[Molecular characterization of full-length genome of Japanese encephalitis virus (02-76) newly isolated in China.].

BACKGROUND

To sequence and analyze the complete nucleotide sequence of the Japanese encephalitis virus (JEV) strain 02-76, newly isolated in 2002 in China and to provide information for the genomic structure of JEV and the characteristics of virulence.

METHODS

Overlapping primers were designed according to the full-length genomes from GenBank. RT-PCR was used to amplify the fragments, sequencing was performed and all the nucleotides were connected to acquire the full-length genome. Computer software was used to analyze the nucleic acid data, deduced amino acid sequence and phylogenetic trees including Clustal X(1.8), DNASTAR, GENEDOC(3.2).

RESULTS

The result of sequence analysis showed that the genome of 02-76 strain was 10,977 nucleotides long. An open reading frame from 95 to 10,391 including 10,296 bases was found capable of coding for a 3432 amino acid polyprotein. Compared with the Beijing 1 strains isolated in 1949 in China, there was a 248 nucleotide divergence and 16 amino acid divergence. Comparison of the complete genome sequences of different JEV isolates showed a 0.6%-15.1% nucleotide sequence divergence among them, which resulted in 0.2%-4.6% amino acid sequence divergence. Phylogenetic analysis through PrM/C,E,3'NTR and full-length genome showed that the 02-76 strain belonged to genotype 3.

CONCLUSION

Analysis based on the complete genome sequences of different JEV isolates showed that the 02-76 isolate in 2002 belonged to genotype 3 and was close to the old Chinese isolates SA-14.