Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses

Tong Zhou, Wanjun Gu, Jianmin Ma, Xiao Sun, Zuhong Lu

Research output: Contribution to journalArticlepeer-review

134 Scopus citations


In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.

Original languageEnglish (US)
Pages (from-to)77-86
Number of pages10
Issue number1
StatePublished - Jul 2005
Externally publishedYes


  • GC content
  • H5N1
  • Influenza A virus
  • Mutational bias
  • Selection pressure
  • Synonymous codon usage

ASJC Scopus subject areas

  • Statistics and Probability
  • Modeling and Simulation
  • General Biochemistry, Genetics and Molecular Biology
  • Applied Mathematics


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