基于全基因组测序技术的新型冠状病毒肺炎疫情传播链分析

Transmission chain analysis of novel coronavirus pneumonia epidemic based on whole genome sequencing technology

目的 对2022年山东省某地级市同一时间内发生点多、涉及范围广的新型冠状病毒肺炎(COVID-19)疫情相关病例鼻咽拭子标本进行全基因组测序并进行传播链分析,为疫情精准防控提供科学依据。方法 对8份流调线路不清晰COVID-19病例的新型冠状病毒(SARS-CoV-2)阳性鼻咽拭子标本(样本编号分别为Boshanqu1107Liuyan、Boshanqu1107langfengsen、Linziqu1107niuyueju、Linziqu 1107liling、Boshanqu1107liudaodong、Linziqu1107chengmaoj、Boshanqu1107songxiaoyun、Jingkaiqu1018caomingwei)进行高通量测序,对测序下机数据使用高通量测序数据分析软件CLC进行拼接并进行测序质量评估,在线对病毒进行分型及变异位点分析,采用MEGA11.0软件构建全基因组序列系统进化树(Neighbor-joining法)进行传播链分析。结果 共获得8条SARS-CoV-2全基因组序列,基因组全长均为29 870 bp,序列缺失碱基数量为236~241,基因组平均测序深度为13 579×,基因组覆盖度均为99.2%,均属于奥密克戎BA.5.2变异株。从系统进化树可以看出,该8例病例共分为2个不同传播分支,其中Jingkaiqu1018caomingwei与新冠序列数据库中Jingkaiqu1010zhanglong、Jingkaiqu1010xingfangjie 2例COVID-19病例共属同一传播分支,并且3例样本序列完全一致;其余7例序列均为同一传播分支,其中Boshanqu1107Liuyan、Boshanqu1107liudaodong、Boshanqu1107songxiaoyun、Boshanqu1107langfengsen4例SARS-CoV-2基因组序列与数据库中Boshanqu20221104songruijuan序列完全一致;Linziqu1107niuyueju、Linziqu1107liling、Linziqu1107chengmaoj序列与数据库中Linziqu1027gaoyongchang等4例样本序列完全一致。结论通过对SARS-CoV-2的全基因组进行系统进化树分析,可有效获得病毒之间的亲缘关系,助力精准开展流行病学调查及传播链分析,为疫情防控提供参考依据。

Objective To analyze the chain of transmission of corona virus disease 2019(COVID-19)in prefecture-level city in Shandong province through whole gene sequencing of nasopharyngeal swab specimens,and provide scientific basis for formulating precise epidemic prevention and control measures.Method High-throughput sequencing method and CLC software were used to determine the sequences of 8 severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)strains from positive nasopharyngeal swab specimens with unclear circulation lines of COVID-19(sample numbers were Boshanqu1107Liuyan,Boshanqu1107langfengsen,Linziqu1107niuyueju,Linziqu/1107liling,Boshanqu1107liudaodong,Linziqu1107chengmaoj,Boshanqu1107songxiaoyun,Jingkaiqu1018caomingwei),and MEGA11.0 software was used to construct the phylogenetic tree(Neighbor-joining method).Results A total of 8 SARS-CoV-2 whole genome sequences were obtained during this sequencing.The full genome lengths were all 29 870 bp.The number of missing bases in the sequences was 236-241.The average genome sequencing depth was 13 579×,and the genome coverage was 99.2%,all belonged to the Omicron BA.5.2 mutant strain.The phylogenetic tree indicated that the 8 cases could be divided into 2 different transmission branches.Among them,Jingkaiqu1018caomingwei and the 2 COVID-19 cases Jingkaiqu1010zhanglong and Jingkaiqu1010xingfangjie in the new coronavirus sequence database belonged to the same transmission branch,and their sequences were completely consistent.The sequences of the remaining 7 cases were all from the same transmission branch.Among them,the genome sequences of Boshanqu1107Liuyan,Boshanqu1107liudaodong,Boshanqu1107songxiaoyun and Boshanqu1107langfengsen,were completely consistent with the Boshanqu20221104songruijuan sequence in the database;the sequences of Linziqu1107niuyueju,Linziqu1107liling and Linziqu1107chengmaoj were consistent with the sequence of Linziqu1027gaoyongchang in the database.Conclusion By conducting phylogenetic tree analysis on the entire genome of SARS-CoV-2,the genetic relationships between viruses were effectively obtained,and facilitated the accurate epidemiological investigations,providing a reference for epidemic prevention and control.