Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus
Identifieur interne : 000101 ( Pmc/Curation ); précédent : 000100; suivant : 000102Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus
Auteurs : Mi Liu [République populaire de Chine] ; Xiang Zhao [République populaire de Chine] ; Sha Hua [République populaire de Chine] ; Xiangjun Du [États-Unis] ; Yousong Peng [République populaire de Chine] ; Xiyan Li [République populaire de Chine] ; Yu Lan [République populaire de Chine] ; Dayan Wang [République populaire de Chine] ; Aiping Wu [République populaire de Chine] ; Yuelong Shu [République populaire de Chine] ; Taijiao Jiang [République populaire de Chine]Source :
- Scientific Reports [ 2045-2322 ] ; 2015.
Abstract
The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution of human influenza A (H1N1) virus is extremely important for its effective surveillance and prevention. Through development of antigenicity inference method for human influenza A (H1N1), named PREDAC-H1, we systematically mapped the antigenic patterns and evolution of the human influenza A (H1N1) virus. Eight dominant antigenic clusters have been inferred for seasonal H1N1 viruses since 1977, which demonstrated sequential replacements over time with a similar pattern in Asia, Europe and North America. Among them, six clusters emerged first in Asia. As for China, three of the eight antigenic clusters were detected in South China earlier than in North China, indicating the leading role of South China in H1N1 transmission. The comprehensive view of the antigenic evolution of human influenza A (H1N1) virus can help formulate better strategy for its prevention and control.
Url:
DOI: 10.1038/srep14171
PubMed: 26412348
PubMed Central: 4585932
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Suzhou Institute of Systems Medicine</institution>, Suzhou, Jiangsu 215123,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences</institution>, Beijing 100101,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zhao, Xiang" sort="Zhao, Xiang" uniqKey="Zhao X" first="Xiang" last="Zhao">Xiang Zhao</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>National Institute for Viral Disease Control and Prevention, China CDC</institution>, Beijing 102206,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Hua, Sha" sort="Hua, Sha" uniqKey="Hua S" first="Sha" last="Hua">Sha Hua</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences</institution>, Beijing 100101,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a4"><institution>University of the Chinese Academy of Sciences</institution>, Beijing 100049,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Du, Xiangjun" sort="Du, Xiangjun" uniqKey="Du X" first="Xiangjun" last="Du">Xiangjun Du</name><affiliation wicri:level="2"><nlm:aff id="a5"><institution>Department of Ecology and Evolution, University of Chicago</institution>, Chicago, IL 60637</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Illinois</region></placeName><wicri:cityArea>, Chicago</wicri:cityArea></affiliation></author><author><name sortKey="Peng, Yousong" sort="Peng, Yousong" uniqKey="Peng Y" first="Yousong" last="Peng">Yousong Peng</name><affiliation wicri:level="1"><nlm:aff id="a6"><institution>College of Information Science and Engineering, Hunan University</institution>, Changsha 410082,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Li, Xiyan" sort="Li, Xiyan" uniqKey="Li X" first="Xiyan" last="Li">Xiyan Li</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>National Institute for Viral Disease Control and Prevention, China CDC</institution>, Beijing 102206,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Lan, Yu" sort="Lan, Yu" uniqKey="Lan Y" first="Yu" last="Lan">Yu Lan</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>National Institute for Viral Disease Control and Prevention, China CDC</institution>, Beijing 102206,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Dayan" sort="Wang, Dayan" uniqKey="Wang D" first="Dayan" last="Wang">Dayan Wang</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>National Institute for Viral Disease Control and Prevention, China CDC</institution>, Beijing 102206,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wu, Aiping" sort="Wu, Aiping" uniqKey="Wu A" first="Aiping" last="Wu">Aiping Wu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005; Suzhou Institute of Systems Medicine</institution>, Suzhou, Jiangsu 215123,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences</institution>, Beijing 100101,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Shu, Yuelong" sort="Shu, Yuelong" uniqKey="Shu Y" first="Yuelong" last="Shu">Yuelong Shu</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>National Institute for Viral Disease Control and Prevention, China CDC</institution>, Beijing 102206,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Jiang, Taijiao" sort="Jiang, Taijiao" uniqKey="Jiang T" first="Taijiao" last="Jiang">Taijiao Jiang</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005; Suzhou Institute of Systems Medicine</institution>, Suzhou, Jiangsu 215123,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences</institution>, Beijing 100101,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution of human influenza A (H1N1) virus is extremely important for its effective surveillance and prevention. Through development of antigenicity inference method for human influenza A (H1N1), named PREDAC-H1, we systematically mapped the antigenic patterns and evolution of the human influenza A (H1N1) virus. Eight dominant antigenic clusters have been inferred for seasonal H1N1 viruses since 1977, which demonstrated sequential replacements over time with a similar pattern in Asia, Europe and North America. Among them, six clusters emerged first in Asia. As for China, three of the eight antigenic clusters were detected in South China earlier than in North China, indicating the leading role of South China in H1N1 transmission. The comprehensive view of the antigenic evolution of human influenza A (H1N1) virus can help formulate better strategy for its prevention and control.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Frost, W H" uniqKey="Frost W">W. H. Frost</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burnet, F" uniqKey="Burnet F">F. Burnet</name></author><author><name sortKey="Clark, E" uniqKey="Clark E">E. Clark</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Johnson, N P A S" uniqKey="Johnson N">N. P. A. S. Johnson</name></author><author><name sortKey="Mueller, J" uniqKey="Mueller J">J. Mueller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kilbourne, E D" uniqKey="Kilbourne E">E. D. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Sci Rep</journal-id><journal-id journal-id-type="iso-abbrev">Sci Rep</journal-id><journal-title-group><journal-title>Scientific Reports</journal-title></journal-title-group><issn pub-type="epub">2045-2322</issn><publisher><publisher-name>Nature Publishing Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26412348</article-id><article-id pub-id-type="pmc">4585932</article-id><article-id pub-id-type="pii">srep14171</article-id><article-id pub-id-type="doi">10.1038/srep14171</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Mi</given-names></name><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Zhao</surname><given-names>Xiang</given-names></name><xref ref-type="aff" rid="a3">3</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Hua</surname><given-names>Sha</given-names></name><xref ref-type="aff" rid="a2">2</xref><xref ref-type="aff" rid="a4">4</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Du</surname><given-names>Xiangjun</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Peng</surname><given-names>Yousong</given-names></name><xref ref-type="aff" rid="a6">6</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Xiyan</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Lan</surname><given-names>Yu</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Dayan</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Aiping</given-names></name><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Shu</surname><given-names>Yuelong</given-names></name><xref ref-type="corresp" rid="c2">b</xref><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Jiang</surname><given-names>Taijiao</given-names></name><xref ref-type="corresp" rid="c3">c</xref><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref></contrib><aff id="a1"><label>1</label><institution>Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005; Suzhou Institute of Systems Medicine</institution>, Suzhou, Jiangsu 215123,<country>China</country></aff><aff id="a2"><label>2</label><institution>Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences</institution>, Beijing 100101,<country>China</country></aff><aff id="a3"><label>3</label><institution>National Institute for Viral Disease Control and Prevention, China CDC</institution>, Beijing 102206,<country>China</country></aff><aff id="a4"><label>4</label><institution>University of the Chinese Academy of Sciences</institution>, Beijing 100049,<country>China</country></aff><aff id="a5"><label>5</label><institution>Department of Ecology and Evolution, University of Chicago</institution>, Chicago, IL 60637</aff><aff id="a6"><label>6</label><institution>College of Information Science and Engineering, Hunan University</institution>, Changsha 410082,<country>China</country></aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email>wuaiping@moon.ibp.ac.cn</email></corresp><corresp id="c2"><label>b</label><email>yshu@cnic.org.cn</email></corresp><corresp id="c3"><label>c</label><email>taijiao@moon.ibp.ac.cn</email></corresp><fn id="n1"><label>*</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="epub"><day>28</day><month>09</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>5</volume><elocation-id>14171</elocation-id><history><date date-type="received"><day>17</day><month>03</month><year>2015</year></date><date date-type="accepted"><day>19</day><month>08</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015, Macmillan Publishers Limited</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Macmillan Publishers Limited</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><abstract><p>The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution of human influenza A (H1N1) virus is extremely important for its effective surveillance and prevention. Through development of antigenicity inference method for human influenza A (H1N1), named PREDAC-H1, we systematically mapped the antigenic patterns and evolution of the human influenza A (H1N1) virus. Eight dominant antigenic clusters have been inferred for seasonal H1N1 viruses since 1977, which demonstrated sequential replacements over time with a similar pattern in Asia, Europe and North America. Among them, six clusters emerged first in Asia. As for China, three of the eight antigenic clusters were detected in South China earlier than in North China, indicating the leading role of South China in H1N1 transmission. The comprehensive view of the antigenic evolution of human influenza A (H1N1) virus can help formulate better strategy for its prevention and control.</p></abstract></article-meta></front><floats-group><fig id="f1"><label>Figure 1</label><caption><title>Methodology and validation of the PREDAC-H1 method.</title><p>(<bold>a</bold>) Workflow of the PREDAC-H1 method, antigenic correlation network was illustrated using Cytoscape software<xref ref-type="bibr" rid="b31">31</xref>. (<bold>b</bold>) Retrospective testing to infer the antigenic relationships between influenza A (H1N1) viruses. (<bold>c</bold>) Comparison of inferred antigenic clusters and predominant clusters in the US from the 1994–1995 to 2013–2014 epidemic seasons as reported by US CDC. Five dominant clusters are colored and labeled.</p></caption><graphic xlink:href="srep14171-f1"></graphic></fig><fig id="f2"><label>Figure 2</label><caption><title>Antigenic and genetic evolution of human influenza A (H1N1) viruses.</title><p>(<bold>a</bold>) Phylogenetic tree of the HA1 region of the H1N1 HA protein. The tree was rooted using A/Brevig Mission/1/1918 strain as outgroup. (<bold>b</bold>) Inferred antigenic correlation network and antigenic clusters of human influenza A (H1N1) viruses. Clusters are colored and named as the abbreviation of vaccine strains. The circulation periods of each cluster are provided in parenthesis. (<bold>c</bold>) Genetic distance (calculated as amino acid substitutions) on HA1 of human influenza A (H1N1) strains to the A/Brevig Mission/1/1918 (H1N1) virus, each dot represents a virus strain. The strains were colored as antigenic clusters in Fig. 2b. The strains from 1918 to 1957, strains from 1977 to 2008, the swine-origin human-infecting strains were separated by gray lines. (<bold>d</bold>) Genetic distance (calculated as amino acid substitutions) on HA1 of human influenza A (H3N2) strains to the A/Hong Kong/1/1968 (H3N2) virus. Strains were colored as the antigenic clusters they belonged to.</p></caption><graphic xlink:href="srep14171-f2"></graphic></fig><fig id="f3"><label>Figure 3</label><caption><title>Comparison of antigenic patterns in different regions from 1980 to 2013.</title><p>Dynamic changes in the percentage of antigenic clusters in Asia, Europe and North America were recorded yearly. The earliest appearance of a new antigenic cluster is marked by a colored bar.</p></caption><graphic xlink:href="srep14171-f3"></graphic></fig><fig id="f4"><label>Figure 4</label><caption><title>Antigenic patterns in South and North China.</title><p>(<bold>a</bold>) Geographic distribution of H1N1 HA sequences provided by the China CDC and obtained from a public database from 1977 to 2008. The map was reconstructed using OpenStreetMap (<ext-link ext-link-type="uri" xlink:href="http://www.openstreetmap.org/">http://www.openstreetmap.org/</ext-link>) with further modification, and is for illustrative purposes only. (<bold>b</bold>) Dynamic changes in the percentage of antigenic clusters in South and North China. The underlying bar represents the circulation period of each antigenic cluster in South and North China and the earliest appearance of a new antigenic cluster is marked with a star. (<bold>c</bold>) Co-circulation of antigenic clusters in South and North China. Co-circulation was measured as the entropy of co-circulating antigenic clusters.</p></caption><graphic xlink:href="srep14171-f4"></graphic></fig></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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