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, Andrew Rambaut

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Abstract

In March and early April 2009, a new swine-origin influenza A (HlNl) 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 Organization 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 timescale 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 emergence in humans, 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about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates.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 humans2.

Original languageEnglish (US)
Pages (from-to)1122-1125
Number of pages4
JournalNature
Volume459
Issue number7250
DOIs
StatePublished - Jun 25 2009

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Genomics
Human Influenza
Swine
Viruses
Pandemics
Disease Outbreaks
Influenza A virus
Medical Genetics
Mexico

ASJC Scopus subject areas

  • General

Cite this

Smith, G. J. D., Vijaykrishna, D., Bahl, J., Lycett, S. J., Worobey, M., Pybus, O. G., ... Rambaut, A. (2009). Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic. Nature, 459(7250), 1122-1125. https://doi.org/10.1038/nature08182

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic. / Smith, Gavin J D; Vijaykrishna, Dhanasekaran; Bahl, Justin; Lycett, Samantha J.; Worobey, Michael; Pybus, Oliver G.; Ma, Siu Kit; Cheung, Chung Lam; Raghwani, Jayna; Bhatt, Samir; Peiris, J. S Malik; Guan, Yi; Rambaut, Andrew.

In: Nature, Vol. 459, No. 7250, 25.06.2009, p. 1122-1125.

Research output: Contribution to journalArticle

Smith, GJD, Vijaykrishna, D, Bahl, J, Lycett, SJ, Worobey, M, Pybus, OG, Ma, SK, Cheung, CL, Raghwani, J, Bhatt, S, Peiris, JSM, Guan, Y & Rambaut, A 2009, 'Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic', Nature, vol. 459, no. 7250, pp. 1122-1125. https://doi.org/10.1038/nature08182
Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic. Nature. 2009 Jun 25;459(7250):1122-1125. https://doi.org/10.1038/nature08182
Smith, Gavin J D ; Vijaykrishna, Dhanasekaran ; Bahl, Justin ; Lycett, Samantha J. ; Worobey, Michael ; Pybus, Oliver G. ; Ma, Siu Kit ; Cheung, Chung Lam ; Raghwani, Jayna ; Bhatt, Samir ; Peiris, J. S Malik ; Guan, Yi ; Rambaut, Andrew. / Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic. In: Nature. 2009 ; Vol. 459, No. 7250. pp. 1122-1125.
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