Tracing the spatiotemporal phylodynamics of Japanese encephalitis virus genotype I throughout Asia and the western Pacific

Abstract

Background: Japanese encephalitis virus (JEV; Flaviridae: Flavivirus) causes Japanese encephalitis (JE), which is the most important arboviral disease in Asia and the western Pacific. Among the five JEV genotypes (GI-V), GI has dominated traditional epidemic regions in the past 20 years. We investigated the transmission dynamics of JEV GI through genetic analyses.

Methods: We generated 18 JEV GI near full length sequences by using multiple sequencing approaches from mosquitoes collected in natural settings or from viral isolates obtained through cell culture. We performed phylogenetic and molecular clock analyses to reconstruct the evolutionary history by integrating our data with 113 publicly available JEV GI sequences.

Results: We identified two subtypes of JEV GI (GIa and GIb), with a rate of 5.94 × 10-4 substitutions per site per year (s/s/y). At present, GIa still circulates within a limited region, exhibited no significant growth, the newest strain was discovered in China (Yunnan) in 2017, whereas most JEV strains circulating belong to the GIb clade. During the past 30 years, two large GIb clades have triggered epidemics in eastern Asia: one epidemic occurred in 1992 [95% highest posterior density (HPD) = 1989-1995] and the causative strain circulates mainly in southern China (Yunnan, Shanghai, Guangdong, and Taiwan) (Clade 1); the other epidemic occurred in 1997 (95% HPD = 1994-1999) and the causative strain has increased in circulation in northern and southern China during the past 5 years (Clade 2). An emerging variant of Clade 2 contains two new amino acid markers (NS2a-151V, NS4b-20K) that emerged around 2005; this variant has demonstrated exponential growth in northern China.

Conclusion: JEV GI stain circulating in Asia have shifted during the past 30 years, spatiotemporal differences were observed among JEV GI subclade. GIa is still circulating within a limited range, exhibite no significant growth. Two large GIb clades have triggered epidemics in eastern Asia, all JEV sequences identified in northern China during the past 5 years were of the new emerging variant of G1b-clade 2.

Fig 1. Time-scaled phylogeographic history of epidemic Japanese encephalitis virus (JEV) genotype I (GI).

Boxes with gradient shading indicate clades GIa and GIb; posterior probabilities for their ancestral nodes are shown. Tip colors represent different sampling locations, according to the map at upper left. The base layer of the modified maps are sourced from Natural Earth, and download in GeoJSON format from website (https://geojson-maps.ash.ms/).

Fig 2

Bayesian skyline plots showing the demographic history of JEV GI including (A) GI, (B) GIa, (C) GIb, (D) GIb clade 1, (E) GIb clade 2, and (F) sub-clades NS2a-151V and NS4b-20K. Each y-axis represents virus effective population size (Ne), which is a measure of genetic diversity based on the number of genomes effectively contributing to new infections. Each x-axis represents time in calendar years. Blue lines are median estimates; purple lines are 95% highest posterior density (HPD) intervals.

Fig 3. Spatial dynamics of JEV GI spread over the past five decades.

Circles indicate sampling locations. Lines between locations represent branches of the maximum clade credibility (MCC) tree along which the relevant location transition occurred. The base layer of the modified maps are sourced from Natural Earth, and download in GeoJSON format from website (https://geojson-maps.ash.ms/).