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Research Article

Dating the emergence of pandemic influenza viruses

Gavin J. D. Smith, Justin Bahl, Dhanasekaran Vijaykrishna, Jinxia Zhang, Leo L. M. Poon, Honglin Chen, Robert G. Webster, J. S. Malik Peiris, and Yi Guan
  1. aState Key Laboratory of Emerging Infectious Diseases & Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China;
  2. bInternational Institute of Infection and Immunity, Shantou University, Shantou, Guangdong 515031, China;
  3. cVirology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38015; and
  4. dHKU-Pasteur Research Centre, The University of Hong Kong, Pokfulam, Hong Kong SAR, China

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PNAS July 14, 2009 106 (28) 11709-11712; https://doi.org/10.1073/pnas.0904991106
Gavin J. D. Smith
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Justin Bahl
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Dhanasekaran Vijaykrishna
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Jinxia Zhang
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Leo L. M. Poon
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Honglin Chen
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Robert G. Webster
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  • For correspondence: yguan@hkucc.hku.hk robert.webster@stjude.org
J. S. Malik Peiris
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Yi Guan
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  • For correspondence: yguan@hkucc.hku.hk robert.webster@stjude.org
  1. Contributed by Robert G. Webster, May 26, 2009

  2. ↵1G.J.D.S., J.B., and D.V. contributed equally to this work. (received for review March 31, 2009)

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    Fig. 1.

    Dated phylogenies of influenza A virus genes. (A) H1-HA, (B) PB2, (C) PB1, (D) PA, (E) H2-HA, and (F) H3-HA gene trees scaled to time (Horizontal Axis) generated using the SRD06 codon model and uncorrelated relaxed clock model. Nodes correspond to mean TMRCAs, and blue horizontal bars at nodes represent the 95% BCIs of TMRCAs. Colored branches represent major influenza A virus lineages. The blue boxes in B and D indicate a period of co-circulation of H2 and H3 viruses. Identical phylogenetic trees with virus names are available online in the supporting information. TMRCAs and BCIs for each of the major influenza A virus lineages are given in Table 1.

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    Table 1.

    Times of most recent common ancestors of human pandemic influenza viruses and related lineages

    GeneSwine/Human H1N1 (node 1)BM/1918 H1N1 (node 2)Seasonal H1N1 (node 3)H1N1 Re-introduction (node 3a)H2N2 (node 5)H3N2 (node 6)
    PB21881 (1813, 1912)1903 (1867, 1918)1910 (1888, 1928)1974 (1967, 1977)H1N1†H2N2†
    PB11906 (1890, 1918)1914 (1906, 1918)BM/1918†1974 (1970, 1977)1954 (1951, 1957)1967 (1965, 1968)
    PA1904 (1888, 1915)1914 (1906, 1918)BM/19181974 (1969, 1977)H1N1H2N2
    HA1885*1916 (1910, 1918)1913 (1895, 1925)1974 (1971, 1976)1955 (1952, 1957)1963 (1959, 1966)
    NP1884*1909 (1884, 1918)BM/19181974 (1969, 1977)H1N1H2N2
    NA1907 (1892, 1918)1913 (1905, 1918)BM/19181975 (1972, 1977)1950 (1945, 1955)H2N2
    M1884 (1841, 1911)1896*1911 (1893, 1926)1972 (1965, 1977)H1N1H2N2
    NS1899 (1876, 1917)1908 (1891, 1918)1915 (1900, 1926)1975 (1971, 1977)H1N1H2N2
    • ↵*Node not supported; therefore BCIs could not be estimated.

    • †These gene segments were derived from BM/1918, seasonal H1N1, and H2N2 viruses, respectively.

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Dating the emergence of pandemic influenza viruses
Gavin J. D. Smith, Justin Bahl, Dhanasekaran Vijaykrishna, Jinxia Zhang, Leo L. M. Poon, Honglin Chen, Robert G. Webster, J. S. Malik Peiris, Yi Guan
Proceedings of the National Academy of Sciences Jul 2009, 106 (28) 11709-11712; DOI: 10.1073/pnas.0904991106

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Dating the emergence of pandemic influenza viruses
Gavin J. D. Smith, Justin Bahl, Dhanasekaran Vijaykrishna, Jinxia Zhang, Leo L. M. Poon, Honglin Chen, Robert G. Webster, J. S. Malik Peiris, Yi Guan
Proceedings of the National Academy of Sciences Jul 2009, 106 (28) 11709-11712; DOI: 10.1073/pnas.0904991106
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