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    Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review

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    Type
    Article
    Authors
    Kim, Kiyeon
    Omori, Ryosuke
    Ueno, Keisuke cc
    Iida, Sayaka
    Ito, Kimihito
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Date
    2016-01-13
    Permanent link to this record
    http://hdl.handle.net/10754/614424
    
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    Abstract
    Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima’s D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima’s D values of viral sequences were different depending on hosts and gene segments. Tajima’s D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima’s D values in rapidly growing viral population were also observed in computer simulations. Tajima’s D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima’s D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.
    Citation
    Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review 2016, 11 (1):e0147021 PLOS ONE
    Sponsors
    This work was supported by CREST (KI) and PRESTO (RO) from Japan Science and Technology Agency (http://www.jst.go.jp/), and by Grants-in-Aid for Scientific Research (B) (KI, 25280080) from the Ministry of Education, Culture, Sports, Science, and Technology in Japan (http://www.mext.go.jp/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Publisher
    Public Library of Science (PLoS)
    Journal
    PLoS ONE
    DOI
    10.1371/journal.pone.0147021
    PubMed ID
    26760775
    Additional Links
    http://dx.plos.org/10.1371/journal.pone.0147021
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pone.0147021
    Scopus Count
    Collections
    Articles; Computational Bioscience Research Center (CBRC)

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