Kaushik Rahul, Kumar Naveen, Yadav Pragya, Sircar Shubhankar, Shete-Aich Anita, Singh Ankur, Tomar Shailly, Launey Thomas, Malik Yashpal Singh
Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates.
Diagnostics and Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462021, Madhya Pradesh, India.
Microorganisms. 2024 Mar 29;12(4):696. doi: 10.3390/microorganisms12040696.
(NeVs) from the family have been linked to enteric diseases in bovines and have been detected worldwide. As viruses rely entirely on the cellular machinery of the host for replication, their ability to thrive in a specific host is greatly impacted by the specific codon usage preferences. Here, we systematically analyzed the codon usage bias in NeVs to explore the genetic and evolutionary patterns. Relative Synonymous Codon Usage and Effective Number of Codon analyses indicated a marginally lower codon usage bias in NeVs, predominantly influenced by the nucleotide compositional constraints. Nonetheless, NeVs showed a higher codon usage bias for codons containing G/C at the third codon position. The neutrality plot analysis revealed natural selection as the primary factor that shaped the codon usage bias in both the VP1 (82%) and VP2 (57%) genes of NeVs. Furthermore, the NeVs showed a highly comparable codon usage pattern to bovines, as reflected through Codon Adaptation Index and Relative Codon Deoptimization Index analyses. Notably, yak NeVs showed considerably different nucleotide compositional constraints and mutational pressure compared to bovine NeVs, which appear to be predominantly host-driven. This study sheds light on the genetic mechanism driving NeVs' adaptability, evolution, and fitness to their host species.
该家族的（牛肠道病毒，NeVs）已与牛的肠道疾病相关联，并且在全球范围内都有检测到。由于病毒完全依赖宿主的细胞机制进行复制，它们在特定宿主中生存的能力受到特定密码子使用偏好的极大影响。在此，我们系统地分析了牛肠道病毒中的密码子使用偏好，以探索其遗传和进化模式。相对同义密码子使用情况和有效密码子数分析表明，牛肠道病毒中的密码子使用偏好略低，主要受核苷酸组成限制的影响。尽管如此，牛肠道病毒在第三个密码子位置含有G/C的密码子上表现出更高的密码子使用偏好。中性绘图分析表明，自然选择是塑造牛肠道病毒VP1（82%）和VP2（57%）基因中密码子使用偏好的主要因素。此外，通过密码子适应指数和相对密码子去优化指数分析发现，牛肠道病毒与牛的密码子使用模式高度相似。值得注意的是，与牛肠道病毒相比，牦牛肠道病毒表现出明显不同的核苷酸组成限制和突变压力，这似乎主要是由宿主驱动的。本研究揭示了驱动牛肠道病毒对宿主物种适应性、进化和适合度的遗传机制。
