Complete genome sequence of two genotype III Japanese encephalitis virus isolates from West Bengal, India

BACKGROUND & OBJECTIVES: Japanese encephalitis (JE), caused by a mosquito-borne virus JE virus (JEV), is a serious health problem in West Bengal, India. In this study, we report the complete genome sequence of two JEV isolates from West Bengal. The amino acid and nucleotide sequence homology was compared with other Indian strains. METHODS: Two JEV isolates (IND-WB-JE1 and IND-WB-JE2) obtained in 2008 and 2010, respectively, from two districts of the State of West Bengal, respectively were analyzed for genetic variations by sequencing the 10934 bp whole genome of the virus. Of these two districts, one was covered under JE vaccination programme in 2007. RESULTS: Phylogenetic analysis showed that both the isolates belonged to the genotype III. A total of 16 mutations were identified in the two isolates studied with respect to Vellore P20778 strain. One unique mutation A3215S was only found in IND-WB-JE2 isolate, but not in the isolate IND-WB-JE1. These two isolates showed maximum homology with P20778 strain of India. INTERPRETATION & CONCLUSIONS: This study reports on complete gene based phylogenetic analysis of JEV isolates from the State of West Bengal. It was evident from the results that JEV was still under circulation in both vaccine covered and not covered districts of West Bengal.