource. Then, the phylogenetic relationships among the representative sequences were calculated using the software tools MEGA 4.1 and RAxML 7.0.4. Lineages and sublineages were classified mainly according to topology of the phylogenetic trees and distribution of the viruses in hosts, regions and time.
The panorama phylogenetic trees of the six internal genes of type A influenza viruses were constructed. Lineages and sublineages within the type based on the six internal genes were classified and designated by a tentative universal numerical nomenclature system. The diversity of influenza viruses circulating in different regions, periods, and hosts based on the panorama trees was analyzed.
This study presents the first whole views to the phylogenetic diversity and distribution of type A influenza viruses based on their six internal genes. It also proposes a tentative universal nomenclature system for the viral lineages and sublineages. These can be a candidate framework to generalize the history and explore the future of the viruses, and will facilitate future scientific communications on the phylogenetic diversity and evolution of the viruses. In addition, it provides a novel phylogenetic view (i.e. the whole view) to recognize the viruses including the origin of the pandemic A(H1N1) influenza viruses.
Url:
DOI: 10.1186/1743-422X-6-137
PubMed: 19737421
PubMed Central: 2746212
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Type A influenza viruses are important pathogens of humans, birds, pigs, horses and some marine mammals. The viruses have evolved into multiple complicated subtypes, lineages and sublineages. Recently, the phylogenetic diversity of type A influenza viruses from a whole view has been described based on the viral external HA and NA gene sequences, but remains unclear in terms of their six internal genes (PB2, PB1, PA, NP, MP and NS).</p>
</sec>
<sec sec-type="methods"><title>Methods</title>
<p>In this report, 2798 representative sequences of the six viral internal genes were selected from GenBank using the web servers in NCBI Influenza Virus Resource. Then, the phylogenetic relationships among the representative sequences were calculated using the software tools MEGA 4.1 and RAxML 7.0.4. Lineages and sublineages were classified mainly according to topology of the phylogenetic trees and distribution of the viruses in hosts, regions and time.</p>
</sec>
<sec><title>Results</title>
<p>The panorama phylogenetic trees of the six internal genes of type A influenza viruses were constructed. Lineages and sublineages within the type based on the six internal genes were classified and designated by a tentative universal numerical nomenclature system. The diversity of influenza viruses circulating in different regions, periods, and hosts based on the panorama trees was analyzed.</p>
</sec>
<sec><title>Conclusion</title>
<p>This study presents the first whole views to the phylogenetic diversity and distribution of type A influenza viruses based on their six internal genes. It also proposes a tentative universal nomenclature system for the viral lineages and sublineages. These can be a candidate framework to generalize the history and explore the future of the viruses, and will facilitate future scientific communications on the phylogenetic diversity and evolution of the viruses. In addition, it provides a novel phylogenetic view (i.e. the whole view) to recognize the viruses including the origin of the pandemic A(H1N1) influenza viruses.</p>
</sec>
</div>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Virol J</journal-id>
<journal-title>Virology Journal</journal-title>
<issn pub-type="epub">1743-422X</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">19737421</article-id>
<article-id pub-id-type="pmc">2746212</article-id>
<article-id pub-id-type="publisher-id">1743-422X-6-137</article-id>
<article-id pub-id-type="doi">10.1186/1743-422X-6-137</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research</subject>
</subj-group>
</article-categories>
<title-group><article-title>Panorama phylogenetic diversity and distribution of type A influenza viruses based on their six internal gene sequences</article-title>
</title-group>
<contrib-group><contrib id="A1" corresp="yes" contrib-type="author"><name><surname>Chen</surname>
<given-names>Ji-Ming</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>jmchen66@yahoo.cn</email>
</contrib>
<contrib id="A2" contrib-type="author"><name><surname>Sun</surname>
<given-names>Ying-Xue</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>sunyingx2004@sina.com</email>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Chen</surname>
<given-names>Ji-Wang</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>jiwang@northwestern.edu</email>
</contrib>
<contrib id="A4" contrib-type="author"><name><surname>Liu</surname>
<given-names>Shuo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>liushuo_z@hotmail.com</email>
</contrib>
<contrib id="A5" contrib-type="author"><name><surname>Yu</surname>
<given-names>Jian-Min</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>yu_jianmin16@live.cn</email>
</contrib>
<contrib id="A6" contrib-type="author"><name><surname>Shen</surname>
<given-names>Chao-Jian</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>shenchaojianyy@hotmail.com</email>
</contrib>
<contrib id="A7" contrib-type="author"><name><surname>Sun</surname>
<given-names>Xiang-Dong</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>sun_xiangdong@hotmail.com</email>
</contrib>
<contrib id="A8" contrib-type="author"><name><surname>Peng</surname>
<given-names>Dong</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>hobohero@hotmail.com</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
The Laboratory of Animal Epidemiological Surveillance, China Animal Health & Epidemiology Center, Qingdao, PR China</aff>
<aff id="I2"><label>2</label>
The Feinberg School of Medicine, Northwestern University, Chicago, USA</aff>
<pub-date pub-type="collection"><year>2009</year>
</pub-date>
<pub-date pub-type="epub"><day>8</day>
<month>9</month>
<year>2009</year>
</pub-date>
<volume>6</volume>
<fpage>137</fpage>
<lpage>137</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.virologyj.com/content/6/1/137"></ext-link>
<history><date date-type="received"><day>6</day>
<month>8</month>
<year>2009</year>
</date>
<date date-type="accepted"><day>8</day>
<month>9</month>
<year>2009</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2009 Chen et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2009</copyright-year>
<copyright-holder>Chen et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p>
<pmc-comment>
Chen
Ji-Ming
jmchen66@yahoo.cn
Panorama phylogenetic diversity and distribution of type A influenza viruses based on their six internal gene sequences
2009 Virology Journal 6(1): 137-. (2009) 1743-422X(2009)6:1<137> urn:ISSN:1743-422X </pmc-comment>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>Type A influenza viruses are important pathogens of humans, birds, pigs, horses and some marine mammals. The viruses have evolved into multiple complicated subtypes, lineages and sublineages. Recently, the phylogenetic diversity of type A influenza viruses from a whole view has been described based on the viral external HA and NA gene sequences, but remains unclear in terms of their six internal genes (PB2, PB1, PA, NP, MP and NS).</p>
</sec>
<sec sec-type="methods"><title>Methods</title>
<p>In this report, 2798 representative sequences of the six viral internal genes were selected from GenBank using the web servers in NCBI Influenza Virus Resource. Then, the phylogenetic relationships among the representative sequences were calculated using the software tools MEGA 4.1 and RAxML 7.0.4. Lineages and sublineages were classified mainly according to topology of the phylogenetic trees and distribution of the viruses in hosts, regions and time.</p>
</sec>
<sec><title>Results</title>
<p>The panorama phylogenetic trees of the six internal genes of type A influenza viruses were constructed. Lineages and sublineages within the type based on the six internal genes were classified and designated by a tentative universal numerical nomenclature system. The diversity of influenza viruses circulating in different regions, periods, and hosts based on the panorama trees was analyzed.</p>
</sec>
<sec><title>Conclusion</title>
<p>This study presents the first whole views to the phylogenetic diversity and distribution of type A influenza viruses based on their six internal genes. It also proposes a tentative universal nomenclature system for the viral lineages and sublineages. These can be a candidate framework to generalize the history and explore the future of the viruses, and will facilitate future scientific communications on the phylogenetic diversity and evolution of the viruses. In addition, it provides a novel phylogenetic view (i.e. the whole view) to recognize the viruses including the origin of the pandemic A(H1N1) influenza viruses.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>République populaire de Chine</li>
<li>États-Unis</li>
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<name sortKey="Yu, Jian Min" sort="Yu, Jian Min" uniqKey="Yu J" first="Jian-Min" last="Yu">Jian-Min Yu</name>
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