四川省40例境外输入新冠肺炎确诊病例病毒全基因组特征分析  

Whole genome sequence analysis of SARS-CoV-2 from 40 imported cases of confirmed COVID-19 in Sichuan

作　　者：徐佳楠[1] 冯玉亮 刘晨霞 杨慧萍[1] 潘明[1] 刘李[1] XU Jia-nan;FENG Yu-liang;LIU Chen-xia;YANG Hui-ping;PAN Ming;LIU Li(Institute of Microbiology,Sichuan Province Center for Disease Control and Prevention,Chengdu,Sichuan 610041,China)

机构地区：[1]四川省疾病预防控制中心微生物检验所,成都610041

出　　处：《中国病毒病杂志》2022年第4期284-289,共6页Chinese Journal of Viral Diseases

基　　金：四川省科技计划项目(2021YFQ0060)。

摘　　要：目的了解四川省2022年1—3月境外输入的新型冠状病毒(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)分子特征。方法选取2022年1—3月经由成都双流国际机场入境的182例境外输入新型冠状病毒肺炎(新冠肺炎)确诊病例的样本进行变异株核酸检测和病毒全基因组测序及其序列分析。对病例的呼吸道样本提取病毒RNA,用突变核酸检测试剂盒进行变异株核酸检测;采用Illumina测序平台进行病毒全基因组测序,采用Nextclade和Pangolin平台判定病毒谱系及型别,分析病毒的变异位点。与NCBI数据库中SARS-CoV-2参考序列进行全基因组遗传进化和抗原变异情况分析并构建系统进化树。结合病例的流行病学资料,分析病毒的来源和相关性。结果在182例确诊病例的样本中,检测出3例B.1.617.2突变和57例B.1.1.529突变。其余122例未检出上述两种变异突变。本研究共获得40条覆盖度>95%的SARS-CoV-2全基因组序列,Nextclade分型结果显示:3条属于21J型(Delta)、5条属于21K型(Omicron)、32条均属于21L型(Omicron);Pangolin分型结果显示:3条21J型(Delta)分别属于AY.4、AY.109和B.1.617.2,5条21K型(Omicron)均属于BA.1.1,32条21L型(Omicron)属于BA.2。这一结果与截至2022年3月GISAID SARS-CoV-2数据库中Omicron变异株的序列占比达到99.7%、具有绝对优势的结果一致。与参考株Wuhan-Hu-1(NC_045512.2)比较,3条21J型(Delta)的核苷酸变异位点分别为45、47和42个,氨基酸变异位点分别为36、25和36个;5条21K型(Omicron)的核苷酸变异位点中位数为59个(26~64个),氨基酸变异位点中位数为48个(10~53个);32条21L型(Omicron)的核苷酸变异位点中位数为71个(66~76个),氨基酸变异位点中位数为53个(40~56个)。进化分析结果显示:40条SARS-CoV-2序列均与目前流行的需要关注的新冠病毒变异株相关。结论四川省持续对境外输入确诊病例的SARS-CoV-2基因组进行全序列测定,使之逐渐形成一套系�Objective To understand the genomic characteristics of SARS-CoV-2 from 40 imported cases with confirmed COVID-19 in Sichuan during January and March 2022.Methods Total viral RNA was extracted from respiratory samples of 182 confirmed COVID-19 cases who entered China through Chendu International Airport from January to March 2022.Mutation nucleic acid detection kit was used to identify the mutant strains and Illumina sequencing platform was applied for whole genome sequence(WGS)of virus.SARS-CoV-2 reference sequences were downloaded from NCBI database for genetic evolution and antigen variation analysis.The Nextclade and Pangolin online virus analysis platform were used to determine the virus family and type,and to analyze the mutation loci of the virus.The phylogenetic tree was constructed,along with the epidemiological data of cases to analyze the source and correlation of viruses.Results Among 182 imported COVID-19 cases,B.1.617.2 mutations were identified in 3 cases and B.1.1.529 mutations were detected in 57 cases.A total of 40 SARS-CoV-2 whole genome sequences with coverage>95%were obtained in this study.Nextclade typing analysis showed that 3 sequences belonged to 21J(Delta),5 sequences belonged to 21K(Omicron)and the remaining 32 sequences belonged to 21L(Omicron).Pangolin typing analysis showed that the 3 sequences of 21J(Delta)belonged to AY.4,AY.109and B.1.617.2,the 5sequences of 21K(Omicron)all belonged to BA.1.1,and the remaining 32 sequences of 21L(Omicron)belonged to BA.2.Our sequence results were99.7%consistency with the Omicron variants sequences in current GISAID database.Compared with the reference sequence strain Wuhan-Hu-1(NC_045512.2),45,47and 42nucleotide variation sites and 36,25 and 36amino acid variation sites were found in the 3 sequences of 21J(Delta).There were average 59(26—64)nucleotide mutation sites and 48(10—53)amino acid mutation sites in the 5sequences of 21K(Omicron).The median number of nucleotide mutation sites of 71(66—76)and amino acid mutation sites of 53(40—56)wer

关 键 词：新型冠状病毒 变异株检测 基因组序列 分子特征 

分 类 号：R183.3[医药卫生—流行病学]