新型冠状病毒基因组的演化分析及谱系划分

作     者：唐小鹿 应若晨 姚欣敏 李广浩 吴长城 汤易雨立 李志达 邝碧姗 伍锋 池昌盛 杜晓满 覃依 高胜寒 胡松年 马俊才 刘天罡 庞星火 王建伟 赵国屏 谭文杰 张亚平 吕雪梅 陆剑 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

作者机构：State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyCenter for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming 650223China Beijing Institute of GenomicsChinese 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 CenterThe Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and Wuhan University School of Pharmaceutical SciencesWuhan 430071China Beijing Center for Disease Prevention and Control(CDC)&Research Center for Preventive Medicine of BeijingBeijing 100013China NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Key Laboratory of Respiratory Disease PathogenomicsChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Key Laboratory of Synthetic BiologyInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200032China NHC Key Laboratory of BiosafetyNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China 

出 版 物：《Science Bulletin》 (科学通报（英文版）)

年 卷 期：2021年第66卷第22期

页      面：2297-2311,M0004页

核心收录：

学科分类：1002[医学-临床医学] 100201[医学-内科学(含：心血管病、血液病、呼吸系病、消化系病、内分泌与代谢病、肾病、风湿病、传染病)] 10[医学] 

基　　金：supported by the National Natural Science Foundation of China(91731301 and U1902201) the Ministry of Science and Technology of the People’s Republic of China(2020YFC0847000) the Light of West China Program of the Chinese Academy of Sciences 

主　　题：COVID-19 Evolutionary analysis Compensatory advantageous mutation Adaptive evolution Lineage designation 

摘      要：新型冠状病毒肺炎(COVID-19,新冠病毒)的流行严重影响了世界经济和人类健康.随着新冠病毒基因组序列的迅速积累,国际上已经检测和发表了成千上万的基因组变异.为了更好地追踪新冠病毒基因组进化轨迹,并实时解析疫情发展进程中的病毒基因组特征,本研究分析了121618个高质量的病毒基因组.基于参考基因组第8782和28144位点上的单核苷酸变异(SNV),首先将这些病毒基因组划分为L和S两个主要谱系;根据第3037、14408和23403位点上的SNV,进一步将L谱系划分为L1和L2两个主要亚谱系.在此基础上,根据另外201个基因组变异位点,逐级划分出了130个亚谱系(S中37个, L1中35个, L2中58个).该谱系/亚谱系划分系统具有层次结构,反映了主要谱系中的亚谱系之间的亲缘关系.本研究同时建立了一个配套网站(***),不仅方便用户查看亚谱系信息,而且提供了谱系划分工具,用户可以通过上传新冠病毒基因组序列,做谱系类型鉴定.最后,本研究讨论了代偿突变和自然选择在新冠病毒进化过程中可能起到的作用.本研究将增进对新冠病毒基因组时空动态进化的理解.