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

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

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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,6 799 transmission chains and 1 766 transmission networks were reconstructed,with chain lengths ranging from 1-9 nodes.The root node samples of the 1 766 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.

SARS-CoV-2Transmission chainTransmission networkAncestor-offspring relationshipDe novo mutationBack mutationSecondary mutation

Chao-Yuan Cheng、Zhi-Bin Zhang

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State Key Laboratory of Integrated Management of Pest Insects and Rodents,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China

CAS Center for Excellence in Biotic Interactions,University of Chinese Academy of Sciences,Beijing 100049,China

Ministry of Science and Technology of the People's Republic of ChinaInstitute of Zoology,Chinese Academy of SciencesInstitute of Zoology,Chinese Academy of Sciences

2021YFC0863400E0517111E122G611

2023

10.24272/j.issn.2095-8137.2022.535

动物学研究
中国科学院昆明动物研究所 中国动物学会

动物学研究

CSTPCDCSCD
影响因子：0.582
ISSN：0254-5853
年,卷(期)：2023.44(3)
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