Insights into the evolutionary history of Japanese encephalitis virus (JEV) based on whole-genome sequences comprising the five genotypes - PubMed (original) (raw)

Insights into the evolutionary history of Japanese encephalitis virus (JEV) based on whole-genome sequences comprising the five genotypes

Xiaoyan Gao et al. Virol J. 2015.

Abstract

Background: Japanese 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.

Findings: In 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.

Conclusions: Genotype 5 is the earliest recognized JEV lineage, and the genetic diversity of JEV has remained high since 2000.

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Figures

Figure 1

Figure 1

Maximum clade credibility (MCC) tree for 100 whole-genome sequences of JEV. Five distinct lineages were identified: G1 (red), G2 (yellow), G3 (blue), G4 (green) and G5 (orange). Estimated TMRCAs of these lineages (with their 95% HPD values in parentheses) are shown, G1: 155(104–315), G2: 530(235–1131), G3: 880(420–1855), G4: 1653(765–3372), and G5: 3255(978–6125).

Figure 2

Figure 2

Bayesian skyline plots for JEV. Highlighted areas correspond to 95% HPD intervals. (A) Populations during the whole evolutionary history; (B) Populations during the later evolutionary history since 1800.

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References

    1. Uchil PD, Satchidanandam V. Phylogenetic analysis of Japanese encephalitis virus: envelope gene based analysis reveals a fifth genotype, geographic clustering, and multiple introductions of the virus into the Indian subcontinent. Am J Trop Med Hyg. 2001;65(3):242–51. - PubMed
    1. Li MH, Fu SH, Chen WX, Wang HY, Guo YH, Liu QY, et al. Genotype V Japanese encephalitis virus is emerging. PLoS Negl Trop Dis. 2011;5(7):e1231. doi: 10.1371/journal.pntd.0001231. - DOI - PMC - PubMed
    1. Solomon T, Ni H, Beasley DW, Ekkelenkamp M, Cardosa MJ, Barrett AD. Origin and evolution of Japanese encephalitis virus in southeast Asia. J Virol. 2003;77(5):3091–8. doi: 10.1128/JVI.77.5.3091-3098.2003. - DOI - PMC - PubMed
    1. Pan XL, Liu H, Wang HY, Fu SH, Liu HZ, Zhang HL, et al. The Emergence of Genotype I of Japanese Encephalitis Virus as the Dominant Genotype in Asia. J Virol. 2011;85(19):9847–53. doi: 10.1128/JVI.00825-11. - DOI - PMC - PubMed
    1. Mohammed MA, Galbraith SE, Radford AD, Dove W, Takasaki T, Kurane I, et al. Molecular phylogenetic and evolutionary analyses of Muar strain of Japanese encephalitis virus reveal it is the missing fifth genotype. Infect Genet Evol. 2011;11(5):855–62. doi: 10.1016/j.meegid.2011.01.020. - DOI - PubMed

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