2009年江西省新分离流行性乙型脑炎病毒株全基因组分子生物学特性研究

Molecular characteristics of full-length genome of Japanese encephalitis virus strain (JX0939) newly isolated in Jiangxi province

目的对2009年分离自江西省蚊虫标本的流行性乙型脑炎(乙脑)病毒JX0939株进行全基因组序列测定,分析其基因组特征。方法使用针对乙脑病毒全基因组测序引物进行PCR扩增基因组片段,PCR产物直接测序,拼接后获得全基因组序列。利用生物信息学软件进行核苷酸序列及氨基酸序列分析和病毒的系统进化分析。结果新分离乙脑病毒JX0939株基因组全长10965个核苷酸,从97位到10392位,共10296个核苷酸编码一个开放阅读框,编码3432个氨基酸。与GenBank中登录的所有59株乙脑病毒全基因组序列比较发现,其核苷酸总体差异率为1%～17%,氨基酸总体差异率为0.1～5%。与目前使用的减毒活疫苗株SA-14-14-2株相比较,只有88%的核苷酸同源性,全基因组共存在1237个核苷酸差异,83个氨基酸差异。提取GenBank登录的及本实验室测定的不同省份的乙脑病毒全基因组序列,进行全基因组序列系统进化分析显示JX0939株属于基因1型乙脑病毒。结论新分离的乙脑病毒JX0939株属于基因1型,与2007年中国分离株SH17M-07进化关系最接近,与疫苗株SA-14-14-2相比关键位点氨基酸未见变异。

Objective To conduct sequencing of full-length genome of Japanese encephalitis virus（JEV） strain（JX0939） isolated in 2009 in Jiangxi province and analyze the characteristics of genome.Methods Overlapping primers were designed according to the full-length genomes in GenBank.RT-PCR was performed to amplify the fragments and the full-length genome was obtained by sequencing and splicing.Bioinformatics software was used to analyze the nucleic acid/amino acid sequence and phylogenetic tree.Results The results showed that the length of the JX0939 strain genome was 10 965 nucleotides.The open reading frame was from 96 nt to 10 392 nt,which coded 3432 amino acid polyprotein.Compared with the live attenuated vaccine strain SA-14-14-2 in China,there was 1237 nucleotide differences and 83 amino acid divergence.Compared with the genome of 59 JEV isolates showed 1%-17% nucleotide sequence divergence among them,which resulted in 0.1%-5% amino acid divergence.Phylogenetic analysis of full-length genome derived from GenBank and database made in our laboratory showed that the JX0939 strain belongs to genotype 1.Conclusion JEV strain（JX0939） isolated in Jiangxi province of China in 2009 belongs to genotype 1 and has close relationship to SH17M-07 isolated in 2007 in China.There were no mutations in the prior antigenic regions.