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    Identifying changes in selective constraints: host shifts in influenza. 
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    Identifying changes in selective constraints: host shifts in influenza.

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    Identifying changes in selective constraints: host shifts in influenza.pdf (243.2Kb)
    Volume
    5
    Pagination
    e1000564 - ?
    DOI
    10.1371/journal.pcbi.1000564
    Journal
    PLoS Comput Biol
    Issue
    11
    Metadata
    Show full item record
    Abstract
    The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic material from waterfowl viruses is introduced into the human population causing worldwide pandemics. Identifying which mutations allow viruses from avian origin to spread successfully in the human population is of great importance in predicting and controlling influenza pandemics. Here we describe a novel approach to identify such mutations. We use a sitewise non-homogeneous phylogenetic model that explicitly takes into account differences in the equilibrium frequencies of amino acids in different hosts and locations. We identify 172 amino acid sites with strong support and 518 sites with moderate support of different selection constraints in human and avian viruses. The sites that we identify provide an invaluable resource to experimental virologists studying adaptation of avian flu viruses to the human host. Identification of the sequence changes necessary for host shifts would help us predict the pandemic potential of various strains. The method is of broad applicability to investigating changes in selective constraints when the timing of the changes is known.
    Authors
    Tamuri, AU; Dos Reis, M; Hay, AJ; Goldstein, RA
    URI
    http://qmro.qmul.ac.uk/xmlui/handle/123456789/14070
    Collections
    • School of Biological and Chemical Sciences [1605]
    Language
    eng
    Copyright statements
    © 2009 Tamuri et al.
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