Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, P.O Box. 400, Al-Ahsa, 31982, Kingdom of Saudi Arabia.
J Mol Evol. 2021 Jul;89(6):341-356. doi: 10.1007/s00239-021-10008-2. Epub 2021 May 15.
Severe Acute Respiratory Syndrome Coronavirus-2 is a zoonotic virus with a possible origin in bats and potential transmission to humans through an intermediate host. When zoonotic viruses jump to a new host, they undergo both mutational and natural selective pressures that result in non-synonymous and synonymous adaptive changes, necessary for efficient replication and rapid spread of diseases in new host species. The nucleotide composition and codon usage pattern of SARS-CoV-2 indicate the presence of a highly conserved, gene-specific codon usage bias. The codon usage pattern of SARS-CoV-2 is mostly antagonistic to human and bat codon usage. SARS-CoV-2 codon usage bias is mainly shaped by the natural selection, while mutational pressure plays a minor role. The time-series analysis of SARS-CoV-2 genome indicates that the virus is slowly evolving. Virus isolates from later stages of the outbreak have more biased codon usage and nucleotide composition than virus isolates from early stages of the outbreak.
严重急性呼吸综合征冠状病毒 2 是一种人畜共患病毒，其可能起源于蝙蝠，可能通过中间宿主传播给人类。当人畜共患病毒跳跃到新宿主时，它们会同时经历突变和自然选择压力，从而导致非同义适应性变化和同义适应性变化，这对于在新宿主物种中有效复制和快速传播疾病是必要的。SARS-CoV-2 的核苷酸组成和密码子使用模式表明存在高度保守的、基因特异性的密码子使用偏好。SARS-CoV-2 的密码子使用模式主要与人类和蝙蝠的密码子使用模式相拮抗。SARS-CoV-2 的密码子使用偏好主要是由自然选择形成的，而突变压力的作用较小。对 SARS-CoV-2 基因组的时间序列分析表明，该病毒正在缓慢进化。与疫情早期的病毒分离株相比，疫情后期的病毒分离株具有更多的偏倚密码子使用和核苷酸组成。
