title: Analysis of synonymous codon usage in hepatitis A virus.
abstract: BACKGROUND
  Hepatitis A virus is the causative agent of type A viral hepatitis, which causes occasional acute hepatitis. Nevertheless, little information about synonymous codon usage pattern of HAV genome in the process of its evolution is available. In this study, the key genetic determinants of codon usage in HAV were examined.
  
  
  RESULTS
  The overall extent of codon usage bias in HAV is high in Picornaviridae. And the patterns of synonymous codon usage are quite different in HAV genomes from different location. The base composition is closely correlated with codon usage bias. Furthermore, the most important determinant that results in such a high codon bias in HAV is mutation pressure rather than natural selection.
  
  
  CONCLUSIONS
  HAV presents a higher codon usage bias than other members of Picornaviridae. Compositional constraint is a significant element that influences the variation of synonymous codon usage in HAV genome. Besides, mutation pressure is supposed to be the major factor shaping the hyperendemic codon usage pattern of HAV.
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, China.
authors.forename: Yiqiang
authors.initials: Y
authors.lastname: Zhang
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Liu
authors.forename: Wenqian
authors.initials: W
authors.lastname: Liu
authors.forename: Jianhua
authors.initials: J
authors.lastname: Zhou
authors.forename: Haotai
authors.initials: H
authors.lastname: Chen
authors.forename: Yin
authors.initials: Y
authors.lastname: Wang
authors.forename: Lina
authors.initials: L
authors.lastname: Ma
authors.forename: Yaozhong
authors.initials: Y
authors.lastname: Ding
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D003062:Codon; D016679:Genome, Viral; D006506:Hepatitis A / Q000821:virology*; D030041:Hepatitis A virus / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010849:Picornaviridae / Q000235:genetics
chemical_list: D003062:Codon