title: Analysis of codon usage and nucleotide composition bias in polioviruses.
abstract: BACKGROUND
  Poliovirus, the causative agent of poliomyelitis, is a human enterovirus and a member of the family of Picornaviridae and among the most rapidly evolving viruses known. Analysis of codon usage can reveal much about the molecular evolution of the viruses. However, little information about synonymous codon usage pattern of polioviruses genome has been acquired to date.
  
  
  METHODS
  The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents and dinucleotides were investigated and a comparative analysis of codon usage pattern for open reading frames (ORFs) among 48 polioviruses isolates including 31 of genotype 1, 13 of genotype 2 and 4 of genotype 3.
  
  
  RESULTS
  The result shows that the overall extent of codon usage bias in poliovirus samples is low (mean ENC = 53.754 > 40). The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in those polioviruses. Depending on the RSCU data, it was found that there was a significant variation in bias of codon usage among three genotypes. Geographic factor also has some effect on the codon usage pattern (exists in the genotype-1 of polioviruses). No significant effect in gene length or vaccine derived polioviruses (DVPVs), wild viruses and live attenuated virus was observed on the variations of synonymous codon usage in the virus genes. The relative abundance of dinucleotide (CpG) in the ORFs of polioviruses are far below expected values especially in DVPVs and attenuated virus of polioviruses genotype 1.
  
  
  CONCLUSIONS
  The information from this study may not only have theoretical value in understanding poliovirus evolution, especially for DVPVs genotype 1, but also have potential value for the development of poliovirus vaccines.
authors: State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu, China.
authors: Jie
authors: J
authors: Zhang
authors: Meng
authors: M
authors: Wang
authors: Wen-qian
authors: WQ
authors: Liu
authors: Jian-hua
authors: JH
authors: Zhou
authors: Hao-tai
authors: HT
authors: Chen
authors: Li-na
authors: LN
authors: Ma
authors: Yao-zhong
authors: YZ
authors: Ding
authors: Yuan-xing
authors: YX
authors: Gu
authors: Yong-sheng
authors: YS
authors: Liu
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D003062:Codon; D019143:Evolution, Molecular; D006801:Humans; D011051:Poliomyelitis / Q000821:virology; D017955:Poliovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D003062:Codon