Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
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DOI：
10.1038/s41564-020-0771-4
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发表时间：
2020-07-28
影响因子：
28.3
通讯作者：
Robertson, David L.
中科院分区：
文献类型：
--
作者：
Boni, Maciej F.;Lemey, Philippe;Robertson, David L.
在这份手稿中，作者解决了SARS-CoV-2出现的进化问题。他们发现，SARS-CoV-2不是迄今为止检测到的任何Sarbecoviruses的重组体，与SARS-CoV-2最密切相关的蝙蝠和穿山甲序列可能在几十年前或更早的时候从人类SARS-CoV-2样本中分离出来。最近出现的人类冠状病毒SARS-CoV-2存在突出的进化问题，包括宿主物种的作用，重组的作用及其与动物病毒的分化时间。我们发现，Sarbecoviruses-病毒亚属包含SARS-CoV和SARS-CoV-2-经历频繁的重组，并表现出空间结构的遗传多样性在中国的区域尺度。SARS-CoV-2本身不是迄今为止检测到的任何Sarbecoviruses的重组体，其受体结合基序对人类ACE 2受体的特异性很重要，似乎是蝙蝠病毒共有的祖先特征，而不是最近通过重组获得的特征。为了采用系统发生年代测定方法，用三种独立的方法去除68个基因组的肉瘤病毒比对的重组区域。贝叶斯进化率和分歧日期估计被证明是一致的，这三种方法和两个不同的先前规范的进化率的基础上HCoV-OC 43和MERS冠状病毒。SARS-CoV-2和蝙蝠Sarbecovirus储库之间的分歧日期估计为1948年（95%最高后验密度（HPD）：1879-1999），1969年（95% HPD：1930-2000）和1982年（95% HPD：1948-2009），表明引起SARS-CoV-2的谱系已经在蝙蝠中传播了几十年而未被注意。
In this manuscript, the authors address evolutionary questions on the emergence of SARS-CoV-2. They find that SARS-CoV-2 is not a recombinant of any sarbecoviruses detected to date, and that the bat and pangolin sequences most closely related to SARS-CoV-2 probably diverged several decades ago or possibly earlier from human SARS-CoV-2 samples.There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses-the viral subgenus containing SARS-CoV and SARS-CoV-2-undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879-1999), 1969 (95% HPD: 1930-2000) and 1982 (95% HPD: 1948-2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.