长沙市GI.6[P11]重组型诺如病毒引起的暴发疫情全基因组序列特征分析

Characteristics of full-length genome sequence of GL6[P11]recombinant norovirus associated with an outbreak in Changsha City

目的对长沙市2017年5月一起诺如病毒暴发疫情中的病毒基因型别进行鉴定,并对病毒全基因组序列特征进行分析。方法采集疫情中4份病例粪便标本和2份饮用井水标本,提取病毒核酸后实时荧光逆转录聚合酶链反应进行诺如病毒GI和GII型检测,逆转录聚合酶链反应扩增病毒开放阅读框(open reading frame,ORF),测定ORF1与ORF2连接区域序列并进行基因型别鉴定,应用二代测序技术对阳性标本进行全基因组序列测定和分析。结果采集的6份标本中有2份病例标本和1份井水标本诺如病毒GI型阳性,基于核酸序列的进化树分析发现ORF1区域序列位于GI.P11型别分支,ORF2区域序列位于GI.6型别分支。3份阳性标本毒株序列之间的同源性为99.8%~100.0%。全基因组序列毒株编号为Hu/CSNV0501/2017,基因组编码区全长为7602 bp。Simplot软件分析重组位点位于ORF1区域序列约5341 bp。结论本次疫情的传染源为井水污染传播,引起此次胃肠炎疫情的病原体为诺如病毒GI.6[P11]重组型。应加强对长沙市诺如病毒少见重组亚型的监测,为重组毒株的遗传进化和疫情防控提供参考。

Objective To identify the genotype of a norovirus outbreak in Changsha in May 2017,and to analyze the molecular characteristics and gene recombination by whole-genome sequencing.Methods Fecal samples of 4 cases and 2 samples of drinking well water were collected.Viral nucleic acid was extracted,norovirus GI/GII genotype was detected by real time RT-PCR,and ORF1-ORF2 junction regions were amplified using specific primers by RT-PCR.Whole genome was sequenced using next generation sequencing.Results Among the 6 samples collected,2 patients and 1 water samples were tested GI norovirus positive.Phylogenetic analysis and BLAST showed that the ORF1 gene was homology with GI.P11,and ORF2 sequence was homology with GI.6.The gene sequences of 3 positive samples were highly homologous(99.8%-100.0%).The complete genome of the Hu/CSNV0501/2017 was 7,602 bp nucleotides long.Simplot analysis indicated that potential recombinant point was located nearby the 5,341 bp site.Conclusion This acute gastroenteritis outbreak was caused by well water pollution,and the pathogen was GI.6[P11]recombinant norovirus.Surveillance of rare recombinant norovirus subtypes should be strengthened in Changsha,which can provide references for genetic evolution and epidemic prevention and control.