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Incorporating structure context of HA protein to improve antigenicity calculation for influenza virus A/H3N2

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  • Incorporating structure context of HA protein to improve antigenicity calculation for influenza virus A/H3N2

    Sci Rep. 2016 Aug 8;6:31156. doi: 10.1038/srep31156.
    Incorporating structure context of HA protein to improve antigenicity calculation for influenza virus A/H3N2.

    Qiu J1, Qiu T1, Yang Y1, Wu D1, Cao Z1.
    Author information

    Abstract

    The rapid and consistent mutation of influenza requires frequent evaluation of antigenicity variation among newly emerged strains, during which several in-silico methods have been reported to facilitate the assays. In this paper, we designed a structure-based antigenicity scoring model instead of those sequence-based previously published. Protein structural context was adopted to derive the antigenicity-dominant positions, as well as the physic-chemical change of local micro-environment in correlation with antigenicity change. Then a position specific scoring matrix (PSSM) profile and local environmental change over above positions were integrated to predict the antigenicity variance. Independent testing showed a high accuracy of 0.875, and sensitivity of 0.986, with a significant ability to discover antigenic-escaping strains. When applying this model to the historical data, global and regional antigenic drift events can be successfully detected. Furthermore, two well-known vaccine failure events were clearly suggested. Therefore, this structure-context model may be particularly useful to identify those to-be-failed vaccine strains, in addition to suggest potential new vaccine strains.


    PMID: 27498613 DOI: 10.1038/srep31156
    [PubMed - in process] Free full text
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