Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model

作     者：Chao-Yuan Cheng Zhi-Bin Zhang Chao-Yuan Cheng;Zhi-Bin Zhang

作者机构：State Key Laboratory of Integrated Management of Pest Insects and RodentsInstitute of ZoologyChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing 100049China 

出 版 物：《Zoological Research》 (动物学研究（英文）)

年 卷 期：2023年第44卷第3期

页      面：494-504页

核心收录：

学科分类：0710[理学-生物学] 1004[医学-公共卫生与预防医学(可授医学、理学学位)] 100401[医学-流行病与卫生统计学] 10[医学] 

基　　金：supported by the Ministry of Science and Technology of the People’s Republic of China(2021YFC0863400) Institute of Zoology,Chinese Academy of Sciences(E0517111,E122G611)。 

主　　题：SARS-CoV-2 Transmission chain Transmission network Ancestor-offspring relationship De novo mutation Back mutation Secondary mutation 

摘      要：The coronavirus disease 2019(COVID-19)pandemic has greatly damaged human society,but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)pathogen remain unclear.Here,we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations.We explored the position(i.e.,root,middle,or tip)of early detected samples in the evolutionary tree of SARS-CoV-2.In total,6799 transmission chains and 1766 transmission networks were reconstructed,with chain lengths ranging from 1-9 nodes.The root node samples of the 1766 transmission networks were from 58 countries or regions and showed no common ancestor,indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected(i.e.,all samples were located at the tip position of the evolutionary tree).No root node sample was found in any sample(n=31,all from the Chinese mainland)collected in the first 15 days from 24 December 2019.Results using six-month data or RaTG13-referenced mutation data were similar.The reconstruction method was verified using a simulation approach.Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan,China.Thus,a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.