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/).
Table 1.
Evidence for adaptive selection on the full open reading frame (ORF) of the JEV genome according to different assessment models.
Table 2.
Amino acid markers and corresponding nucleotide changes identified for different clades.of JEV GI.