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The variable codons of H5N1 avian influenza A virus haemagglutinin genes

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Abstract

We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 1997 to 2007, except viruses from 2000. The haemagglutinin sequences of viruses from southeast Asia, Hong Kong and mainland China were the most polymorphic and had similar nonsynonymous profiles. Some sites were positively selected in viruses from most regions and a few of these sites displayed different amino acid patterns. Selection appeared to produce different outcomes in viruses from Europe, Africa and Russia and from different host types. One position was found to be positively selected for human isolates only. Although the functions of some positively selected positions are unknown, our analysis provided evidence of different temporal, spatial and host adaptations for H5N1 avian influenza viruses.

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Authors and Affiliations

  1. Institute of Life Sciences, Taishan Medical College, Taian, 271000, China

    WeiFeng Shi & NaNa Yang

  2. School of Botany and Zoology, Faculty of Science, Australian National University, ACT, 0200, Australia

    Mark J. Gibbs

  3. Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China

    YanZhou Zhang & ChaoDong Zhu

  4. Department of Basic Medicine, Taishan Medical College, Taian, 271000, China

    DongMing Zhuang, AiShe Dun & GuangFu Yu

  5. Department of Natural History, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada

    Robert W. Murphy

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  1. WeiFeng Shi
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  2. Mark J. Gibbs
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  3. YanZhou Zhang
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  4. DongMing Zhuang
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  6. GuangFu Yu
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  7. NaNa Yang
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  9. ChaoDong Zhu
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Correspondence to WeiFeng Shi or ChaoDong Zhu.

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Shi, W., Gibbs, M.J., Zhang, Y. et al. The variable codons of H5N1 avian influenza A virus haemagglutinin genes. SCI CHINA SER C 51, 987–993 (2008). https://doi.org/10.1007/s11427-008-0131-8

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  • DOI: https://doi.org/10.1007/s11427-008-0131-8

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