Transmission chain analysis of novel coronavirus pneumonia epidemic based on whole genome sequencing technology
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 579x,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.
SARS-CoV-2Next generation sequencingThe traceability analysisVariable site
NETL
NSTL
万方数据
