Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

Gavin J. D. Smith, Dhanasekaran Vijaykrishna, Justin Bahl, Samantha J. Lycett, Michael Worobey, Oliver G. Pybus, Siu Kit Ma, Chung Lam Cheung, Jayna Raghwani, Samir Bhatt, J. S. Malik Peiris, Yi Guan () and Andrew Rambaut ()
Additional contact information
Gavin J. D. Smith: Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
Dhanasekaran Vijaykrishna: Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
Justin Bahl: Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
Samantha J. Lycett: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King’s Buildings, Edinburgh EH9 3JT, UK
Michael Worobey: University of Arizona, Tucson, Arizona 85705, USA
Oliver G. Pybus: University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Siu Kit Ma: Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
Chung Lam Cheung: Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
Jayna Raghwani: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King’s Buildings, Edinburgh EH9 3JT, UK
Samir Bhatt: University of Oxford, South Parks Road, Oxford OX1 3PS, UK
J. S. Malik Peiris: Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
Yi Guan: Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
Andrew Rambaut: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King’s Buildings, Edinburgh EH9 3JT, UK

Nature, 2009, vol. 459, issue 7250, 1122-1125

Abstract: H1N1 pandemic virus analysed A phylogenetic analysis of swine-origin H1N1 influenza A virus provides evidence that the virus is a reassortment possessing genes from avian, swine and human origin viruses. The pandemic virus appears to have evolved in way typical of swine flu sequences prior to entering humans, and is derived from several viruses circulating in swine. Initial transmission to humans appears to have occurred several months before recognition of the outbreak. An estimate of the gaps in genetic surveillance points to a period of years between the reassortment of swine lineages and the transfer to humans and the multiple genetic ancestry is inconsistent with an artificial origin for the virus. The gaps in out knowledge revealed by this work highlight the need for the systematic surveillance of influence in swine as a means of identifying potentially pandemic strains before they cross into human populations.

Date: 2009
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DOI: 10.1038/nature08182

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