基于宏基因组高通量测序分析1起聚集性新型冠状病毒感染疫情的基因组及传播特征  

Analysis of the genome and transmission characteristics of an aggregated novel coronavirus infection based on metagenomic next-generation sequencing

作　　者：杨玉荣[1] 万寒兵 康耀霞[1] 彭景贤[1] 高蒙[1] 刘欣 郭晓奎[2] 朱泳璋[2] Yang Yurong;Wan Hanbing;Kang Yaoxia;Peng Jingxian;Gao Meng;Liu Xin;Guo Xiaokui;Zhu Yongzhang(Microbiology Laboratory,Baotou Center for Disease Control and Prevention,Baotou 014030,China;School of Global Health,Chinese Centre for Tropical Diseases Research,Shanghai Jiao Tong University School of Medicine,Shanghai 200025,China)

机构地区：[1]包头市疾病预防控制中心微生物检验科,包头014030 [2]上海交通大学医学院国家热带病研究中心全球健康学院,上海200025

出　　处：《中华地方病学杂志》2023年第2期152-156,共5页Chinese Journal of Endemiology

基　　金：包头市科技计划项目(2020Z1003)。

摘　　要：目的分析包头市新型冠状病毒感染者的病毒基因组序列,了解新型冠状病毒在病例间传播过程中基因组的突变特征,探索新型冠状病毒在聚集性人群中的传播规律。方法采集2020年1月25日至2月21日包头市确诊的10例新型冠状病毒感染者的9份咽拭子样本(1~7、9、10号),2份痰液样本(8、11号,11号样本来自10号病例)及1份物表涂抹物样本(12号,来自10号病例),1、3号样本为单发病例样本,其余样本为聚集性病例样本。采用宏基因组高通量测序(mNGS)进行病毒基因组测序,与新型冠状病毒参考毒株NC045512序列比对筛选单核苷酸多态性(SNP)突变位点;并结合流行病学相关信息,进行基因突变、病毒分型和进化溯源分析。结果病毒基因组mNGS结果显示,与参考毒株NC045512序列比对,12份样本共检出76个SNP突变位点,突变类型包括转换3个(3.95%)、颠换73个(96.05%);包含19个(25.00%)同义突变和57个(75.00%)非同义突变。核苷酸及氨基酸变异位点分析结果显示,在全部聚集性病例(2、4~10号病例)中,T2821C、C6548T、T16464C、G16858A、T251C 5个位点均出现突变;单发病例1号样本在C9245T和A15340T位点、3号样本在C13T位点出现突变。病毒分型分析结果显示,1、3号样本均属于新型冠状病毒L型,其余样本均属于新型冠状病毒S型。基因组进化关系分析结果显示,所有样本可分为2个分支,1、3号样本分支属于单发病例,其余样本分支属于家庭聚集性病例。结论包头市新型冠状病毒感染聚集性病例基因组特征与流行病学调查结果基本吻合,病毒的传播主要与近距离接触和家庭聚集有关。Objective To analyze the viral genome sequence of novel coronavirus infected persons in Baotou City,understand the mutation characteristics of novel coronavirus genome in the process of transmission among cases,and explore the transmission rule of novel coronavirus in the clustered populations.Methods Nine throat swabs samples(No.1-7,No.9,and No.10),two sputum samples(No.8,No.11,and No.11 sample was from No.10 case),and one surface smear sample(No.12,and No.12 sample was from No.10 case)were collected from 10 confirmed cases of novel coronavirus infection in Baotou City from January 25 to February 21,2020.Samples 1 and 3 were from single cases,and the rest were from clustered cases.The virus genome was sequenced by metagenomic next-generation sequencing(mNGS),and single nucleotide polymorphism(SNP)mutation sites were screened by comparing with NC_045512,a reference strain of novel coronavirus.Combined with relevant epidemiological information,gene mutation,virus typing,and evolutionary traceability analysis were carried out.Results The results of viral genome mNGS showed that 76 SNP mutation sites were detected in 12 samples compared with the reference strain NC_045512,including 3(3.95%)transitions and 73(96.05%)reversals.There were 19(25.00%)synonymous mutations and 57(75.00%)non-synonymous mutations.The analysis of nucleotide and amino acid variation sites showed that mutations were found at five sites(T2821C,C6548T,T16464C,G16858A and T251C)in all the clustered cases(cases 2,4-10).In the single cases,sample 1 had mutations at C9245T and A15340T,and sample 3 had mutation at C13T.The virus typing analysis showed that the samples 1 and 3 belonged to the L type of novel coronavirus,while the rest belonged to the S type of novel coronavirus.The results of genomic evolutionary relationship analysis showed that all the samples could be divided into two branches.The branches of sample 1 and 3 belonged to single cases,and the rest belonged to family clustered cases.Conclusion The genomic characteristics of the clustere

关 键 词：新型冠状病毒感染 聚集性病例 宏基因组高通量测序 基因特征 

分 类 号：R511[医药卫生—内科学] R181.3[医药卫生—临床医学]