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

Xiao Yan Gao, Hai Yan Wang, Huan Yu Wang, Shi Hong Fu, Gui Fang Liu, Yan Li, Ming Hua Li, Ai Qiang Xu, Guo Dong Liang

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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. RT-PCR 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. CONCLUSION: 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.

Original languageEnglish (US)
Pages (from-to)242-244
Number of pages3
JournalZhonghua shi yan he lin chuang bing du xue za zhi = Zhonghua shiyan he linchuang bingduxue zazhi = Chinese journal of experimental and clinical virology
Issue number4
StatePublished - Aug 2009
Externally publishedYes

ASJC Scopus subject areas

  • General Medicine


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