山东省新分离乙脑病毒（SD08—10株）全基因组序列特征

Molecular characterization of full-length genome of Japanese Encephalitis virus（SD08-10） newly isolated in Shandong province

目的对山东省新分离乙脑病毒SD08—10株进行全基因组序列测定和分析，全面了解其基因组特征。方法设计乙脑病毒全基因组序列扩增引物，RT-PCR扩增片段，PCR产物直接测序，拼接后获得全基因组序列。采用Clustal X（1．8）、DNAStar、GENEDOC（3．2）、Mega（4．0）等生物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SD08—10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0．7％～18．9％，氨基酸总体差异率为0．1％-5．2％。与目前使用的减毒活疫苗株SA-14—14．2株相比较，全基因组共存在1253个核苷酸差异，82个氨基酸差异。全基因组序列系统进化分析显示SD08．10属于基因Ⅰ型乙脑病毒。结论新分离的乙脑病毒SD08—10株属于基因Ⅰ型，与2007年中国分离株SH17M-07进化关系最接近。

Objective Sequence and analysis the complete nucleotide of the Japanese encephalitis virus （JEV） newly strain SD08-10, isolated in 2008 in Shandong, China in order to understand the characterization of the virus. Methods Overlapping primers were designed according to the full-length genomes in GenBank. RTPCR was used to amplify the fragments and the full-length genome was obtained by sequencing and splicing. Using the computer software to analysis the nucleic acid data, deduced amino acid sequence and phylogenetic tree, including Clustal X （1.8）, DNASTAR, GENEDOC （3.2）. Results The result of sequence analysis shows that the genome of SD08-10 strain was 10 965 nucleotides long. An open reading frame from 96 to 10 392 including 10 296 nucleotides is capable of coding for a 3432 amino acid polyprotein. Compared with the live attenuated vaccine strain SA-14-14-2 in China, there was 1253 nucleotide difference and 82 amino acid divergence. Comparison of the complete genome sequences with 59 different JEV isolates showed a 0.7%--18.9% nucleotide sequence divergence among them, which resulted in 0.1%--5.2% amino acid sequence divergence. Phylogenetic analysis of full-length genome showed that the SD08-10 strain was belonging to genotype Ⅰ .Condusion Analysis based on the complete genome sequences of different JEV isolates showed that the SD08-10 strain isolated in 2008 in Shandong was belonging to genotype Ⅰ and close to SH17M-07 isolated in 2007 in China.