Genetic Variation of Japanese Encephalitis Virus in Nature

Abstract

Forty-six strains of Japanese encephalitis (JE) virus from a ovariety of geographic areas in Asia were examined by primer-extension sequencing of the RNA template. A 240 nucleotide sequence from the pre-M gene region was selected for study because it provided sufficient information for determining genetic relationships among the virus isolates. Using 12 % divergence as a cutoff point for virus relationships, the 46 isolates fell into three distinct genotypic groups. One genotypic group consisted of JE virus isolates from northern Thailand and Cambodia. A second group was composed of isolates from southern Thailand, Malaysia, Sarawak and Indonesia. The remainder of the isolates, from Japan, China, Taiwan, the Philippines, Sri Lanka, India and Nepal, made up a third group. The implications of these findings in relation to the epidemiology of JE are discussed. Results of this study demonstrate that the comparison of short nucleotide sequences can provide insight into JE virus evolution, transmission and, possibly, pathogenesis.

Antigenic and Genetic Variations among Japanese Encephalitis Virus Strains Belonging to Genotype 1

“…The results of pair-wise comparisons of 240 nucleotides from the 67 JE virus isolates from different geographic regions indicated that the 12 Thai strains belonged to genotype 1 of Chen et al (9), which contains virus strains from northern Thailand and Cambodia (Fig. 2).…”

“…By pair-wise sequence comparison of 67 nucleotide sequences, a dendrogram of the virus relationship was constructed with the aid of the "Cluster Analysis" computer program (48). The prM nucleotide sequence information of 56 JE strains was obtained from previous publications (9,10). The nucleotide sequence data of the E protein genes of Nakayama, Beijing-1, Kamiyama, 691004 and Muar were obtained from Hasegawa et al (18) and ThCMAr4492 and ThCMAr6793 from our previous report (1).…”

“…Critical B-cell epitopes of the E protein produce neutralizing antibodies that are either type-specific, cross-reacting to the same antigenic complex, or common to all flaviviruses (22 (4,26). Recently, Chen et al (9,10) identified four genotypes of JE virus by analyzing 240 nucleotides from the prM gene region, and tried to explain the transmission, evolution, epidemiology and possible pathogenesis of JE virus.…”

Isolation of Japanese encephalitis virus from mosquitoes (Diptera: Culicidae) collected in the Western Province of Papua New Guinea, 1997-1998.

“…Genotype I is found primarily in Laos, northern Thailand, Cambodia, and Malaysia; Genotype II consists of isolates from southern Thailand, Malaysia, and Indonesia; Genotype III appears to be the most widely distributed and includes isolates from Japan, Korea, China, Malaysia, Philippines, Indonesia, India, and Sri Lanka; and Genotype IV appears to be restricted to Indonesia. [8][9][10] Comparison of the genetic sequence of the 1995 isolates of JE virus in the prM region revealed they probably had a common source and were most closely related to a 1970 isolate from Malaysia and a 1981 isolate from Indonesia, both of which belonged to Genotype II. 5 Sequence comparison of an overlapping region of the non-structural and 3Ј untranslated region (NS5-3Ј UTR) confirmed the relationship between the Australian, Indonesian, and Malaysian isolates, and also revealed the Australian isolates had a unique eleven base deletion immediately following the stop codon in the 3Ј untranslated region.…”

Evidence of intratypic recombination in natural populations of hepatitis C virus

“…Accordingly, the vast majority of work on flaviviruses, including vaccine studies and phylogenetic analyses in which genotypes were identified and sometimes correlated with disease severity (Chen et al, 1990;Leitmeyer et al, 1999;Rico-Hesse, 1990), has rested on the implicit assumption that evolution in the family Flaviviridae is clonal, with diversity generated through the accumulation of mutational changes.…”