一起无菌性脑膜炎疫情中埃可病毒30型的全基因组分析

Whole Genome Analysis of Echovirus 30 in A Aseptic Meningitis Outbreak

对引起一起无菌性脑膜炎的埃可病毒30型(Echovirus 30,E30)毒株进行全基因组测序,并分析其遗传变异和分子进化特征。提取病毒RNA,荧光RT-PCR确定为肠道病毒,再扩增其VP1区,测序确定为E30,设计针对E30全基因组的引物,RT-PCR扩增和序列测定获得全基因序列。利用DNAMAN 9.0、MEGA X、RDP 5和SimPlot 3.5.1软件分析全基因序列。E30无锡株基因组全长7 425 bp个核苷酸(nt),5′端和3′端分别为743 nt和97 nt的UTR,二个UTR之间为一个6 585 nt长的开放阅读框,编码一个含2 195个氨基酸(aa)的多聚蛋白。与GenBank中基因组序列比对,最同源的是毒株USA/2017/CA-RGDS-1048 (基因登录号:MN153801),核苷酸同源性为97.5%,氨基酸同源性为99.1%。VP1基因进化树分析显示,E30无锡株属于h型,并可归类于h型下分的基因簇GroupⅣ。种系进化分析和同源性分析提示E30无锡株可上溯到中国江苏毒株FDJS03毒株。分析还发现E30无锡株在非结构区存在重组,重组序列可能来自E30毒株(KY888274)和E18毒株(MN815813)。E30无锡株归类为h型E30,它是一个包含了E30毒株和E18毒株序列的重组病毒。

We sequenced the whole genome of the human Echovirus 30 strain(E30) isolated from an aseptic meningitis patient and analyzed its genetic variation and molecular evolution. Viral RNA was extracted and identified as enterovirus by fluorescence RT-PCR. The VP1 gene was amplified and identified as E30 by sequencing. Primers were designed for the whole genome of E30, and the whole genome sequence was obtained by RT-PCR and sequenced. Phylogenetic and pairwise alignment analyses based on whole genome and complete VP1 regions were conducted using DNAMAN 9.0, Mega X, RDP 5, and SimPlot 3.5.1 software.The genome of the E30 Wuxi strain consists of 7,425 bp with 743 nt and 97 nt non-coding regions at the 5’ and 3’ ends, respectively. The entire open reading frame between the two non-coding regions spans 6,585 nt, encoding a 2195 amino acid polyprotein. Compared with genome sequences in GenBank, the most homologous strain was USA/2017/CA-RGDS-1048(gene login number: MN153801), with nucleotide identity of 97.5%and amino acid identity of 99.1%. The E30 Wuxi strain belongs to lineage h of E30 and can be classified into Group Ⅳ within lineage h. Phylogenetic and homology analyses suggested that the E30 Wuxi strain could be traced back to strain FDJS03 found in Jiangsu Province, China, in 2003. Intertypic recombination was observed between the E30 Wuxi strain, another E30 strain(KY888274), and the E18 strain(MN815813) in non-structural protein-coding regions of the genome. The E30 Wuxi strain belongs to lineage h of E30, and it is a recombinant enterovirus composed of Echovirus E30 and Echovirus E18 genome segments.