Nucleotide and deduced amino acid sequence of the structural protein genes of Japanese encephalitis viruses from different geographical locations

Strain variation among Japanese encephalitis (JE) virus isolates has been previously demonstrated by many workers using different methods. We report the nucleotide sequence of the 5' non-coding region and the nucleotide and deduced amino acid sequences of structural protein genes for eight wild-type JE virus strain isolated from different Asian countries (Vietnam, Nepal, Indonesia, Thailand, India, Japan and China). We compare these with five other published wild-type JE virus strains isolated from Japan and the mainland of China. No strain variation could be related to geographical location on the basis of the wild-type JE virus strains studied. The viruses differed from each other by between 21 (0.9%) and 111 (4.6%) nucleotides and by between 3 (0.4%) and 31 (4.2%) amino acids over the 2434 nucleotides examined. The amino acid divergence of the envelope (E) protein gene of the viruses was 4.2% or less among the 13 strains compared. Thus there is little genetic divergence in the strains studied. However, four variable E protein amino acids (E-51, E-209, E-244 and E-366) were identified. Residue positions E-51, E-244 and E-366 are found in peptides with functional T helper cell epitopes in two other flaviviruses. Therefore, these amino acids may be important in defining the various immunotypes of JE virus identified by antibody reactivity patterns.