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Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia


A highly pathogenic avian influenza virus, H5N1, caused disease outbreaks in poultry in China and seven other east Asian countries between late 2003 and early 2004; the same virus was fatal to humans in Thailand and Vietnam1. Here we demonstrate a series of genetic reassortment events traceable to the precursor of the H5N1 viruses that caused the initial human outbreak in Hong Kong in 1997 (refs 2–4) and subsequent avian outbreaks in 2001 and 2002 (refs 5, 6). These events gave rise to a dominant H5N1 genotype (Z) in chickens and ducks that was responsible for the regional outbreak in 2003–04. Our findings indicate that domestic ducks in southern China had a central role in the generation and maintenance of this virus, and that wild birds may have contributed to the increasingly wide spread of the virus in Asia. Our results suggest that H5N1 viruses with pandemic potential have become endemic in the region and are not easily eradicable. These developments pose a threat to public and veterinary health in the region and potentially the world, and suggest that long-term control measures are required.

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Figure 1
Figure 2: Seasonality of the isolation of avian H5N1 viruses from domestic poultry in mainland China during July 2000 to January 2004 (see Table 1).
Figure 3: The genotypes of H5N1 influenza virus reassortants from eastern Asia.
Figure 4: Phylogenetic relationships of the haemagglutinin (a) and matrix protein (b) genes of representative influenza A viruses isolated in southeastern Asia, including 2 of 6 from Indonesia, 5 of 8 from Thailand and 4 of 12 from Vietnam.


  1. World Health Organization, Avian influenza A (H5N1). Weekly Epidemiol. Rev. 79, 65–70 (2004)

    Google Scholar 

  2. Xu, X., Subbarao, K., Cox, N. J. & Guo, Y. Genetic characterization of the pathogenic influenza A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks in Hong Kong. Virology 261, 15–19 (1999)

    CAS  Article  PubMed  Google Scholar 

  3. Claas, E. C. J. et al. Human influenza A H5N1 virus related to a highly pathogenic avian influenza virus. Lancet 351, 472–477 (1998)

    CAS  Article  PubMed  Google Scholar 

  4. Guan, Y., Shortridge, K. F., Krauss, S. & Webster, R. G. Molecular characterization of H9N2 influenza viruses: were they the donors of the “internal” genes of H5N1 viruses in Hong Kong? Proc. Natl Acad. Sci. USA 96, 9363–9367 (1999)

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. Guan, Y. et al. Emergence of multiple genotypes of H5N1 avian influenza viruses in Hong Kong SAR. Proc. Natl Acad. Sci. USA 99, 8950–8955 (2002)

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. Guan, Y. et al. H5N1 Influenza: A protean pandemic threat. Proc. Natl Acad. Sci. USA 101, 8156–8161 (2004)

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. Shortridge, K. F. et al. Characterization of avian H5N1 influenza viruses from poultry in Hong Kong. Virology 252, 331–342 (1998)

    CAS  Article  PubMed  Google Scholar 

  8. Matrosovich, M., Zhou, N. N., Kawaoka, Y. & Webster, R. G. The surface glycoproteins of H5 influenza viruses isolated from humans, chickens, and wild aquatic birds have distinguishable properties. J. Virol. 73, 1146–1155 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Hien, T. T. et al. Avian influenza A (H5N1) in 10 patients in Vietnam. N. Engl. J. Med. 350, 1179–1188 (2004)

    CAS  Article  Google Scholar 

  10. Li, K. S. et al. Characterization of H9 subtype influenza viruses from the ducks of southern China: a candidate for the next influenza pandemic in humans? J. Virol. 77, 6988–6994 (2003)

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Presgraves, D. C., Balagopalan, L., Abmayr, S. M. & Orr, H. A. Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila. Nature 423, 715–719 (2003)

    ADS  CAS  Article  PubMed  Google Scholar 

  12. Webster, R. G., Bean, W. J., Gorman, O. T., Chambers, T. M. & Kawaoka, Y. Evolution and ecology of influenza A viruses. Microbiol. Rev. 56, 152–179 (1992)

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Scholtissek, C., Quack, G., Klenk, H. D. & Webster, R. G. How to overcome resistance of influenza A viruses against adamantane derivatives. Antiviral Res. 37, 83–95 (1998)

    CAS  Article  PubMed  Google Scholar 

  14. Holsinger, L. J., Shaughnessy, M. A., Micko, A., Pinto, L. H. & Lamb, R. A. Analysis of the posttranslational modifications of the influenza virus M2 protein. J. Virol. 69, 1219–1225 (1995)

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Thomas, J. M., Stevens, M. P., Percy, N. & Barclay, W. S. Phosphorylation of the M2 protein of influenza A virus is not essential for virus viability. Virology 252, 54–64 (1998)

    CAS  Article  PubMed  Google Scholar 

  16. Ha, Y., Stevens, D. J., Skehel, J. J. & Wiley, D. C. X-ray structures of H5 avian and H9 swine influenza virus hemagglutinins bound to avian and human receptor analogs. Proc. Natl Acad. Sci. USA 98, 11181–11186 (2001)

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. Kaverin, N. V. et al. Structure of antigenic sites on the haemagglutinin molecule of H5 avian influenza virus and phenotypic variation of escape mutants. J. Gen. Virol. 83, 2497–2505 (2002)

    CAS  Article  PubMed  Google Scholar 

  18. Iwatsuki-Horimoto, K., Kanazawa, R., Sugii, S., Kawaoka, Y. & Horimoto, T. The index influenza A virus subtype H5N1 isolated from a human in 1997 differs in its receptor-binding properties from a virulent avian influenza virus. J. Gen. Virol. 85, 1001–1005 (2004)

    CAS  Article  PubMed  Google Scholar 

  19. Hatta, M., Gao, P., Halfmann, P. & Kawaoka, Y. Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses. Science 293, 1773–1775 (2001)

    Article  Google Scholar 

  20. Fouchier, R. A. M. et al. Avian influenza A virus (H7N7) associated with conjunctivitis and a fatal case of acute respiratory distress syndrome. Proc. Natl Acad. Sci. USA 101, 1356–1361 (2004)

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. Seo, S. H., Hoffmann, E. & Webster, R. G. Lethal H5N1 influenza viruses escape host anti-viral cytokine responses. Nature Med. 8, 950–954 (2002)

    CAS  Article  PubMed  Google Scholar 

  22. Peiris, J. S. M. et al. Co-circulation of avian H9N2 and contemporary “human” H3N2 influenza viruses in pigs in southeastern China: potential for genetic reassortment? J. Virol. 75, 9679–9686 (2001)

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. Sims, L. D. et al. Avian influenza in Hong Kong 1977–2002. Avian Dis. 47, 832–838 (2003)

    CAS  Article  PubMed  Google Scholar 

  24. Guan, Y. et al. H9N2 influenza viruses possessing H5N1-like internal genomes continue to circulate in poultry in southeastern China. J. Virol. 74, 9372–9380 (2000)

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Swofford, D. L. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta (Sinauer Associates, Sunderland, USA, 2001)

    Google Scholar 

  26. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245 (2001)

    CAS  Article  PubMed  Google Scholar 

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We acknowledge K. Stöhr and the World Health Organization for facilitating the study; L. J. Zhang, C. L. Cheung and Y. H. C. Leung for technical assistance; N. Ng and colleagues for provision of computing facilities; and T. M. Ellis, K. Dyrting, W. Wong, P. Li and C. Li of the Department of Agriculture, Fisheries and Conservation of Hong Kong for their support of field work and W. Lim, for virus isolates. We also thank S. Naron for editorial assistance. These studies were supported by a grant from the National Institutes of Health, a grant from The Wellcome Trust, the Ellison Foundation, the Li Ka Shing Foundation, and grants from the Research Grants Council of Hong Kong.

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Correspondence to Y. Guan.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Figure 1

Phylogenetic relationships of the NA, NP, PA, PB1 and PB2 genes. (PDF 87 kb)

Supplementary Figure 2

Phylogenetic tree of the NS gene. (PDF 80 kb)

Supplementary Figure 3

Location of a potential additional glycosylation site superimposed on the 3D structure of the hemagluttinin molecule. (PDF 73 kb)

Supplementary Table 1

Results of the Ka/Ks rates of substitution analysis for genotype Z viruses. (DOC 52 kb)

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Li, K., Guan, Y., Wang, J. et al. Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature 430, 209–213 (2004).

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