Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2
Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2
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DOI：
10.1002/jmv.25731
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发表时间：
2020-06-01
影响因子：
12.7
通讯作者：
Chaillon, Antoine
中科院分区：
文献类型：
--
作者：
Li, Xingguang;Zai, Junjie;Chaillon, Antoine
为了研究中国最近爆发的严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的进化历史，分析了2019年12月24日至2020年2月3日期间来自中国和其他地方的70株病毒株的基因组。为了探索SARS-CoV-2病毒的潜在中间动物宿主，我们重新分析了穿山甲和代表性SARS相关冠状病毒蝙蝠分离株的病毒组数据集，特别关注刺突糖蛋白基因。我们进行了系统发育，分裂网络，传输网络，似然映射，和基因组的比较分析。基于使用tip-dating方法的贝叶斯时间尺度系统发育分析，我们估计了SARS-CoV-2最近共同祖先的时间和进化速率，分别为2019年11月22日至24日和每年每个位点1.19至1.31 x 10（-3）次替换。我们的研究结果还表明，BetaCoV/bat/Yunnan/RaTG 13/2013病毒与SARS-CoV-2病毒的相似性高于从两个穿山甲样品（SRR 10168377和SRR 10168378）中获得的冠状病毒。我们还确定了一个独特的肽（PRRA）插入在人类SARS冠状病毒-2，这可能是参与了由细胞蛋白酶的刺突蛋白的蛋白水解裂解，因此可能会影响宿主范围和传播性。有趣的是，穿山甲携带的冠状病毒没有RRAR基序。因此，我们得出结论，导致最近COVID-19爆发的人类SARS-CoV-2病毒并非直接来自穿山甲。
To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 x 10(-3) substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.