JVI Accepts, published online ahead of print on 20 September 2006

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J. Virol. doi:10.1128/JVI.01414-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Comparison between avian and human influenza A virus reveals a mutational bias on the viral genomes

Raul Rabadan, Arnold J. Levine, and Harlan Robins^*

Institute for Advanced Study, Einstein Dr., Princeton, NJ 08540, USA; Computational Biology Group, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA

^* To whom correspondence should be addressed. Email: hrobins{at}fhcrc.org.

In the last few years, the genomic sequence data has become publicly available for thousands of influenza A virus strains including the 1918 pandemic strain and hundreds of isolates of the avian H5N1 which is causing an increasing number of human fatalities. This large quantity of sequence data allows us to do comparative genomics with the human and avian versions of the virus. We find that the nucleotide composition of influenza A viruses infecting the two hosts are sufficiently different that we can determine the host at almost 100% accuracy. This assignment works at the segment level which allows us to construct the reassortment history of individual segments within each strain. We suggest that the different nucleotide composition can be explained by a host dependent mutation bias. To support this idea we estimate the fixation rates for the different polymerase segments and the ratios of synonymous to non-synonymous changes. Additionally, we provide evidence supporting the hypothesis that the H1N1 influenza virus entered the human population just prior to the 1918 outbreak with an earliest bound of 1910.

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