遂宁市8例本土新型冠状病毒肺炎确诊病例病毒全基因组特征分析  

Genome characterization of 8 local confirmed cases of COVID-19 in suining of Sichuan Province

作　　者：徐佳楠[1] 陈器[2] 刘李[1] 杨慧萍[1] 潘明[1] 周琳琳[3] 冯玉亮 XU Jia-nan;CHEN Qi;LIU Li;YANG Hui-ping;PAN Ming;ZHOU Lin-lin;FENG Yu-liang(Sichuan Province Center for Disease Control and Prevention,Chengdu 610041,Sichuan Province,China;Suining Center for Disease Control and Prevention,Suining 629000,Sichuan Province,China;West China School of Preclinical and Forensic Medicine,Sichuan University,Chengdu 610017,Sichuan Province,China)

机构地区：[1]四川省疾病预防控制中心,成都610041 [2]遂宁市疾病预防控制中心,四川遂宁629000 [3]四川大学华西基础医学与法医学院,成都610017

出　　处：《预防医学情报杂志》2023年第1期113-118,共6页Journal of Preventive Medicine Information

基　　金：四川省科技厅重点研发项目(项目编号:2021YFQ0060)。

摘　　要：目的对引起遂宁市本土新型冠状病毒肺炎(COVID-19,简称新冠肺炎)疫情的新型冠状病毒(SARS-CoV-2)进行全基因组测序溯源、分子特征和变异情况分析。方法对2022年3月31日—4月9日采集的遂宁市新冠肺炎本土疫情8例确诊病例的呼吸道样本提取病毒RNA,采用Illumina测序平台进行病毒全基因组测序,运用CLC Genomics Workbench(Version 20.0)软件进行序列拼接。从NCBI数据库中下载新冠病毒参考序列进行全基因组遗传进化和抗原变异情况分析。应用Nextclade和Pangolin在线病毒分析平台,判定病毒家系及型别,分析病毒的变异位点。应用进化分析软件构建病毒进化树分析病毒的来源和相关性。结果病例1~8的SARS-CoV-2全基因组序列同武汉参考株(NC_045512)序列相比,分别有69、68、68、69、70、70、70和70个变异位点,8条SARS-CoV-2全基因组序列均属于BA.2(Omicron)支系,是VOC/Omicron变异株(B.1.1.529进化分支)。病例1与外省部分本土病例SARS-CoV-2序列共享全部68个变异位点,新增加1个变异位点(A27898T)。本起疫情的全部8例病例均出现A27898T变异位点。病例1出现了C14724T变异位点,属于杂合突变,比例仅为19.75%;随后在病例2~8中均出现C14724T变异位点,杂合突变比例逐渐增高,病例7和病例8的C14724T变异位点,突变比例达到100.00%。病例3和病例4出现了A15002G变异位点,但突变比例仅为7.90%和50.00%,但在病例8中,A15002G变异位点的突变比例为100.00%。病例8出现C16915T变异位点,突变比例为73.30%,这个变异位点是首次在本起疫情中出现。进化分析结果显示:遂宁市本起疫情的全部8例病例均属于同一传播链,位于同一进化分支。结论遂宁市本起疫情的全部8例病例SARS-CoV-2基因序列溯源结果提示来源于外省新冠肺炎病例持续传播地区。常态化疫情防控期间应持续加强四川省本土和境外输入型新冠肺炎病例的病毒分子动态实时监测。Objective To analyze molecular characteristic,sequencing traceability and genetic variation of a local COVID-19 outbreak induced by Novel Coronavirus CoV-2 in Suining city,Sichuan province.Methods Total viral RNA was extracted from respiratory samples of eight cases in Suining city from March 31 to April 9,2022.Eight cases were sequenced by using Illumina sequencing platform and CLC Genomics Workbench(Version 20.0)software was used for sequence splicing.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 analyzed the mutation loci of the virus.The Phylogenetic tree was constructed by using evolutionary analysis software to analyze the source and correlation of viruses.Results The Wuhan reference strain(NC_045512)were compared,the whole genome sequence of SARS-CoV-2 in cases 1-8 has 69,68,68,69,70,70,70,70 mutation sites.Among 8 cases of SARS-CoV-2 sequences belonged to the BA.2(Omicron)clade,which was a VOC/Omicron variant strain(B.1.1.529 clade).Case 1 shared all 68 mutation sites with the SARS-CoV-2 sequence of some local cases in other provinces and a new mutation site(A27898T)was detected.Mutation site A27898T was found in all 8 cases of this outbreak.All 8 cases in this local COVID-19 outbreak had the A27898T mutation site.C14724T mutation site was found in case1,which was a heterozygous mutation,accounting for only 19.75%.C14724T mutation site was also found in case 2 and case 8.The percentage of heterozygous mutations had gradually increased.The C14724T mutation site in both case 7 and case 8 was 100.00%.In case 3 and case 4,the mutation proportion of A15002G mutation site was only 7.90%and 50.00%,but in case 8,the mutation proportion of A15002G mutation site was 100.00%.C16915T mutation site was found in case 8,and the mutation proportion was 73.30%.C16915T mutation site was the first to appear in this local COVID-19 outbreak.Phyl

关 键 词：新型冠状病毒 基因组序列 分子特征 

分 类 号：R563.1[医药卫生—呼吸系统]