Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, WalesWales SY3 3FL, UK.
The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
Viruses. 2020 Dec 30;13(1):49. doi: 10.3390/v13010049.
In 2019, a novel coronavirus, SARS-CoV-2/nCoV-19, emerged in Wuhan, China, and has been responsible for the current COVID-19 pandemic. The evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development. As part of the international "CoronaHack" in April 2020, we employed a collection of contemporary methodologies to compare the genomic sequences of coronaviruses isolated from human (SARS-CoV-2; n = 163), bat (bat-CoV; n = 215) and pangolin (pangolin-CoV; n = 7) available in public repositories. We have also noted the pangolin-CoV isolate MP789 to bare stronger resemblance to SARS-CoV-2 than other pangolin-CoV. Following de novo gene annotation prediction, analyses of gene-gene similarity network, codon usage bias and variant discovery were undertaken. Strong host-associated divergences were noted in ORF3a, ORF6, ORF7a, ORF8 and S, and in codon usage bias profiles. Last, we have characterised several high impact variants (in-frame insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and may be highlighting loci of potential functional relevance.
2019 年，一种新型冠状病毒 SARS-CoV-2/nCoV-19 在我国武汉出现，并引发了当前的 COVID-19 大流行。该病毒的进化起源仍不清楚，了解其复杂的突变特征可能有助于指导疫苗的设计和开发。作为 2020 年 4 月国际“CoronaHack”的一部分，我们采用了一系列当代方法，比较了公共数据库中分离出的来自人类（SARS-CoV-2；n = 163）、蝙蝠（bat-CoV；n = 215）和穿山甲（pangolin-CoV；n = 7）的冠状病毒的基因组序列。我们还注意到，穿山甲-CoV 分离株 MP789 与 SARS-CoV-2 的相似度强于其他穿山甲-CoV。在进行从头基因注释预测后，我们进行了基因-基因相似性网络、密码子使用偏好和变异发现分析。在 ORF3a、ORF6、ORF7a、ORF8 和 S 以及密码子使用偏好谱中观察到强烈的宿主相关分歧。最后，我们在蝙蝠-CoV 和穿山甲-CoV 群体中鉴定出了几个具有高影响的变异（框内插入/缺失或终止增益），其中一些位于相同的氨基酸位置，可能突出了潜在功能相关的基因座。
