Molecular characterization of full-length genome of Japanese encephalitis virus strain 47 isolated from patient's cerebrospinal fluid in China.

Abstract

Objective To sequence and analyze the whole genome of Japanese encephalitis virus (JEV) strain named 47 which was isolated from patient's cerebrospinal fluid sample in Heilongjiang province in 1950. Methods RNA was extracted from the recovery strain 47 and amplified with self-designed JEV genome sequencing primers. The differentiation analysis for nucleotides and coding amino acids and phylogenetic analysis were performed by the software of DNAStar, Modeltest, and Phylip. Results The whole genome of strain 47 has 10 977 nucleotides. An open reading frame from 95 to 10 391 including 10 296 nucleotides is capable of coding a 3432 amino acid pelyprotein. The nucleotide difference between strain 47 and 5 vaccine strains is 2.4%-4.4%, the amino acid difference between strain 47 and 5 vaccine strains is 0.3 %-1.1%. The best evolution model for the whole genome is GTR + I + G. Based on the phylogenetic analysis, strain 47 belongs to the geuotype Ⅲ JEV Conclusion Strain 47 is highly conserved on whole genome nucleotide and amino acid sequence. And it is belongs to the genotype Ⅲ JEV. Key words: Japanese encephalitis virus; Phylogeny; Gene amplification; Sequence analysis