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    A complete analysis of HA and NA genes of influenza A viruses.

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    Authors
    Shi, Weifeng
    Lei, Fumin
    Zhu, Chaodong
    Sievers, Fabian
    Higgins, Desmond G
    Affiliation
    The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland. weifeng.shi@ucd.ie
    Issue Date
    2010-12
    MeSH
    Animals
    Birds
    Databases, Genetic
    Evolution, Molecular
    Genetic Variation
    Geography
    Hemagglutinins
    Humans
    Influenza A virus
    Influenza in Birds
    Influenza, Human
    Multivariate Analysis
    Neuraminidase
    Phylogeny
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    Citation
    A complete analysis of HA and NA genes of influenza A viruses. 2010, 5 (12):e14454 PLoS ONE
    Journal
    PloS one
    URI
    http://hdl.handle.net/10147/135989
    DOI
    10.1371/journal.pone.0014454
    PubMed ID
    21209922
    Additional Links
    http://www.ncbi.nlm.nih.gov/pubmed/21209922
    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 18,975 HA sequences and divided them into 280 subgroups according to multivariate and phylogenetic analyses. Similarly, we divided 11,362 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.
    Item Type
    Article
    Language
    en
    ISSN
    1932-6203
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pone.0014454
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