深圳市首例本土新型冠状病毒Omicron变异株BA.1和BA.2亚型的基因组特征分析  

Molecular Characterization of the First Local BA.1 and BA.2 Omicron Strains of SARS⁃CoV⁃2 in Shenzhen,China

作　　者：屈雅丽 陈龙[2] 唐秀娟[3] 陈建成 吕秋莹[3] 孙颖 魏欣仪 卢清菊 高玮[3] 朱灿 李诗敏 周莎 张仁利[2] 胡贵方[1] 何雅青[1,2] QU Yali;CHEN Long;TANG Xiujuan;CHEN Jiancheng;LYU Qiuying;SUN Ying;WEI Xinyi;LU Qingju;GAO Wei;ZHU Can;LI Shimin;ZHOU Sha;ZHANG Renli;HU Guifang;HE Yaqing(Department of Epidemiology,School of Public Health,Southern Medical University,Guangzhou 510515,China;Institute of Pathogen Biology,Shenzhen Center for Disease Control and Prevention,Shenzhen 518055,China;Department of Communicable Diseases Control and Prevention,Shenzhen Center for Disease Control and Prevention,Shenzhen 518055,China;School of Public Health,University of South China,Hengyang 421001,China)

机构地区：[1]南方医科大学公共卫生学院流行病学系,广州510515 [2]深圳市疾病预防控制中心病原生物研究所,深圳518055 [3]深圳市疾病预防控制中心传染病预防控制所,深圳518055 [4]南华大学公共卫生学院,衡阳421001

出　　处：《病毒学报》2022年第4期769-775,共7页Chinese Journal of Virology

基　　金：深圳市科技创新委员会技术攻关重点项目(项目号:JSGG20200225152648408),题目:基于SARS⁃CoV⁃2冠状病毒表面Spike蛋白的早期快检技术研发;深圳市科技创新委员会技术攻关重点项目(项目号JSGG20210901145004012),题目:新冠病毒变异株快速检测试剂盒关键技术研发。

摘　　要：为了解本土新型冠状病毒(SARS⁃CoV⁃2)变异株的分子特征,本研究对深圳市首次确认的本土Omicron变异株的BA.1和BA.2亚型毒株进行了基因组特征分析。通过Illumina测序,2022年1月16号和1月18号分别获得了深圳市首次确认的本土Omicron变异株BA.1亚型和BA.2亚型毒株的基因组长度分别为29862nt和29391nt。与参考株Wuhan⁃Hu⁃1(NC_045512.2)比较,深圳BA.1亚型毒株hCoV⁃19/Shenzhen/IVDC⁃01⁃16/2022有60个核苷酸变异位点,深圳本土BA.2亚型毒株hCoV⁃19/Shenzhen/IVDC⁃01⁃18/2022有67个核苷酸变异位点。通过与GISAID数据库序列比对发现,深圳BA.1亚型毒株hCoV⁃19/Shenzhen/IVDC⁃01⁃16/2022与2021年12月加拿大的毒株hCoV⁃19/Canada/NB⁃CHUDGLD⁃1312⁃MM01207R/2021相似性最高,基因组序列一致性为100%。深圳本土BA.2亚型毒株hCoV⁃19/Shenzhen/IVDC⁃01⁃18/2022与2021年12月日本的毒株hCoV⁃19/Japan/IC⁃2879/2021相似性最高,基因组序列仅在ORF6基因上表现出1个核苷酸差异(C27297T)。开展本土的SARS⁃CoV⁃2病毒的分子监测,对预防与控制本地新型冠状病毒肺炎(COVID⁃19)暴发与流行具有重要意义。We wished to investigate the origin of indigenous severe acute respiratory syndrome coronavirus 2(SARS⁃CoV⁃2)variants.Using an Illumina platform for sequencing,the first confirmed indigenous BA.1 and BA.2 Omicron variants were obtained in Shenzhen(China)on 16 and 18 January 2022,respectively.The genome length of the two indigenous Omicron variants was 29,862 nt and 29,391 nt,respectively.Compared with the reference strain(Wuhan⁃HU⁃1(NC_045512.2)),the BA.1 Omicron strain hCoV⁃19/Shenzhen/IVDC⁃01⁃16/2022 had 60 nucleotide mutation sites.The BA.2 Omicron strain hCoV⁃19/Shenzhen/IVDC⁃01⁃18/2022 had 67 nucleotide mutation sites.Comparison of sequences using the GISAID database revealed the BA.1 strain hCoV⁃19/Shenzhen/IVDC⁃01⁃16/2022 to have the highest similarity with the December 2021 Canadian strain hCoV⁃19/Canada/NB⁃CHUDGLD⁃1312⁃MM01207R/2021,and the genome sequence was 100%identical.The BA.2 strain hCoV⁃19/Shenzhen/IVDC⁃01⁃18/2022 had the highest similarity with the Japanese strain hCoV⁃19/Japan/IC⁃2879/2021,with only one nucleotide difference in ORF6(C27297T).Molecular surveillance of local SARS⁃CoV⁃2 is crucial for the prevention and control of local outbreaks and epidemics of COVID⁃19.

关 键 词：Omicron变异株 BA.1亚型 BA.2亚型 基因组流行病学 新型冠状病毒(SARS⁃CoV⁃2) 

分 类 号：R373.1[医药卫生—病原生物学]