Analysis of codon usage of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and its adaptability in dog
Analysis of codon usage of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and its adaptability in dog
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DOI：
10.1016/j.virusres.2020.198113
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发表时间：
2020-10-15
期刊：
影响因子：
5
通讯作者：
Borah, Probodh
中科院分区：
文献类型：
--
作者：
Dutta, Rupam;Buragohain, Lukumoni;Borah, Probodh
严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）被认为是造成本世纪最具破坏性大流行的危及生命的病毒之一。这种病毒的起源尚不清楚。为了阐明其分子进化和基因表达调控，了解密码子的使用是一个先决条件。在这项研究中，我们试图记录人类和狗的SARS-CoV-2的全基因组密码子使用情况以及影响密码子使用模式的各种因素。SARS-CoV-2基因组中A和U核苷酸相对丰富，同义密码子使用分析显示首选同义密码子多以A/U结尾。对c- gc3s、中立和奇偶规则2图的分析表明，自然选择和其他未定义因素主导了SARS-CoV2的密码子使用偏好，而突变压力的影响相对较小。SARS-CoV-2的密码子适应指数和密码子相对失优指数揭示了人类比狗更适合适应宿主。这些结果增强了我们对新型人类SARS-CoV-2的进化及其在狗中的适应性的理解。
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is recognized as one of the life-threatening viruses causing the most destructive pandemic in this century. The genesis of this virus is still unknown. To elucidate its molecular evolution and regulation of gene expression, the knowledge of codon usage is a prerequisite. In this study, an attempt was made to document the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SARS-CoV-2 in human and dog. The SARS-CoV-2 genome showed relative abundance of A and U nucleotides and relative synonymous codon usage analysis revealed that the preferred synonymous codons mostly end with A/U. The analysis of ENc-GC3s, Neutrality and Parity rule 2 plots indicated that natural selection and other undefined factors dominate the overall codon usage bias in SARS-CoV2 whereas the impact of mutation pressure is comparatively minor. The codon adaptation index and relative codon deoptimization index of SARS-CoV-2 deciphered that human is more favoured host for adaptation compared to dog. These results enhance our understanding of the factors involved in evolution of the novel human SARS-CoV-2 and its adaptability in dog.