Phylogenetic analysis of the envelope gene of Japanese encephalitis virus

Variation among Japanese encephalitis virus (JEV) strains has been documented in a number of studies by employing a variety of techniques like HI, NT, CF, RNA fingerprinting and sequencing of prM region. We report the complete envelope (E) gene sequence and the deduced amino acid sequence of four strains of JEV from the Indian subcontinent. These sequences were compared with published E gene sequences of 16 strains of JEV. Pairwise comparisons of the E gene nucleotide and deduced amino acid sequences of these strains indicated an overall sequence conservation. A majority of the differences in the four strains were located in domain A and domain C (Mandl et al., 1989). Phylogenetic analysis of the E gene sequences by a variety of tree building methods identified four clusters. Viral groupings did not correspond to geographic origin, isolation host or virulence. Evidence for positive selection operating on some strains belonging to different clusters was obtained.