Gu Haogao, Chu Daniel K W, Peiris Malik, Poon Leo L M
School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR.
Virus Evol. 2020 May 14;6(1):veaa032. doi: 10.1093/ve/veaa032. eCollection 2020 Jan.
Coronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genus , which also includes severe acute respiratory syndrome-related coronavirus (SARSr-CoV) and Middle East respiratory syndrome-related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses helped identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, we compared the codon usage bias using global correspondence analysis (CA), within-group CA and between-group CA. We found that the bat RaTG13 virus best matched the overall codon usage pattern of SARS-CoV-2 in orf1ab, spike and nucleocapsid genes, while the pangolin P1E virus had a more similar codon usage in membrane gene. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.
2019冠状病毒病（COVID-19）是一个全球卫生问题，因为它继续在中国境内外传播。这种疾病的病原体，严重急性呼吸综合征冠状病毒2（SARS-CoV-2），属于冠状病毒属，该属还包括严重急性呼吸综合征相关冠状病毒（SARSr-CoV）和中东呼吸综合征相关冠状病毒（MERSr-CoV）。据信病毒基因的密码子使用在不同宿主环境中受到不同的选择压力。先前关于甲型流感病毒密码子使用的研究有助于确定病毒的宿主来源和进化趋势，然而，缺乏对冠状病毒的类似研究。在本研究中，我们使用全局对应分析（CA）、组内CA和组间CA比较了密码子使用偏好。我们发现蝙蝠RaTG13病毒在orf1ab、刺突和核衣壳基因中与SARS-CoV-2的整体密码子使用模式最匹配，而穿山甲P1E病毒在膜基因中有更相似的密码子使用。一般发现SARS-CoV-2的氨基酸使用模式与蝙蝠和人类SARSr-CoV相似。然而，我们发现SARS-CoV-2与其系统发育亲属在刺突和膜基因上的同义密码子使用差异更大，这表明SARS-CoV-2的这两个基因受到不同的进化压力。
