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Evolutionary analysis and lineage designation of SARS-CoV-2 genomes

Science Bulletin 2021年第22期66卷 2297-2311,M0004页

作者： Xiaolu Tang Ruochen Ying Xinmin Yao Guanghao Li Changcheng Wu Yiyuli Tang Zhida Li Bishan Kuang Feng Wu Changsheng Chi Xiaoman Du Yi Qin Shenghan Gao Songnian Hu Juncai Ma Tiangang Liu Xinghuo Pang Jianwei Wang Guoping Zhao Wenjie Tan Yaping Zhang Xuemei Lu Jian Lu State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyCenter for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming 650223China Beijing Institute of Genomics Chinese Academy of SciencesBeijing 100101China Yuxi Rongjian Information Technology Co. Ltd.Yuxi 653100China State Key Laboratory of Microbial Resources(SKLMR) The Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China the microresource and big data center The Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical SciencesWuhan 430071China Beijing center for Disease Prevention and Control(CDC)&Research center for Preventive Medicine of Beijing Beijing 100013China NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Key Laboratory of Synthetic Biology Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200032China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China

The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global *** the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly *** improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 *** divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and ***,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic *** lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major *** also provide a companion website(***)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage ***,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s *** efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.

关键词： COVID-19 Evolutionary analysis Compensatory advantageous mutation Adaptive evolution Lineage designation

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