Japanese encephalitis/West Nile virus group, Microbial Containment Complex Campus, Sus Road, Pashan, Pune-411021, India.
We analyzed genetic relationship between 39 isolates of Japanese encephalitis virus obtained from human patients, pigs and various mosquito species during 1956–2005 from different geographic regions (9 different states) of India. Representative JE virus strains from Japan, Sri Lanka and China were included as experimental controls. The partial sequence from the nucleocapsid – premembrane and envelope regions of these strains were used to determined their genetic relationships. The phylogenetic analysis of partial C-prM and envelope sequences classified all the Indian isolates in genotype III which were further clustered in to different sub-clusters. Tree topologies obtained with C-prM fragments indicated clustering of Indian strains according to their year of isolation and geographic distribution. The envelope sequence based analysis does not precisely correlate with the geographic distribution. The study divides Indian viruses in to three different groups: 1) Southern Indian strains isolated up to 1978; 2) strains isolated from central, northern and western India and 3) Strains isolated from southern India including Goa after 1978. One strain isolated from Karnataka in 1990 does not cluster with any of these groups. As complete genomic sequence of only 2 Indian strains (P20778 from Vellore and GP78 from Gorakhpur) was available, the study also sequenced and analyzed complete genome sequence of JE virus isolates from northern India (Lakhimpur, 2001; Gorakhpur, 2005), central India (Bhandara, 2002), and southern India (Bellary, 1990) sequenced and analyzed. All the Indian JE virus strains grouped in to three major groups diverged by 3–6%. The study indicates utility of both C-preM and envelope protein sequences in determining the phylogenetic relationship between JE virus strains.
