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

Author

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  • 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)

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.

Suggested Citation

  • 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, 2009. "Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic," Nature, Nature, vol. 459(7250), pages 1122-1125, June.
    • Handle: RePEc:nat:nature:v:459:y:2009:i:7250:d:10.1038_nature08182
    DOI: 10.1038/nature08182
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    Cited by:

    1. Mario Arturo Ruiz Estrada & Evangelos Koutronas & Donghyun Park & Alam Khan & Muhammad Tahir, 2023. "The impact of COVID-19 on the economic performance of Wuhan, China (2019–2021)," Quality & Quantity: International Journal of Methodology, Springer, vol. 57(1), pages 847-862, February.
    2. Shanshan Chen & Yijun Ran & Hebo Huang & Zhenzhen Wang & Ke-ke Shang, 2022. "Epidemic Dynamics of Two-Pathogen Spreading for Pairwise Models," Mathematics, MDPI, vol. 10(11), pages 1-18, June.
    3. Igor Balaz & Taichi Haruna, 2018. "Evolution Of Influenza A Nucleotide Segments Through The Lens Of Different Complexity Measures," Advances in Complex Systems (ACS), World Scientific Publishing Co. Pte. Ltd., vol. 21(05), pages 1-24, August.
    4. Guo, Zun-Guang & Sun, Gui-Quan & Wang, Zhen & Jin, Zhen & Li, Li & Li, Can, 2020. "Spatial dynamics of an epidemic model with nonlocal infection," Applied Mathematics and Computation, Elsevier, vol. 377(C).
    5. Goulas, Sofoklis & Megalokonomou, Rigissa, 2016. "Swine Flu and The Effect of Compulsory Class Attendance on Academic Performance," MPRA Paper 75395, University Library of Munich, Germany.
    6. Cecilia Solér, 2012. "Conceptualizing Sustainably Produced Food for Promotional Purposes: A Sustainable Marketing Approach," Sustainability, MDPI, vol. 4(3), pages 1-47, March.
    7. Finlay Campbell & Anne Cori & Neil Ferguson & Thibaut Jombart, 2019. "Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data," PLOS Computational Biology, Public Library of Science, vol. 15(3), pages 1-20, March.

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