Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales

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

Research output: Contribution to journalArticlepeer-review

181 Scopus citations


In this study, we calculated the codon usage bias in severe acute respiratory syndrome Coronavirus (SARSCoV) and performed a comparative analysis of synonymous codon usage patterns in SARSCoV and 10 other evolutionary related viruses in the Nidovirales. Although there is a significant variation in codon usage bias among different SARSCoV genes, codon usage bias in SARSCoV 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 synonymous codon usage pattern in these virus genes was virus specific and phylogenetically conserved, but it was not host specific. Phylogenetic analysis based on codon usage pattern suggested that SARSCoV was diverged far from all three known groups of Coronavirus. 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)155-161
Number of pages7
JournalVirus Research
Issue number2
StatePublished - May 2004


  • Base pair
  • CA
  • Correspondence analysis
  • ENC
  • Effective number of codons
  • GC
  • RSCU
  • Relative synonymous codon usage
  • Severe acute respiratory syndrome Coronavirus
  • The frequency of G+C at the synonymous third position of sense codons
  • bp

ASJC Scopus subject areas

  • Cancer Research
  • Virology
  • Infectious Diseases


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