一起入境航班关联新冠肺炎聚集性疫情病毒全基因组特征分析  

Genomic characteristics of SARS-CoV-2 from an outbreak in inbound flight

作　　者：段玮[1] 王东[1] 冯兆民 李夫 崔淑娟[1] 吕冰[1] 梁志超[1] 张代涛[1] 杨鹏[1] 王全意[1] 潘阳[1] Duan Wei;Wang Dong;Feng Zhaomin;Li Fu;Cui Shujuan;Lyu Bing;Liang Zhichao;Zhang Daita Yang Peng;Wang Quanyi;Pan Yang(Beijing Center for Disease Prevention and Control,Beijing 100013,China)

机构地区：[1]北京市疾病预防控制中心,北京100013

出　　处：《中华实验和临床病毒学杂志》2023年第2期140-145,共6页Chinese Journal of Experimental and Clinical Virology

基　　金：北京市科技计划(Z211100002521015,Z211100002521019)。

摘　　要：目的分析2021年8月北京市一起入境航班关联新冠肺炎聚集性疫情中新型冠状病毒(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)基因组特征及变异情况,为疫情防控和风险评估提供参考。方法收集此次疫情全部50例关联病例的呼吸道标本,使用数字PCR方法对病毒载量进行测定,使用高通量测序对病毒全基因组进行测定分析,对基因组数据拼接整理后进行变异位点分析及系统发生分析。结果全部50例样本中病毒载量中位数为5.57×10^(4)拷贝/ml(ORF1ab基因)和5.85×10^(4)拷贝/ml(N基因)。共测定获得SARS-CoV-2病毒全基因组序列46份,均为Omicron变异株BA.5分支。其中21例与7例形成两个进化簇,内部全基因组核苷酸相似度高于99.993%和99.997%。结论该起聚集性疫情可能由两个传播链和其他散在感染共同构成,疫情病毒为境外流行的Omicron变异株BA.5分支。Objective To analyze the genomic characteristics and variations of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)derived from an outbreak in inbound flight in Aug,2022 in Beijing,and provide reference data for disease prevention and control and risk assessment.Methods Fifty respiratory tract specimens from all cases in this outbreak were collected.The digital PCR(ddPCR)was used to determine the viral loads of the specimens.The full genome of the viruses were sequenced by Next-generation sequencing.Then analuses were performed on the genetic identity,variations and phylogenesis.Results The median of viral loads in all 50 samples were 5.57×10^(4) copies/ml and 5.85×10^(4) copies/ml,for ORF1ab gene and N gene,respectively.A total of 46 SARS-CoV-2 genomes were obtained,which all belonged to Omicron/BA.5.Two genome clusters were observed,involving 21 and 7 cases,with a nucleotide sequence identities of 99.993%and 99.997%,respectively.Conclusions The studied outbreak was composed of two main clusters and other individual cases with Omicron/BA.5 virus overseas.

关 键 词：新型冠状病毒 基因组 病毒载量 系统发育分析 变异 

分 类 号：R181.8[医药卫生—流行病学] R563.1[医药卫生—公共卫生与预防医学]