State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu, China.
Virol J. 2011 Mar 30;8:146. doi: 10.1186/1743-422X-8-146.
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.
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.
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.
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.
脊髓灰质炎病毒是引起脊髓灰质炎的病原体，是一种人类肠道病毒，属于小核糖核酸病毒科，是已知进化最快的病毒之一。对密码子使用的分析可以揭示病毒的分子进化情况。然而，迄今为止，有关脊髓灰质炎病毒基因组同义密码子使用模式的信息还很少。
研究了相对同义密码子使用（RSCU）值、有效密码子数（ENC）值、核苷酸含量和二核苷酸，并对包括 31 株 1 型、13 株 2 型和 4 株 3 型在内的 48 株脊髓灰质炎病毒分离株的开放阅读框（ORF）的密码子使用模式进行了比较分析。
结果表明，脊髓灰质炎病毒样本中的密码子使用偏倚程度总体较低（平均 ENC=53.754>40）。碱基组成与密码子使用偏倚之间的一般相关性表明，突变压力而不是自然选择是决定这些脊髓灰质炎病毒密码子使用偏倚的主要因素。根据 RSCU 数据，发现三种基因型之间的密码子使用偏倚存在显著差异。地理因素也对密码子使用模式有一定影响（存在于脊髓灰质炎病毒 1 型中）。在病毒基因中，同义密码子使用的变化与基因长度或疫苗衍生脊髓灰质炎病毒（DVPV）、野生病毒和减毒活病毒无关。在脊髓灰质炎病毒 ORFs 中，二核苷酸（CpG）的相对丰度远低于预期值，尤其是在 DVPV 和脊髓灰质炎病毒 1 型减毒病毒中。
本研究提供的信息不仅在理解脊髓灰质炎病毒进化，特别是 DVPV 1 型方面具有理论价值，而且在脊髓灰质炎病毒疫苗的开发方面也具有潜在价值。
