The variable codons of H5N1 avian influenza A virus haemagglutinin genes.
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.
Shi
Weifeng
W
Institute of Life Sciences, Taishan Medical College, Taian, 271000, China. weifeng_cau@sina.com
Gibbs
Mark J
MJ
Zhang
Yanzhou
Y
Zhuang
Dongming
D
Dun
Aishe
A
Yu
Guangfu
G
Yang
Nana
N
Murphy
Robert W
RW
Zhu
Chaodong
C
D000818:Animals; D001717:Birds; D003062:Codon; D030541:Databases, Genetic; D005814:Genes, Viral; D014644:Genetic Variation; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D006801:Humans; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000821:virology; D007251:Influenza, Human / Q000821:virology; D016013:Likelihood Functions; D008322:Mammals; D008957:Models, Genetic; D009976:Orthomyxoviridae Infections / Q000821:virology; D012641:Selection, Genetic; D013045:Species Specificity
D003062:Codon; D019267:Hemagglutinin Glycoproteins, Influenza Virus