State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China.
Infect Genet Evol. 2013 Aug;18:8-12. doi: 10.1016/j.meegid.2013.03.043. Epub 2013 Apr 22.
The adaptation of the overall codon usage pattern of hepatitis C virus (HCV) to that of human is estimated by the synonymous codon usage value (RSCU). The synonymous codon usage biases for the translation initiation region (TIR) of this virus are also analyzed by calculation of usage fluctuation of each synonymous codon along the TIR (the first 30 codon sites of the whole coding sequence of HCV). As for the overall codon usage pattern of HCV, this virus has a significant tendency to delete the codons with CpG or TpA dinucleotides. Turning to the adaptation of the overall codon usage of HCV to that of human, over half part of codons has a similar usage pattern between this virus and human, suggesting that the host cellular environment of the overall codon usage pattern influences the formation of codon usage for HCV. In addition, there is no obvious phenomenon that the codons with relatively low energy tend to be highly selected in the TIR of HCV, suggesting that the synonymous codon usage patterns for the TIR of HCV might be not affected by the secondary structure of nucleotide sequence, however, the formation of synonymous codons usage in the TIR of HCV is influenced by the overall codon usage patterns of human to some degree.
丙型肝炎病毒（HCV）的整体密码子使用模式适应人类的程度可以通过同义密码子使用值（RSCU）来估计。还通过计算 TIR 中每个同义密码子的使用波动（HCV 整个编码序列的前 30 个密码子位点）来分析该病毒 TIR 的同义密码子使用偏好。对于 HCV 的整体密码子使用模式，该病毒具有显著删除 CpG 或 TpA 二核苷酸密码子的趋势。至于 HCV 整体密码子使用的适应，该病毒与人类有一半以上的密码子具有相似的使用模式，表明宿主细胞环境对 HCV 密码子使用的形成有影响。此外，在 HCV 的 TIR 中，没有明显的现象表明相对低能量的密码子被高度选择，这表明 HCV 的 TIR 同义密码子使用模式可能不受核苷酸序列二级结构的影响，然而，TIR 中同义密码子的形成 HCV 的使用在一定程度上受到人类整体密码子使用模式的影响。
