威海市一例输入性新型冠状病毒奥密克戎BA.2的全基因组测序分析

Whole-genome sequencing analysis of an imported novel coronavirus omicron BA.2 in Weihai city

目的结合高通量测序技术和生物信息学技术,从新冠肺炎感染者咽拭子标本中直接测定病毒基因组序列,并从基因组水平上了解输入性新型冠状病毒(novel coronavirus 2019,2019-nCoV)的全基因组特征和变异情况,从而进行病毒的分型和溯源。方法选取1例威海市境外输入性2019-nCoV感染病例的咽拭子标本,采用2019-nCoV全基因组序列捕获结合NGS高通量测序技术进行全基因组测序。所得测序数据使用病毒变异分析软件,进行序列拼接和变异位点分析;对病毒进行分型,并构建进化树,追踪病毒的潜在来源。结果成功获得2019-nCoV的全基因组序列,基因组全长29808 bp,平均测序深度达5013.11×;全基因组共发生51处核苷酸突变,分布于8个编码区(ORF1ab、S、ORF3a、E、M、ORF6、ORF7a和N);病毒分型结果显示病毒属于奥密克戎BA.2型;进化分析显示,该病毒序列与来自日本的参考株共同处于同一分支。结论本研究构建的测序方法和分析结果可用于2019-nCoV的变异分析和病例溯源,对COVID-19疫情防控具有重要意义。

Objective To identify the genome-wide characteristics and variations of the novel coronavirus 2019(2019-nCoV)by combining high-throughput sequencing and bioinformatics techniques,to type and trace the virus.Methods Pharyngeal swab sample of one 2019-nCoV infection case imported from Weihai city was selected for 2019-nCoV whole-genome sequence capture and NGS high-throughput sequencing.The obtained sequencing data were sequenced and analyzed using virus mutation analysis software,we classify viruses and build phylogenetic trees to track their potential sources.Results The complete genome sequence of 2019-nCoV was obtained,with a total length of 29808 bp and an average sequencing depth of 5013.11×.A total of 51 nucleotide mutations were found in 8 coding regions(ORF1ab,S,ORF3a,E,M,ORF6,ORF7a and N).The result of virus typing showed that the virus belonged to Omicron BA.2.Evolutionary analysis showed that the virus sequence was in the same clade as the reference strains from Japan.Conclusions The sequencing method and analysis result established in this study can be used for mutation analysis of 2019-nCoV and case tracing,which is of great significance for the prevention and control of COVID-19.