The mean divergence within all Vietnamese viral sequences was 0.3%, but there was 3.3 11.3% nucleotide divergence over the N-450 region compared with WHO reference strains (Fig. 1).
Both clades show low differentiation (maximum haplotype divergence being under 1% in SAF and under 3% in NAF) over a broad geographical range (see Figure 2), but are highly divergent from one another (mean divergence 6.6%), with haplotypes differing by 7% separated by less than 200 km.
Estimates of the mean divergence times with 95% highest posterior density regions HPD and posterior probabilities represented as percentages are noted on the chronogram.
TreeAnnotator v1.5.4 [ 125] was used to summarize the set of post-burn-in trees and their parameters, in order to produce a maximum clade credibility (MCC) chronogram showing mean divergence time estimates with 95% HPD intervals.
TreeAnnotator, part of the BEAST package, was then used to create a maximum clade credibility tree, with the mean divergence ages shown for all nodes with >95% highest posterior density.
When filtering the TE families with mean divergence >20% and standard deviation >5%, as well as copies with >20% divergence (supplementary table S-6, Supplementary Material online), or when focusing separately on the three Alu families (supplementary table S-7, Supplementary Material online), the conclusions remain unchanged.
Mean divergence estimates (t) (calibrated with mutation rates of 2 and 4% divergence per Ma) ranged from 91 182 (HPD 24 320) kya.
FigTree v.1.3.1 was used to visualize tree structure, with mean divergence times.
Importantly, RETA had a mean divergence of 56% compared with other rickettsial genomes, just below Neorickettsia (57%) and not atypical from other rickettsial lineages.
Based on these results the first 12.5 million generations were discarded as burn-in, and remaining samples were summarized as a maximum clade credibility tree with mean divergence times and HPD intervals of age estimates using TreeAnnotator v.1.6.1 [ 130].
