Molecular epidemiological analysis of a HFMD epidemic caused by CV-A6

Abstract

Objective To identify the pathogen that caused the cluster of HFMD epidemic in a middle school of Fuxin City in September 2019, and to find out the homogeneity of the pathogen. Methods The samples were preliminary identified by real-time PCR. Partial VP1 sequences were amplified by nested PCR. The virus type was identified by sequencing and blast comparison. and the homology and phylogenetic analyes of VP1 region were performed by bioinformatics software with CV-A6 reference sequences. Results Samples of 5 cases were tested by real-time fluorescent PCR, and the results showed that the enterovirus universal nucleic acid was positive, and both CV-A16 and EV71 nucleic acids were negative. They were judged to be non-CV-A16 and non-EV71 enterovirus infection. Online BLAST comparison of partial nucleotide sequences of the enterovirus VP1 region showed that samples of 5 cases were all positive for CV-A6 enterovirus, The homology of VP1 nucleotide sequence among 5 samples were 100%. Phylogenetic analysis showed that 5 samples in this study belonged to the CV-A6 D3 subtype which was widely epidemic in China, and they were clustered with the dominant strains in recent years in Liaoning province. Conclusion This cluster of HFMD epidemic is induced by CV-A6. It is closely related to the prevalent CV-A6 strains in Liaoning province in recent years, and no significant variation is detected. 摘要：目的 对2019年9月辽宁省阜新市某中学一起手足口病聚集性疫情的未分型肠道病毒进行病原学鉴定, 分 析其种系发生情况。 方法 使用实时荧光PCR对标本进行初步病原学鉴定, 使用巢式PCR对未分型肠道病毒VP1区 部分核苷酸序列进行扩增和测序, BLAST比对确定肠道病毒型别, 利用生物信息学软件将VP1区全长序列与柯萨奇病 毒A6型(CV-A6)各亚型参考序列进行同源性和系统进化分析。 结果 5份标本经实时荧光PCR检测, 结果 显示肠道 病毒通用型核酸阳性 , CV-A16型和EV71型核酸均为阴性 , 判断为非CV-A16非EV71型肠道病毒感染。对肠道病毒 VP1区部分核苷酸序列进行在线BLAST比对 , 结果 显示5例患者标本均为CV-A6型肠道病毒阳性, 其VP1区核苷酸序 列同源性为100%。系统进化分析显示, 5例标本属于我国广泛流行的CV-A6 D3亚型 , 且与辽宁省近几年的优势流行 株在同一个进化树分支上。 结论 引起此次聚集性手足口病疫情的病原体为CV-A6型肠道病毒, 与近年来辽宁省流 行的CV-A6毒株亲缘关系密切, 未发生明显变异。