Identification of the host reservoir of SARS-CoV-2 and determining when it spilled over into humans
Identification of the host reservoir of SARS-CoV-2 and determining when it spilled over into humans
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DOI：
10.1101/2023.11.25.568670
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发表时间：
2024-03
期刊：
影响因子：
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通讯作者：
Vidyavathi Pamjula;Norval J.C Strachan;F. Pérez-Reche
中科院分区：
文献类型：
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作者：
Vidyavathi Pamjula;Norval J.C Strachan;F. Pérez-Reche
自2019年武汉出现SARS-CoV-2以来，其宿主库尚未建立。对71株冠状病毒和1株布雷达病毒的全基因组序列（WGS）进行了系统发育分析。使用贝叶斯进化分析抽样树（BEAST），将包括两种SARS-CoV-2武汉病毒和8种最密切相关的冠状病毒序列的子集用于宿主库分析。在这些基因组中，20个核心基因组片段被组合成两组，每组具有相似的时钟速率（5.9×10−3和1.1×10−3 subs/site/year）。将这些片段组的结果合并，得到了SARS-COV-2和蝙蝠分离株RaTG 13在2007年左右共享的最近共同祖先（MRCA）（95% HPD：2003，2011）。此外，MRCA的宿主最有可能是蝙蝠（概率为0.64 - 0.87）。因此，对人类的溢出一定发生在2007年至2019年之间的某个时候，蝙蝠可能是最有可能的宿主。
Since the emergence of SARS-CoV-2 in Wuhan in 2019 its host reservoir has not been established. Phylogenetic analysis was performed on whole genome sequences (WGS) of 71 coronaviruses and a Breda virus. A subset comprising two SARS-CoV-2 Wuhan viruses and 8 of the most closely related coronavirus sequences were used for host reservoir analysis using Bayesian Evolutionary Analysis Sampling Trees (BEAST). Within these genomes, 20 core genome fragments were combined into 2 groups each with similar clock rates (5.9×10−3 and 1.1×10−3 subs/site/year). Pooling the results from these fragment groups yielded a most recent common ancestor (MRCA) shared between SARS-COV-2 and the bat isolate RaTG13 around 2007 (95% HPD: 2003, 2011). Further, the host of the MRCA was most likely a bat (probability 0.64 - 0.87). Hence, the spillover into humans must have occurred at some point between 2007 and 2019 and bats may have been the most likely host reservoir.