2022年12月-2023年1月四川省境外输入病例新型冠状病毒全基因组特征分析  

Whole-genome sequencing of SARS-CoV-2 variants isolated from imported cases in Sichuan Province from December 2022 to January 2023

作　　者：杨慧萍[1] 潘颜 田绿波 邝玉[4] 张磊 王利辉 周琳琳[2] 潘明[1] Yang Huiping;Pan Yan;Tian Lyubo;Kuang Yu;Zhang Lei;Wang Lihui;Zhou Linlin;Pan Ming(Institute of Microbiological Detection,Sichuan Center for Disease Control and Prevention,Chengdu 610041,China;Department of Pathogenic Biology,West China School of Basic Medical Sciences&Forensic Medicine,Sichuan University,Chengdu 610041,China;Sichuan International Travel Healthcare Center(Chengdu Customs Port Clinic),Chengdu 610000,China;National Experimental Teaching Demonstration Center,West China School of Basic Medical Sciences&Forensic Medicine,Sichuan University,Chengdu 610041,China;Department of Public Health,Southwest Medical University,Luzhou 646000,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 [2]四川大学华西基础医学与法医学院病原生物学系,成都610041 [3]四川国际旅行卫生保健中心(成都海关口岸门诊部),成都610000 [4]四川大学华西医学基础国家级实验教学示范中心,成都610041 [5]西南医科大学公共卫生学院,泸州646000

出　　处：《中华微生物学和免疫学杂志》2024年第7期601-607,共7页Chinese Journal of Microbiology and Immunology

基　　金：国家自然科学基金(82374291);四川省科技厅重点研发项目(2022ZDZX0017)。

摘　　要：目的分析2022年12月-2023年1月四川省境外输入新型冠状病毒(severe acute respiratory syndrome coronavirus 2, SARS-CoV-2)变异株分布情况和全基因组特征。方法选取2022年12月-2023年1月核酸检测荧光阈值(Ct)≤32的四川省境外输入SARS-CoV-2阳性病例鼻、咽拭子样本108份。采用全基因组靶向扩增结合Illumina NextSeq™ 2000测序系统进行病毒全基因组测序;Nextclade和Pangolin平台判定病毒谱系及型别, 分析病毒基因组变异特征;应用最大似然法构建系统进化树。结果本研究共获得55株覆盖度>95%的SARS-CoV-2全基因组序列, 均为Omicron变异株, 与Wuhan-Hu-1参考株基因组序列相比较, 21L、22B、22D、22E和22F基因型的核苷酸突变和氨基酸突变中位数分别为93、75、92、78、92个和68、53、68、69、65个。2022年12月-2023年1月, 四川省境外输入SARS-CoV-2的主要流行株为BA.5.2(10.91%, 6/55)、XBB.1.1(9.09%, 5/55)、BF.7.14(7.27%, 4/55)和BQ.1.1(7.27%, 4/55)。结论变异株分布情况在一定程度上能够反映全球流行趋势, 但跟国内本土流行变异株分布存在较大差异, 具有流行优势的XBB变异株在成为全国范围内(不包括中国港澳台地区)主要流行株之前, 即在入境旅客中大量检出。Objective To analyze the distribution and genomic characteristics of SARS-CoV-2 variants isolated from imported cases of COVID-19 in Sichuan Province from December 2022 to January 2023.Methods This study selected 108 nasal and throat swab samples with fluorescence threshold(Ct)≤32 that were collected from imported COVID-19 cases in Sichuan Province from December 2022 to January 2023.Targeted amplification and Illumina NextSeq™2000 system were used for whole-genome sequencing.Nextclade and Pangolin online platforms were used to determine the virus genotypes and analyze the mutation loci.A phylogenetic tree was constructed using maximum likelihood.Results A total of 55 SARS-CoV-2 whole genome sequences with coverage of>95%were obtained,and all of the strains were Omicron variants.Compared with the sequence of reference strain Wuhan-Hu-1,the median number of nucleotide mutation sites of 21L,22B,22D,22E,and 22F genotypes were 93,75,92,78,and 92,and the median number of amino acid mutation sites were 68,53,68,69,and 65,respectively.From December 2022 to January 2023,the predominant circulating SARS-CoV-2 variants from imported cases in Sichuan Province were BA.5.2(10.91%,6/55),XBB.1.1(9.10%,5/55),BF.7.14(7.23%,4/55),and BQ.1.1(7.23%,4/55).Conclusions The distribution of SARS-CoV-2 variants can reflect the global epidemic trend to a certain extent.However,it is different from the distribution of local circulating variants in the Chinese mainland.The XXB variants with transmission advantages can be detected in large numbers of inbound travelers before becoming the predominant circulating strains in the Chinese mainland.

关 键 词：新型冠状病毒 境外输入病例 全基因组 

分 类 号：R511[医药卫生—内科学]