Complete nucleotide sequence of an Indian strain of Japanese encephalitis virus: Sequence comparison with other strains and phylogenetic analysis

The RNA genome of an Indian strain of Japanese encephalitis virus (JEV), GP 78, was reverse transcribed and the cDNA fragments were cloned in bacterial plasmids. Nucleotide sequencing of the cDNA clones covering the entire gen ome of the virus established that the GP78 genome was 10,976 nucleotides lo ng. An open reading frame of 10,296 bases, capable of coding for a 3,432 am ino acid polyprotein, was flanked by 95- and 585-base long 5'- and 3'-non-c oding regions, respectively. When compared with the nucleotide sequence of the JaOArS982 strain, the JEV GP78 genome had a number of nucleotide substi tutions that were scattered throughout the genome except for the 5'-noncodi ng region, the sequence of which was fully conserved. Comparison of the com plete genome sequences of different JEV isolates showed a 1.3-4.1% nucleoti de sequence divergence among them, which resulted in 0.6-1.8% amino acid se quence divergence. Analysis based on the complete genome sequences of diffe rent JEV isolates showed that the GP78 isolate from India was phylogenetica lly closer to the Chinese SA14 isolate.