2株人副肠孤病毒1型山东地方株的全基因组序列分析

Complete genome analysis of two human parechovirus 1 strains in Shandong province,China

目的了解人副肠孤病毒1型(human parechovirus 1,HPeV1)山东地方株的遗传背景和进化特征,为国内HPeV的流行病学调查及预防提供科学依据。方法山东省疾病预防控制中心脊髓灰质炎实验室对来自2019年和2021年山东省急性弛缓性麻痹监测系统报告病例的1319份粪便标本按照监测方案要求进行病毒分离,病毒分离物应用下一代测序技术测定其全基因组序列。使用BioEdit 7.0.9.0软件进行同源性分析,使用MEGA 11.0软件构建系统发生树,使用SimPlot 3.5.1软件进行重组分析。结果成功分离到2株HPeV1(19225和21031),其基因组全长分别为7324 nt和7328 nt(未包括多聚腺苷酸尾),编码区长6540 nt,可编码一个含2179个氨基酸的多聚蛋白,衣壳蛋白VP1羧基端含有精氨酸-甘氨酸-天冬氨酸基序。2株山东分离株间的核苷酸同源性为91.4%,与国内外其他地区HPeV1分离株的核苷酸同源性为77.3%~95.4%。VP1区系统发生分析结果显示,山东分离株位于HPeV1B基因簇内,与其他地区HPeV1分离株的平均遗传距离为0.153。重组分析结果显示,21031株在3C和3D区与HPeV5毒株CH-ZXY1存在重组信号,19225株不存在基因重组现象。结论山东地方株与国内外其他HPeV1分离株存在不同程度的序列变异,研究结果为HPeV的基因组流行病学研究和诊断试剂研发提供了科学依据。

Objective To understand the genetic background and evolutionary characteristics of human parechovirus 1(HPeV1)in Shandong province of China and to provide a scientific basis for epidemiological investigation and prevention of HpeV-related diseases.Methods A total of 1319 stool specimens collected during acute flaccid paralysis surveillance in Shandong province of China in 2019 and 2021 were processed by the Polio Laboratory of Shandong Center for Disease Control and Prevention according to standard protocols recommended by the WHO.Nextgeneration sequencing technology was used to obtain the complete genome sequences of virus isolates.Similarity comparison was carried out by BioEdit 7.0.9.0 software.Phylogenetic trees were constructed by Mega 11.0 software.The potential recombination was analyzed using Simplot 3.5.1 program.Results Strains 19225 and 21031 had genomes of 7324 nt and 7328 nt in length(excluding a poly(A)tail),respectively,with a single,large open reading frame encoding a polyprotein of 2179 amino acids.A arginine-glycine-aspartic acid(RGD)motif in the VP1C-terminus region was identified in 19225 and 21031.Strains 19225 and 21031 had 91.4%genomic nucleotide similarity with each other and 77.3%-95.4%with other complete genome sequences available from GenBank.Phyloge-netic analysis of the entire VP1 coding region showed that all HPe V1 strains were divided into two clades(1A and 1B),and the strains of this study were classified into clade 1B.The mean p-distance between Shandong strains and all other HPe V1 strains was 0.153.Simplot and bootscanning analyses on HPe V1 genome sequences reflected evidence of recombination in 3C and 3D regions for 21031 and CH-ZXY1 for the HPe V5 strain.Conclusions Shandong HPe V1 strains have genetic variability with other HPe V1 strains.These results can provide essential data for further study on the genomic epidemiology of HPe V and the development of diagnostic reagents.