Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
Infect Genet Evol. 2013 Mar;14:396-400. doi: 10.1016/j.meegid.2013.01.001. Epub 2013 Jan 16.
West Nile virus (WNV) is a member of the family Flaviviridae and its genome consists of an 11-kb single-stranded, positive-sense RNA. WNV is maintained in an enzootic cycle between mosquitoes and birds, but can also infect and cause disease in horses and humans, which serve as incidental dead-end hosts. Understanding the extent and causes of biases in codon usage is essential to the comprehension of viral evolution. In this study, we performed a comprehensive analysis of 449 WNV strains, for which complete genome sequences are available. Effective number of codons (ENC) indicates that the overall codon usage among WNV strains is only slightly biased. Codon adaptation index (CAI) values found for WNV genes are different from the CAI values found for human genes. The relative synonymous codon usage among WNV strains isolated from birds, equines, humans and mosquitoes are roughly similar and are influenced by the relative dinucleotide frequencies. Taking together, the results of this work suggest that WNV genomic biases are the result of the evolution of genome composition, the need to escape the antiviral cell responses and a dynamic process of mutation and selection to re-adapt its codon usage to different environments.
西尼罗河病毒（WNV）属于黄病毒科，其基因组由 11kb 的单链、正义 RNA 组成。WNV 在蚊子和鸟类之间维持着地方性循环，但也可以感染和引起马和人类的疾病，马和人类是偶然的末端宿主。了解密码子使用偏倚的程度和原因对于理解病毒进化至关重要。在这项研究中，我们对 449 株 WNV 进行了全面分析，这些毒株的全基因组序列均可获得。有效密码子数（ENC）表明，WNV 株之间的整体密码子使用仅略有偏向。WNV 基因的密码子适应指数（CAI）值与人类基因的 CAI 值不同。从鸟类、马、人类和蚊子中分离出的 WNV 株之间的相对同义密码子使用大致相似，受相对二核苷酸频率的影响。总的来说，这项工作的结果表明，WNV 基因组的偏倚是基因组组成进化、逃避抗病毒细胞反应的需要以及突变和选择的动态过程重新适应不同环境的结果。
