Exploring the molecular epidemiology and evolutionary dynamics of influenza A virus in Taiwan
The evolution and population dynamics of human influenza in Taiwan is a microcosm of the viruses circulating worldwide, which has not yet been studied in detail. We collected 343 representative full genome sequences of human influenza A viruses isolated in Taiwan between 1979 and 2009. Phylogenetic...
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| description | The evolution and population dynamics of human influenza in Taiwan is a microcosm of the viruses circulating worldwide, which has not yet been studied in detail. We collected 343 representative full genome sequences of human influenza A viruses isolated in Taiwan between 1979 and 2009. Phylogenetic and antigenic data analysis revealed that H1N1 and H3N2 viruses consistently co-circulated in Taiwan, although they were characterized by different temporal dynamics and degrees of genetic diversity. Moreover, influenza A viruses of both subtypes underwent internal gene reassortment involving all eight segments of the viral genome, some of which also occurred during non-epidemic periods. The patterns of gene reassortment were different in the two subtypes. The internal genes of H1N1 viruses moved as a unit, separately from the co-evolving HA and NA genes. On the other hand, the HA and NA genes of H3N2 viruses tended to segregate consistently with different sets of internal gene segments. In particular, as reassortment occurred, H3HA always segregated as a group with the PB1, PA and M genes, while N2NA consistently segregated with PB2 and NP. Finally, the analysis showed that new phylogenetic lineages and antigenic variants emerging in summer were likely to be the progenitors of the epidemic strains in the following season. The synchronized seasonal patterns and high genetic diversity of influenza A viruses observed in Taiwan make possible to capture the evolutionary dynamic and epidemiological rules governing antigenic drift and reassortment and may serve as a "warning" system that recapitulates the global epidemic. |
| doi_str_mv | 10.1371/journal.pone.0061957 |
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We collected 343 representative full genome sequences of human influenza A viruses isolated in Taiwan between 1979 and 2009. Phylogenetic and antigenic data analysis revealed that H1N1 and H3N2 viruses consistently co-circulated in Taiwan, although they were characterized by different temporal dynamics and degrees of genetic diversity. Moreover, influenza A viruses of both subtypes underwent internal gene reassortment involving all eight segments of the viral genome, some of which also occurred during non-epidemic periods. The patterns of gene reassortment were different in the two subtypes. The internal genes of H1N1 viruses moved as a unit, separately from the co-evolving HA and NA genes. On the other hand, the HA and NA genes of H3N2 viruses tended to segregate consistently with different sets of internal gene segments. In particular, as reassortment occurred, H3HA always segregated as a group with the PB1, PA and M genes, while N2NA consistently segregated with PB2 and NP. Finally, the analysis showed that new phylogenetic lineages and antigenic variants emerging in summer were likely to be the progenitors of the epidemic strains in the following season. The synchronized seasonal patterns and high genetic diversity of influenza A viruses observed in Taiwan make possible to capture the evolutionary dynamic and epidemiological rules governing antigenic drift and reassortment and may serve as a "warning" system that recapitulates the global epidemic.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0061957</identifier><identifier>PMID: 23613982</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Antigenic drift ; Antigenic variants ; Antigens ; Biodiversity ; Biological evolution ; Biology ; Data analysis ; Data processing ; Epidemics ; Epidemiology ; Evolution ; Female ; Gene sequencing ; Genes ; Genetic diversity ; Genomes ; Genomics ; Humans ; Influenza ; Influenza A ; Influenza A virus - pathogenicity ; Influenza, Human - epidemiology ; Influenza, Human - virology ; Information management ; Male ; Medical laboratories ; Medicine ; Molecular dynamics ; Molecular Epidemiology - methods ; Pandemics ; Phylogenetics ; Phylogeny ; Population biology ; Segments ; Taiwan - epidemiology ; Viruses</subject><ispartof>PloS one, 2013-04, Vol.8 (4), p.e61957-e61957</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Lin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Lin et al 2013 Lin et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-e0571ac6c5fabed46e0f6ed8d835fd5bd4a94febe25476e193643da1cf3331b63</citedby><cites>FETCH-LOGICAL-c758t-e0571ac6c5fabed46e0f6ed8d835fd5bd4a94febe25476e193643da1cf3331b63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628583/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628583/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23613982$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Khudyakov, Yury E.</contributor><creatorcontrib>Lin, Jih-Hui</creatorcontrib><creatorcontrib>Chiu, Shu-Chun</creatorcontrib><creatorcontrib>Lin, Yung-Cheng</creatorcontrib><creatorcontrib>Cheng, Ju-Chien</creatorcontrib><creatorcontrib>Wu, Ho-Sheng</creatorcontrib><creatorcontrib>Salemi, Marco</creatorcontrib><creatorcontrib>Liu, Hsin-Fu</creatorcontrib><title>Exploring the molecular epidemiology and evolutionary dynamics of influenza A virus in Taiwan</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The evolution and population dynamics of human influenza in Taiwan is a microcosm of the viruses circulating worldwide, which has not yet been studied in detail. We collected 343 representative full genome sequences of human influenza A viruses isolated in Taiwan between 1979 and 2009. Phylogenetic and antigenic data analysis revealed that H1N1 and H3N2 viruses consistently co-circulated in Taiwan, although they were characterized by different temporal dynamics and degrees of genetic diversity. Moreover, influenza A viruses of both subtypes underwent internal gene reassortment involving all eight segments of the viral genome, some of which also occurred during non-epidemic periods. The patterns of gene reassortment were different in the two subtypes. The internal genes of H1N1 viruses moved as a unit, separately from the co-evolving HA and NA genes. On the other hand, the HA and NA genes of H3N2 viruses tended to segregate consistently with different sets of internal gene segments. In particular, as reassortment occurred, H3HA always segregated as a group with the PB1, PA and M genes, while N2NA consistently segregated with PB2 and NP. Finally, the analysis showed that new phylogenetic lineages and antigenic variants emerging in summer were likely to be the progenitors of the epidemic strains in the following season. The synchronized seasonal patterns and high genetic diversity of influenza A viruses observed in Taiwan make possible to capture the evolutionary dynamic and epidemiological rules governing antigenic drift and reassortment and may serve as a "warning" system that recapitulates the global epidemic.</description><subject>Analysis</subject><subject>Antigenic drift</subject><subject>Antigenic variants</subject><subject>Antigens</subject><subject>Biodiversity</subject><subject>Biological evolution</subject><subject>Biology</subject><subject>Data analysis</subject><subject>Data processing</subject><subject>Epidemics</subject><subject>Epidemiology</subject><subject>Evolution</subject><subject>Female</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic diversity</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Humans</subject><subject>Influenza</subject><subject>Influenza A</subject><subject>Influenza A virus - pathogenicity</subject><subject>Influenza, Human - 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We collected 343 representative full genome sequences of human influenza A viruses isolated in Taiwan between 1979 and 2009. Phylogenetic and antigenic data analysis revealed that H1N1 and H3N2 viruses consistently co-circulated in Taiwan, although they were characterized by different temporal dynamics and degrees of genetic diversity. Moreover, influenza A viruses of both subtypes underwent internal gene reassortment involving all eight segments of the viral genome, some of which also occurred during non-epidemic periods. The patterns of gene reassortment were different in the two subtypes. The internal genes of H1N1 viruses moved as a unit, separately from the co-evolving HA and NA genes. On the other hand, the HA and NA genes of H3N2 viruses tended to segregate consistently with different sets of internal gene segments. In particular, as reassortment occurred, H3HA always segregated as a group with the PB1, PA and M genes, while N2NA consistently segregated with PB2 and NP. Finally, the analysis showed that new phylogenetic lineages and antigenic variants emerging in summer were likely to be the progenitors of the epidemic strains in the following season. The synchronized seasonal patterns and high genetic diversity of influenza A viruses observed in Taiwan make possible to capture the evolutionary dynamic and epidemiological rules governing antigenic drift and reassortment and may serve as a "warning" system that recapitulates the global epidemic.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23613982</pmid><doi>10.1371/journal.pone.0061957</doi><tpages>e61957</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Antigenic drift Antigenic variants Antigens Biodiversity Biological evolution Biology Data analysis Data processing Epidemics Epidemiology Evolution Female Gene sequencing Genes Genetic diversity Genomes Genomics Humans Influenza Influenza A Influenza A virus - pathogenicity Influenza, Human - epidemiology Influenza, Human - virology Information management Male Medical laboratories Medicine Molecular dynamics Molecular Epidemiology - methods Pandemics Phylogenetics Phylogeny Population biology Segments Taiwan - epidemiology Viruses |
| title | Exploring the molecular epidemiology and evolutionary dynamics of influenza A virus in Taiwan |
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