Analysis on the molecular characteristics of Japanese encephalitis virus isolated in Northwestern Yunnan province / 中华流行病学杂志

ABSTRACT

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 nueleotide 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 eodon in genotype Ⅰ and Ⅲ isolates, respectively. Conclusion 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.