Shahhosseini Nariman, Wong Gary, Kobinger Gary P, Chinikar Sadegh
Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada.
Pasteur Institute of Shanghai, China.
Gene Rep. 2021 Jun;23:101045. doi: 10.1016/j.genrep.2021.101045. Epub 2021 Feb 16.
In late 2019, a novel Coronavirus emerged in China. Perceiving the modulating factors of cross-species virus transmission is critical to elucidate the nature of virus emergence. Using bioinformatics tools, we analyzed the mapping of the SARS-CoV-2 genome, modeling of protein structure, and analyze the evolutionary origin of SARS-CoV-2, as well as potential recombination events. Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV. However, the Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats. Further recombination analysis revealed the pathway for spillover transmission from Bat-SL-CoV-2 and Pangolin-CoV. Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2. Nevertheless, the role of mutations should be noted as another influencing factor in the continuing evolution and resurgence of novel SARS-CoV-2 variants.
2019年末，一种新型冠状病毒在中国出现。了解跨物种病毒传播的调节因素对于阐明病毒出现的本质至关重要。我们使用生物信息学工具，分析了严重急性呼吸综合征冠状病毒2（SARS-CoV-2）基因组的图谱、蛋白质结构建模，并分析了SARS-CoV-2的进化起源以及潜在的重组事件。系统发育树分析表明，在完整病毒基因组层面，SARS-CoV-2与蝙蝠严重急性呼吸综合征冠状病毒2（Bat-SL-CoV-2，即RaTG13）具有最密切的进化关系，与穿山甲冠状病毒的相似性较低。然而，SARS-CoV-2的受体结合域（RBD）在氨基酸水平上与穿山甲冠状病毒几乎相同，这表明溢出传播可能直接来自穿山甲，而非蝙蝠。进一步的重组分析揭示了从Bat-SL-CoV-2和穿山甲冠状病毒溢出传播的途径。在此，我们为Bat-SL-CoV-2和穿山甲冠状病毒之间的重组事件提供了证据，该事件导致了SARS-CoV-2的出现。尽管如此，应注意到突变在新型SARS-CoV-2变体持续进化和再次出现中的作用，它是另一个影响因素。
