Genetic variation of Japanese encephalitis virus in Taiwan

A 280-nucleotide sequence from the capsid-premembrane (C/preM) gene region of 44 Japanese encephalitis (JE) virus strains isolated in Taiwan from mosq uitoes from 1983 to 1994, and 3 strains, (Ling [1965], Chang [1965], and HV 1 [1958]) isolated from human brain were analyzed by direct sequencing of r everse transcription-polymerase chain reaction (RT-PCR) amplified products and compared with the corresponding sequences of reference strains. The ove rall sequence homology of the 47 isolates was greater than or equal to 93.3 %. Taking 12% nucleotide divergence as a cut-off value, all isolates fell i nto genotype 3, which included strains from Japan, China, the Philippines, Sri Lanka, India, and Nepal. High nucleotide homology was observed among is olates from different regions of Taiwan and different time periods; on the other hand, high variation existed among isolates from the same region and time period. Phylogenetic analysis showed that the 47 Taiwan isolates fell into three clusters. Twenty-Eve isolates formed cluster 1, 18 isolates clus ter 2, and four isolates cluster 3. Isolates in cluster I showed greater (l ess than or equal to 2.9%) intragroup divergence compared to those in clust er 2 (less than or equal to 1.1%) or cluster 3 (less than or equal to 0.7%) . The majority of isolates from northern (73.3%) and central (60%) Taiwan b elonged to cluster 1, whereas most isolates (66.7%) from southern Taiwan be longed to cluster 2. Comparison with other Asian JE virus strains showed th at isolates of cluster 1 were more specific to Taiwan than isolates of clus ter 2 and cluster 3.