College of Animal Science and Technology, Hainan University, Haikou 570228, China.
College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
Viruses. 2022 May 16;14(5):1055. doi: 10.3390/v14051055.
Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes to virus evolvability remains elusive. In this paper, we characterize how the Senecavirus A (SVA), a picornavirus, utilizes synonymous codon mutations to influence its evolution, resulting in the adaptive evolution of the virus to adverse environments. The phylogenetic tree and Median-joining (MJ)-Network of these SVA lineages worldwide were constructed to reveal SVA three-stage genetic development clusters. Furthermore, we analyzed the codon bias of the SVA genome of selected strains and found that SVA could increase the GC content of the third base of some amino acid synonymous codons to enhance the viral RNA adaptive evolution. Our results highlight the impact of recessive mutation of virus codon bias on the evolution of the SVA and uncover a previously underappreciated evolutionary strategy for SVA. They also underline the importance of understanding the genetic evolution of SVA and how SVA adapts to the adverse effects of external stress.
同义密码子偏好在病毒基因组中影响蛋白质翻译和基因表达，表明同义密码子突变体在影响病毒毒力和进化方面起着至关重要的作用。然而，隐性突变体形式如何有助于病毒的进化能力仍然难以捉摸。在本文中，我们描述了微小 RNA 病毒科（Picornaviridae）的塞内卡病毒 A（SVA）如何利用同义密码子突变来影响其进化，从而导致病毒对不利环境的适应性进化。构建了这些 SVA 谱系的系统发育树和中值连接（MJ）网络，以揭示 SVA 的三个阶段遗传发育簇。此外，我们分析了选定菌株的 SVA 基因组的密码子偏好性，发现 SVA 可以增加一些氨基酸同义密码子第三碱基的 GC 含量，以增强病毒 RNA 的适应性进化。我们的研究结果强调了病毒密码子偏好性的隐性突变对 SVA 进化的影响，并揭示了 SVA 的一种以前未被充分认识的进化策略。它们还强调了了解 SVA 的遗传进化以及 SVA 如何适应外部压力的不利影响的重要性。
