The variable codons of H5N1 avian influenza A virus haemagglutinin genes

• Published in: Science China. Life sciences 2008-11, Vol.51 (11), p.987-993
• Main Authors: Shi, WeiFeng, Gibbs, Mark J., Zhang, YanZhou, Zhuang, DongMing, Dun, AiShe, Yu, GuangFu, Yang, NaNa, Murphy, Robert W., Zhu, ChaoDong
• Format: Article
• Language: English
• Subjects: Adaptation; Amino acids; Animals; Avian flu; Biomedical and Life Sciences; Birds; Codon; Codons; Databases, Genetic; Genes, Viral; Genetic Variation; Hemagglutinin Glycoproteins, Influenza Virus - genetics; Hemagglutinins; Humans; Influenza A; Influenza A virus; Influenza A Virus, H5N1 Subtype - genetics; Influenza A Virus, H5N1 Subtype - isolation & purification; Influenza in Birds - virology; Influenza, Human - virology; Life Sciences; Likelihood Functions; Mammals; Models, Genetic; Orthomyxoviridae; Orthomyxoviridae Infections - virology; Positive selection; Selection, Genetic; Species Specificity; Viruses
• ISSN: 1006-9305; 1674-7305; 1862-2798; 1869-1889
• DOI: 10.1007/s11427-008-0131-8

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.