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Reference: Gavin J. D. Smith, Dhanasekaran Vijaykrishna, Justin Bahl et al., (2009). Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature.Citable link to this page:


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

Abstract: In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organisation to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the time-scale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before human emergence, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans.

Publication status:PublishedPeer Review status:Peer reviewed Funder: National Institutes of Health   Funder: Hong Kong SAR Government   Notes:This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.

Bibliographic Details

Publisher: Nature Publishing Group (Macmillan Publishers Ltd)

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Host: Naturesee more from them

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Issue Date: 2009

Copyright Date: 2009 Identifiers


Issn: 0028-0836

Eissn: 1476-4687

Urn: uuid:59acf805-c510-433f-92f5-4bcf0f749464 Item Description

Type: Article: post-print;

Language: en Keywords: swine-origin influenza A (H1N1) virusSubjects: Infectious diseases Biology Zoological sciences Tiny URL: ora:2833


Author: Gavin J. D. Smith - institutionUniversity of Hong Kong, Hong Kong, China facultyState Key Laboratory of Emerging Infectious Disea



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