北京市朝阳区1例输入性SARS-CoV-2全基因组序列分析  

Analysis of Complete Genome Sequence of an Imported Case of SARS-CoV-2 in Chaoyang District,Beijing,China

作　　者：韩桃利 王海滨[1] 焦洋[1] 雷娜[1] 高艳[1] 赵剑虹[1] 田甜[1] 董歧[1] 段杉[1] 孙灵利[1] HAN Taoli;WANG Haibin;JIAO Yang;LEI Na;GAO Yan;ZHAO Jianhong;TIAN Tian;DONG Qi;DU AN Shan;SUN Lingli(Center for Disease Control and Prevention of Chaoyang District,Beijing 100021,China)

机构地区：[1]北京市朝阳区疾病预防控制中心,北京100021

出　　处：《病毒学报》2020年第5期745-750,共6页Chinese Journal of Virology

基　　金：环境模拟与污染控制国家重点联合实验室(清华大学)2020年度开放课题(项目号:20K01ESPCT),题目:污水中新型冠状病毒检测与风险识别;社会发展计划(项目号:CYSF2011),题目:2022年冬奥会突发公共卫生事件应急保障技术平台建设。

摘　　要：北京市朝阳区在连续40d没有新增本土COVID-19确诊病例的情况下,出现了1例潜伏期超过14d的境外回国COVID-19确诊病例。为分析北京市朝阳区1例COVID-19患者是否为输入病例,进行了全基因组序列测定和遗传特性分析,本研究采用高通量测序技术配合Ion Torrent系列仪器和试剂对患者咽拭子中的SARS-CoV-2进行测序,同时应用对应插件或软件分析其全基因组同源性和变异情况。结果显示,该病例标本中测得1株SARS-CoV-2毒株,共29 876 bp,BLAST结果显示与其他国家和地区分离株的相似性高于与中国分离株的相似性。系统进化树中该毒株与2003年感染人的SARS冠状病毒和蝙蝠中分离的SARS冠状病毒明显不同,分处不同进化分支;该毒株与中国分离株分处不同的簇,而和美国分离株聚集在一簇。另外,突变分析显示存在3个改变氨基酸性质的非同义突变。本研究提示,该病例为美国输入的SARS-CoV-2感染病例,应注意境外输入性COVID-19的传播,并适当延长隔离观察期限;该毒株在患者的1例关联病例中发生了部分核苷酸突变,对SARS-CoV-2的致病力等的影响有待进一步研究。One imported confirmed case of COVID-19 with incubation period exceeding 14 days was found after 40 consecutive days without new confirmed case of COVID-19 in Chaoyang District,Beijing,China. To analyze whether one patient with coronavirus disease 2019(COVID-19)in Chaoyang District,Beijing,China,was an imported case and explore the complete genomics characteristics of SARS-CoV-2 that causes COVID-19,SARS-CoV-2 was sequenced by high-throughput sequencing combined with the Ion Torrent ? series of instruments and reagents. The homology and variation of the whole genome were analyzed by the corresponding plug-ins. A total of 29,876 bp of SARS-CoV-2 was detected. Blast results showed that the homology with the isolates from other countries and regions was higher than that of the isolates from China. In the phylogenetic tree,the strain was different from that of SARS-CoV from 2003 that infected humans and bats,and had different evolutionary branches;it had different clusters to those of the Chinese strain,but had a cluster close to that of the American strain. Mutation analyses showed three non-synonymous mutations which changed the properties of amino acids. The present study suggested that this was a SARS-CoV-2 infection case imported from the USA. And so we should pay attention to the transmission and infection of imported COVID-19 cases,and prolong the period of medical observation appropriately. Some base mutations are noted in patients’ families,and the impact on SARS-CoV-2 pathogenicity merits further study.

关 键 词：SARS-CoV-2 COVID-19 高通量测序 Ion Torrent 输入病例 

分 类 号：R373.1[医药卫生—病原生物学] R511[医药卫生—基础医学]