JVI Accepts, published online ahead of print on 18 March 2009

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J. Virol. doi:10.1128/JVI.02565-08
Copyright (c) 2009, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses

Eleca J. Dunham, Vivien G. Dugan, Emilee K. Kaser, Sarah E. Perkins, Ian H. Brown, Edward C. Holmes, and Jeffery K. Taubenberger^*

Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA, USA; Virology Department, Veterinary Laboratories Agency - Weybridge, Addlestone, Surrey, UK; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA

^* To whom correspondence should be addressed. Email: taubenbergerj{at}niaid.nih.gov.

In 1979 a lineage of avian-like H1N1 influenza A virus emerged in European swine populations independently from the ‘classical’ swine H1N1 virus lineage that had circulated in pigs since the ‘Spanish’ influenza pandemic of 1918. To determine whether these two distinct lineages of swine-adapted A/H1N1 viruses have evolved in similar ways, as might be expected given their common host species and origin from avian-like A/H1N1 ancestors, we compared patterns of nucleotide and amino acid change in whole genome sequences of both groups. An analysis of nucleotide compositional bias across all 8 genomic segments for the two swine lineages showed a clear lineage-specific bias, although a segment-specific effect was also apparent. As such, there only appears to be a relatively weak host-specific selection pressure. Strikingly, despite each lineage evolving in the same species host for decades, amino acid analysis revealed little evidence for either parallel or convergent changes. These findings suggest that although adaptation due to evolutionary lineages can be distinguished, there are functional and structural constraints on all gene segments, and that the evolutionary trajectory of each lineage of swine A/H1N1 virus has a strong historical contingency. Thus, in the context of emergence of an influenza A virus strain via a host-switch event, it is difficult to predict what specific polygenic changes are needed for mammalian adaptation.

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