2022年北京市新型冠状病毒分支BA.5.2的流行特征与基因组学特征分析

Comparative analysis of epidemiological characteristics of 206 imported COVID-19 cases in Beijing

目的了解北京市2022全年新型冠状病毒分支BA.5.2流行特征与基因组学特征,为科学监测和防控新冠病毒感染提供依据。方法收集北京市2022全年新冠病毒感染病例呼吸道标本,过滤后采用高通量测序法进行全基因组测序,测序数据进行比对、分析并构建系统发育树。结果截止2022年12月中旬累计获得2881条新冠病毒全长序列,其中BA.5.2占比12.22%,与Wuhan-Hu-1参考基因组的核苷酸和氨基酸序列一致性中位数分别为99.2%和99.0%。352条BA.5.2新冠序列共发现271个氨基酸突变位点,其中常见突变位点有ORF1ab区域的S135R和S蛋白区的D614G等35个;常见缺失位点有ORF1a基因的3675~3677位、ORF9b基因的27~29位和S基因的69~70位等;未发现插入变异。系统发育分析显示,北京市2022全年的BA.5.2的病毒基因组均位于GR进化支,与GISAID上的其他分支以及北京监测的其他分支存在一定的进化距离。结论北京市2022年BA.5.2变异株的流行规律基本与全球流行趋势相一致。352条新冠病毒序列由于时间跨度长、多波输入和本土局部传播疫情共同构成,进化树存在多个进化分支并且存在高达271个氨基酸突变位点。加强对新冠病毒感染等呼吸道传染病的常规监测和全基因组测序,及时了解北京市新冠流行毒株的变化,为及时调整疾病防控策略提供指引。

Objective To understand the epidemiological and genomic characteristics of Omicron sub-variant BA.5.2 in Beijing in 2022,so as to provide scientific evidences for scientific prevention and control of coronavirus disease 2019(COVID-19).Methods The respiratory tract samples of COVID-19 cases in Beijing throughout 2022 were collected.High-throughput sequencing method was performed on filtered samples.The sequences were used for alignment and analysis and to construct phylogenetic tree.Results A total of 2881 whole genome sequences of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)were obtained till mid-December 2022.The SARS-CoV-2 omicron sub-variant BA.5.2 accounted for 12.22%,and the median values of nucleotide sequence and amino acid sequence identity with the reference genome Wuhan-Hu-1 was 99.2%and 99.0%,respectively.Among 352 sequences of omicron sub-variant BA.5.2,271 amino acid mutation were identified and S135R in the ORF1ab region and D614G in the S protein region were the most common mutations.The common sites of deletion included nt3675-3677 in ORF1a gene,nt27-29 in ORF9b gene,and nt69-70 in S gene.No insertion was found.Phylogenetic analysis showed all genomes of omicron sub-variant BA.5.2 in Beijing in 2022 belonged to GR branch and maintained certain evolutionary distance from other branches on GISAID and other branches observed in Beijing.Conclusions The epidemiological trend of omicron sub-variant BA.5.2 in Beijing in 2022 was generally consistent with the global trend.The 352 sequences of SARS-CoV-2 consisted of strained obtained from long-time surveillance,multiple imported and local outbreaks.The phylogenetic analysis exhibited multiple evolutionary branches and up to 271 amino acid mutation sites.Strengthen routine surveillance and whole genome sequencing of SARS-CoV-2,as well as timely understand the changes of epidemic sub-variants of SARS-CoV-2 in Beijing will provide guidance for adjustment of disease prevention and control strategies.