2023年白银市200例新型冠状病毒全基因组测序与基因特性分析

Whole-genome sequencing and genetic characterization of 200 novel coronavirus cases in Baiyin city in 2023

目的分析2023年新冠病毒(SARS-CoV-2)变异株在甘肃省白银市的流行特点及其基因变异情况,为疫情防控和疫苗研发提供科学依据。方法选取2023年1—9月在甘肃省白银市医疗卫生机构就诊、住院和监测的新冠病毒感染(COVID-19)病例鼻(口)咽拭子样本200份,采用二代测序技术进行全基因组测序,利用MGI metargetCOVID软件进行序列组装分析、Pangolin平台分型,使用FREEBAYES检测变异位点、基于NIRVANA进行注释,使用MAFFT软件进行多序列比对和IQTREE构建系统进化树,并采用GGTREE和GGTREEEXTRA软件对进化树和相关的临床信息进行可视化分析。结果2023年1—9月白银市检出SARS-CoV-2均为Omicron变异株,其中第1季度(1—3月)为BA.5.2(32例,100.00%),第2季度(4—6月)主要为XBB(56例,62.92%)和FL(20例,22.47%)家族,第3季度(7—9月)主要由EG.5.1.1(52例,65.82%)主导;在中型病例中显著富集了42个突变位点,包括ORF1ab基因突变25个、S基因突变9个、ORF3a和ORF8基因突变各3个以及N基因突变2个。结论白银市流行的SARS-CoV-2基因组与武汉参考株处于不同分支,并与Pangolin分型谱系和输入时间基本一致,不同临床症状之间存在遗传关联,接种疫苗和既往感染与进化树的关联不显著。

Objective To analyze the prevalence and genetic variations of SARS-CoV-2 variants in Baiyin city,Gansu province in 2023,and provide scientific basis for epidemic prevention and control and vaccine development.Methods A total of 200 nasal/oropharyngeal swab samples were collected from COVID-19 cases who visited medical institutions,were hospitalized,or under monitoring in Baiyin city,Gansu province from January to September 2023.Next-generation sequencing technology was used for whole-genome sequencing.MGI metargetCOVID software was used for sequence assembly analysis and Pangolin platform for typing.FREEBAYES was used to detect mutation sites,and annotation was performed based on NIRVANA.MAFFT software was used for multiple sequence alignment,and IQTREE was used to construct the phylogenetic tree.GGTREE and GGTREEEXTRA software were used for visualization analysis of the phylogenetic tree and related clinical information.Results From January to September 2023,all detected SARS-CoV-2 in Baiyin city were Omicron variants,with BA.5.2(32 cases,100.00%)in the first quarter(January-March),mainly XBB(56 cases,62.92%)and FL(20 cases,22.47%)families in the second quarter(April-June),and mainly dominated by EG.5.1.1(52 cases,65.82%)in the third quarter(July-September).Forty-two mutation sites were significantly enriched in moderate cases,including 25 mutations in the ORF1ab gene,9 mutations in the S gene,3 mutations each in the ORF3a and ORF8 genes,and 2 mutations in the N gene.Conclusion The SARS-CoV-2 genomes circulating in Baiyin city were in different branches from the Wuhan reference strain and were basically consistent with the Pangolin typing lineages and input time.There were genetic associations between different clinical symptoms,and the association of vaccination and previous infection with the phylogenetic tree was not significant.