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Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics

摘要DEAR EDITOR,The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a tremendous threat to human society.SARS-CoV-2 is airborne and transmits primarily through social contact;however,whether cold chain-related transmission has occurred remains highly debated(Han&Liu,2022;Lewis,2021;Ma et al.,2021;Mallapaty et al.,2021;Pang et al.,2020;Wu et al.,2021).Here,we present a novel method and identify two transmission routes based on lineage-specific reductions in the SARS-CoV-2 evolutionary rate.After analyzing 4 039 521 SARS-CoV-2 genomic sequences,we identified two outbreaks in Xinfadi-Beijing and Auckland that may be cold-chain related,caused by two mutation-dormant variants,respectively.A mutation-dormant variant represents a variant with a(nearly)identical genomic sequence repeatedly isolated over a long period of time.Dalian outbreak in July 2020 and Yingkou outbreak ten months later were epidemiologically connected and derived from a mutation-dormant variant.Furthermore,the earliest SARS-CoV-2 variant(i.e.,the most recent common ancestor of SARS-CoV-2)was also found to be a mutation-dormant variant.Its spillover events were repeatedly observed during the last two years,indicating that the COVID-19 outbreak in Wuhan may be associated with spillover events from cold-chains.In all observed cases,the virus re-started mutating after spillover events from cold-chains.Systematic identification of spillover events revealed that the frequency of cold-chain related transmission is in the order of 0.1%-10%.Our results indicate that that cold-chain related transmission is rare but may have occurred globally.

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作者 Dalang Yu [1] Junwei Zhu [2] Jianing Yang [1] Yi-Hsuan Pan [3] Hailong Mu [4] Ruifang Cao [4] Bixia Tang [2] Guangya Duan [5] Zi-Qian Hao [1] Long Dai [6] Guo-Ping Zhao [7] Ya-Ping Zhang [8] Wenming Zhao [5] Guoqing Zhang [1] Haipeng Li [1] 学术成果认领
作者单位 National Genomics Data Center&Bio-Med Big Data Center,CAS Key Laboratory of Computational Biology,Shanghai Institute of Nutrition and Health,Chinese Academy of Sciences,Shanghai 200031,China;University of Chinese Academy of Sciences,Beijing 100049,China [1] National Genomics Data Center,Beijing Institute of Genomics,Chinese Academy of Sciences and China National Center for Bioinformation,Beijing 100101,China [2] Key Laboratory of Brain Functional Genomics of Ministry of Education,School of Life Science,East China Normal University,Shanghai 200062,China [3] National Genomics Data Center&Bio-Med Big Data Center,CAS Key Laboratory of Computational Biology,Shanghai Institute of Nutrition and Health,Chinese Academy of Sciences,Shanghai 200031,China [4] National Genomics Data Center,Beijing Institute of Genomics,Chinese Academy of Sciences and China National Center for Bioinformation,Beijing 100101,China;University of Chinese Academy of Sciences,Beijing 100049,China [5] National Genomics Data Center&Bio-Med Big Data Center,CAS Key Laboratory of Computational Biology,Shanghai Institute of Nutrition and Health,Chinese Academy of Sciences,Shanghai 200031,China;Shanghai Southgene Technology Co.Ltd,Shanghai 201203,China [6] National Genomics Data Center&Bio-Med Big Data Center,CAS Key Laboratory of Computational Biology,Shanghai Institute of Nutrition and Health,Chinese Academy of Sciences,Shanghai 200031,China;Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences,Shanghai 200032,China;School of Life and Health Sciences,Hangzhou Institute for Advanced Study,University of Chinese Academy of Sciences,Hangzhou,Zhejiang 310024,China [7] State Key Laboratory of Genetic Resources and Evolution,Yunnan Laboratory of Molecular Biology of Domestic Animals,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming,Yunnan 650223,China [8]
发布时间 2022-11-18
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2022年43卷5期

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