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


CONCLUSIONS
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.
Gao
Xiao-Yan
XY
Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China.
Wang
Hai-Yan
HY
Wang
Huan-Yu
HY
Fu
Shi-Hong
SH
Liu
Gui-Fang
GF
Li
Yan
Y
Li
Ming-Hua
MH
Xu
Ai-Qiang
AQ
Liang
Guo-Dong
GD
D002681:China; D004664:Encephalitis Virus, Japanese / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D004672:Encephalitis, Japanese / Q000821:virology*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny