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. 2012 Apr 15;1(4):385-90.
doi: 10.1242/bio.2012281. Epub 2012 Feb 16.

A comprehensive analysis of reassortment in influenza A virus

U Chandimal de Silva  1 , Hokuto Tanaka, Shota Nakamura, Naohisa Goto, Teruo Yasunaga
Affiliations

A comprehensive analysis of reassortment in influenza A virus

U Chandimal de Silva et al. Biol Open. .

Abstract

Genetic reassortment plays a vital role in the evolution of the influenza virus and has historically been linked with the emergence of pandemic strains. Reassortment is believed to occur when a single host - typically swine - is simultaneously infected with multiple influenza strains. The reassorted viral strains with novel gene combinations tend to easily evade the immune system in other host species, satisfying the basic requirements of a virus with pandemic potential. Therefore, it is vital to continuously monitor the genetic content of circulating influenza strains and keep an eye out for new reassortants. We present a new approach to identify reassortants from large data sets of influenza whole genome nucleotide sequences and report the results of the first ever comprehensive search for reassortants of all published influenza A genomic data. 35 of the 52 well supported candidate reassortants we found are reported here for the first time while our analysis method offers new insight that enables us to draw a more detailed picture of the origin of some of the previously reported reassortants. A disproportionately high number (13/52) of the candidate reassortants found were the result of the introduction of novel hemagglutinin and/or neuraminidase genes into a previously circulating virus. The method described in this paper may contribute towards automating the task of routinely searching for reassortants among newly sequenced strains.

Keywords: Influenza A; Matrix; Neighbourhood; Phylogeny; Reassortment.

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Figures

Fig. 1.
Fig. 1.. Neighbourhoods of strain t in segments i, j and k.
t falls on different lineages in segments i and j and have no common elements in their neighbourhoods except for strain t itself. Conversely, t has identical roots in segments i and k, giving rise to identical r-neighbourhoods.
See this image and copyright information in PMC

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