[Analysis on the molecular characteristics of Japanese encephalitis virus isolated in northwestern Yunnan province].
OBJECTIVE
To analyze the molecular characteristics of Japanese encephalitis virus (JEV) isolated in Northwestern Yunnan province, and to clarify the differences between the strains isolated in Northwestern and other parts of Yunnan province.


METHODS
PrM, E and 3' untranslated region nucleotide acid sequences of the isolates were amplified by RT-PCR and then sequenced. Sequence alignment and phylogenetic analysis were performed by using Clustal 1.8X, DNASTAR, GENEDOC and Mega 3.1 programs.


RESULTS
12 of the 13 isolates of JEV obtained in Northwestern Yunnan were identified as genotype I, only one strain was genotype III of JEV. The 12 strains of genotype I were clustered in different branches with other isolates obtained in other parts of Yunnan province. Data from sequence analysis on E gene found that the nucleotide identity was 0.2%-13.9% between the Northwestern isolates and other Yunnan strains. There were two kinds of nucleotides deletion patterns at 3' untranslated region with three and one deletions was found after termination codon in genotype I and III isolates, respectively.


CONCLUSIONS
There were two genotypes of I and III in 13 strains of JEV in this study and genotype I isolates were predominant (12/13). There were no apparent differences in E gene sequence between isolates obtained in the Northwestern and other parts of Yunnan. Three deletions were found in 3' untranslated region in genotypes I isolates and one deletion was in genotypes III.
Sun
Xiao-Hong
XH
Institute for Viral Diseases Control and Prevention, Chinese Center for Diseases Control and Prevention, Beijing, China.
Wang
Huan-Yu
HY
Pan
Xiao-Ling
XL
Fu
Shi-Hong
SH
Feng
Yun
Y
Meng
Wei-Shan
WS
Liang
Guo-Dong
GD
D001483:Base Sequence; D002681:China; D004664:Encephalitis Virus, Japanese / Q000235:genetics* / Q000302:isolation & purification; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D020506:Untranslated Regions
D020506:Untranslated Regions