河南省首起奥密克戎COVID-19疫情全基因组特征与溯源分析  

Whole-genome characterization and traceability analysis of the first COVID-19 outbreak caused by Omicron variant in Henan Province

作　　者：宋云 卢世栋 胡晓 朱琳 张白帆[1] 潘静静[1] 李东晓 卫海燕[1] 李懿[1] 赵升[2] 王海峰[1] 叶莹[1] 黄学勇[1] 马红霞[1] Song Yun;Lu Shidong;Hu Xiao;Zhu Lin;Zhang Baifan;Pan Jingjing;Li Dongxiao;Wei Haiyan;Li Yi;Zhao Sheng;Wang Haifeng;Ye Ying;Huang Xueyong;Ma Hongxia(Henan Provincial Key Laboratory of Infectious Disease Microbiology,Infectious Disease Control and Prevention Institute,Henan Provincial Center for Disease Control and Prevention,Zhengzhou 450016,China;Institute of Immunization Prevention and Planning,Henan Provincial Center for Disease Control and Prevention,Zhengzhou 450016,China)

机构地区：[1]河南省疾病预防控制中心传染病预防控制所,河南省传染病病原生物重点实验室,郑州450016 [2]河南省疾病预防控制中心免疫预防与规划所,郑州450016

出　　处：《中华微生物学和免疫学杂志》2023年第4期271-278,共8页Chinese Journal of Microbiology and Immunology

基　　金：新型冠状病毒防控应急攻关首批项目(201100310800);河南省中青年卫生健康科技创新领军人才培养项目(YXKC2020006);河南省医学科技攻关计划联合共建项目(LHGJ20220150);河南省医学科技攻关项目(23050103)。

摘　　要：目的对河南省首起本土奥密克戎COVID-19确诊病例的呼吸道标本进行SARS-CoV-2全基因组测序, 分析基因组突变及分子溯源情况。方法采用全基因组测序技术对2022年1月7日—1月29日疫情相关的COVID-19病例阳性样本进行全基因组测序和序列比对分析, 分析病毒全基因组序列的一致性和变异进化情况。结果通过SARS-CoV-2基因组高通量测序, 共获得120例病例的SARS-CoV-2全基因组序列, 占安阳COVID-19疫情总病例数的25.64%(120/468)。与武汉参考株(NC045512.2)相比, 120例病例的全基因组序列存在57~59个核苷酸突变位点, 在共享57个核苷酸位点的基础上增加1~2个核苷酸突变位点, 均属于VOC/Omicron变异株(BA.1.1进化分支), 基因组序列高度同源。其中, 首发病例A全基因组序列含有57个核苷酸突变位点, 首发病例B全基因组序列在含有57个相同的核苷酸突变位点基础上, 增加1个特有变异位点(C1594T), 提示二者为同一传播链。经中国疾病预防控制中心和河南省疾病预防控制中心与国内本土病例和输入病例数据库比对, 发现与外省现有本地疫情属同一传播链。同时流行病学调查显示, 病例A在1月2日接触从外省返回的表弟及其家人, 有明确的外省疫区暴露史。结论结合病毒基因组学及流行病学综合分析表明, 判定河南省安阳市COVID-19疫情是由2021年12月28日从外省返回安阳市的1名在校大学生导致的本土疫情, 与外省现有本地疫情属同一传播链。Objective To analyze the whole genome of Omicron variants causing the first local Omicron outbreak in Henan Province and to investigate the mutations in the SARS-CoV-2 genome for source tracing.Methods Respiratory tract samples from COVID-19 cases in the Omicron outbreak in Henan Province from January 7 to 29,2022 were subjected to whole-genome sequencing and sequence alignment analysis.Whole-genome identity,variations and evolution of the Omicron variants were analyzed.Results Through high-throughput sequencing,the whole-genome sequences of SARS-CoV-2 were obtained from 120 cases,which accounted for 25.64%(120/468)of all COVID-19 cases in Anyang during the same period.Compared with the genome of Wuhan reference strain(NC_045512.2),there were 57-59 nucleotide mutation sites in the 120 whole genome sequences,and one or two nucleotide mutation sites were added to the shared 57 nucleotide sites.All of the 120 strains were VOC/Omicron(BA.1.1)variants and shared high homology.The whole-genome sequence obtained from the first case A contained 57 nucleotide mutation sites,while apart from the 57 identical nucleotide mutation sites,one specific mutation site(C1594T)was found in the whole-genome sequence obtained from the first case B,suggesting that the two cases were in the same transmission chain.After comparing with the database of domestic and imported cases by the Chinese Center for Disease Control and Prevention and the Henan Provincial Center for Disease Control and Prevention,it was found that the current outbreak was linked with the same transmission chain as the existing local epidemics in other provinces.Moreover,epidemiological investigation showed that on January 2,case A had come into contact with her cousin and his family who returned from an affected area outside the province.Conclusions Based on the gene sequencing results and epidemiological investigation,the COVID-19 outbreak in Anyang city,Henan Province was a local epidemic and the source of it was a college student who returned to Anyang city from o

关 键 词：SARS-CoV-2 奥密克戎变异株 基因组特征 

分 类 号：R373[医药卫生—病原生物学]