Molecular characteristics of full-length genome of Japanese encephalitis virus strain (JX0939) newly isolated in Jiangxi province

Objective To conduct sequencing of full-length genome of Japanese encephalitis virus (JEV) strain (JX0939) isolated in 2009 in Jiangxi province and analyze the characteristics of genome. Methods Overlapping primers were designed according to the full-length genomes in GenBank. RT-PCR was performed to amplify the fragments and the full-length genome was obtained by sequencing and splicing. Bioinformatics software was used to analyze the nucleic acid/ amino acid sequence and phylogenetic tree. Results The results showed that the length of the JX0939 strain genome was 10 965 nucleotides. The open reading frame was from 96 nt to 10 392 nt, which coded 3432 amino acid polyprotein. Compared with the live attenuated vaccine strain SA-14-14-2 in China, there was 1237 nucleotide differences and 83 amino acid divergence. Compared with the genome of 59 JEV isolates showed 1%-17% nucleotide sequence divergence among them, which resulted in 0.1%-5% amino acid divergence. Phylogenetic analysis of full-length genome derived from GenBank and database made in our laboratory showed that the JX0939 strain belongs to genotype 1. Conclusion JEV strain (JX0939) isolated in Jiangxi province of China in 2009 belongs to genotype 1 and has close relationship to SH17M-07 isolated in 2007 in China. There were no mutations in the prior antigenic regions.