The high diversity of SARS-CoV-2-related coronaviruses in pangolins alters potential ecological risks
Min‐Sheng Peng, 中国科学院昆明动物研究所遗传资源与进化国家重点实验室, 云南省畜禽分子生物学重点实验室, 云南 昆明 650201, 中国, Jianbo Li, Zheng‐Fei Cai, Hang Liu, Xiaolu Tang, Ruochen Ying, Jianan Zhang, Jiajun Tao, Tingting Yin, Tao Zhang, Jingyang Hu, Ru‐Nian Wu, Zhongyin Zhou, Zhigang Zhang, Li Yu, Yong‐Gang Yao, Zheng‐Li Shi, Xuemei Lu, Jian Lü, Ya‐Ping Zhang, 中国科学院大学昆明生命科学学院, 云南 昆明 650204, 中国, 中国科学院昆明动物研究所 中国科学院明动物研究所-香港中文大学生物资源与疾病分子机理联合实验室, 云南 昆明 650201, 中国, 云南大学云南生物资源保护与利用国家重点实验室, 云南 昆明 650091, 中国, 北京大学生命科学学院蛋白质与植物基因研究国家重点实验室, 生物信息中心, 北京 100871, 中国, 博瑞迪生物技术有限公司, 河北 石家庄 050035, 中国, 中国科学院昆明动物研究所中国科学院-云南省动物模型与人类疾病机理重点实验室, 云南 昆明 650201, 中国, 中国科学院武汉病毒研究所中国科学院高致病性病原生物学与生物安全重点实验室, 湖北 武汉 430071, 中国, 中国科学院动物进化与遗传前沿交叉卓越创新中心, 云南 昆明 650201, 中国
Abstract
Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks. A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses (SC2r-CoVs). Here, we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species, and detected positive signals in muscles of four <i>Manis javanica</i> and, for the first time, one <i>M. pentadactyla</i>. Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia. Using in-solution hybridization capture sequencing, we assembled a partial pangolin SC2r-CoV (pangolin-CoV) genome sequence of 22895 bp (MP20) from the <i>M. pentadactyla</i> sample. Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in <i>M. javanica</i> seized by Guangxi Customs. A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated. Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated. Given the potential infectivity of pangolin-CoVs, the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.