Abstract
BackgroundJapanese encephalitis virus (JEV) is the etiological agent of Japanese encephalitis (JE), one of the most serious viral encephalitis worldwide. Five genotypes have been classified based on phylogenetic analysis of the viral envelope gene or the complete genome. Previous studies based on four genotypes have reported that in evolutionary terms, genotype 1 JEV is the most recent lineage. However, until now, no systematic phylogenetic analysis was reported based on whole genomic sequence of all five JEV genotypes.FindingsIn this study, phylogenetic analysis using Bayesian Markov chain Monte Carlo simulations was conducted on the whole genomic sequences of all five genotypes of JEV. The results showed that the most recent common ancestor (TMRCA) for JEV is estimated to have occurred 3255 years ago (95% highest posterior density [HPD], −978 to−6125 years). Chronologically, this ancestral lineage diverged to produce five recognized virus genotypes in the sequence 5, 4, 3, 2 and 1. Population dynamics analysis indicated that the genetic diversity of the virus peaked during the following two periods: 1930–1960 and 1980–1990, and the population diversity of JEV remained relatively high after 2000.ConclusionsGenotype 5 is the earliest recognized JEV lineage, and the genetic diversity of JEV has remained high since 2000.
Highlights
Japanese encephalitis virus (JEV) is the etiological agent of Japanese encephalitis (JE), one of the most serious viral encephalitis worldwide
The the most recent common ancestor (TMRCA) of JEV was estimated to be 1690 years when calculations were based on the complete sequence of four genotypes (G1-G4) [4], whereas, analysis of JEV using a limited number of whole genomic sequences from five genotypes indicated that
In order to improve our understanding of the evolutionary progress and population diversity of JEV, a comprehensive dataset was established for evolutionary analysis of JEV in this study
Summary
Genotype 5 is the earliest recognized JEV lineage, and the genetic diversity of JEV has remained high since 2000. The phylogenetic characteristics of JEV were analyzed and the most recent common ancestor (TMRCA) was estimated. The TMRCA of JEV was estimated to be 1690 years when calculations were based on the complete sequence of four genotypes (G1-G4) [4], whereas, analysis of JEV using a limited number of whole genomic sequences from five genotypes indicated that. 100 whole genomic sequences of JEV representing all five genotypes of JEV, isolated from various hosts (humans, pigs and bats) and vectors (mosquitoes and midges) were collected and analyzed. Two G5 JEV full-length genome sequences (Muar and XZ0934) were downloaded from GenBank (GB No HM596272 and JF915894, respectively) and added to the database established in a previous report [4], forming a new database for analysis (Table 1).
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