Fig 1.
Recombination and selection analysis of JEV genomes.
Top legend indicates the locations of protein coding genes, bottom legend indicates position in the genome alignment. Graph A depicts recombination break point probability per site, light grey indicates 99% probability, the mid grey area indicates 95% probability while the dark grey represents non-significant break points. Marginally significant break points were observed in structural protein E and Nonstructural protein 5. Graph B depicts nucleotide diversity (π) calculated using a sliding window analysis.
Fig 2.
Phylogeny of JEV genome sequences, showing the five monophyletic genotypes of JEV.
Branching order in the current analysis is confirmatory of prior studies of evolution of JEV. Node labels indicate bootstrap support, scale is in substitutions per site. The MDV sequence is a Murray Valley encephalitis virus sequence used as an outgroup for the phylogenetic analysis.
Table 1.
Recombinant strains as detected by RDP5 analysis.
All events were between isolates of the same genotype with the exception of those with unknown parents, and event 16. R–RDP, G–GENECONV, B–Bootscan, M–MaxChi, C–Chimaera, S–SiScan, T– 3Seq, Major parent–major presumed donor of recombined sequence, Minor parent–minor presumed donor of recombined sequence (if more than one recombination event detected).
Table 2.
Results of selection analysis.
Test of neutrality was conducted using an averaged codon based, two tailed Z test; Episodic selection was determined using a Branch-site Unrestricted Statistical Test for Episodic Selection; and codon positions under diversifying selection were determined using a Mixed Effects Model of Evolution analysis. The most prevalent amino acid substitution is indicated after each position when non-synonymous.