Fig. 5: Global geographic history of DENV-2 lineage 2 detected in Kenya.

Bayesian maximum clade credibility trees from phylogeographic analyses of 355 sequences were used to reconstruct the geographic history of DENV-2 lineage 1 circulating in Kenya detected in this study. Geolocation data from sequences was grouped into one of 16 study categories (Supplementary Table 3) to improve analytic tractability. a Each arrow in the map corresponds to a node on the MCC tree ancestral to the detected Kenyan lineage indicated in the plot, where a geographic transition between two locations occurred. Lines are annotated with inferred MRCA node date and 95% high posterior density (HPD) intervals. b Markov jump history between locations was recorded for inferred trees and is summarized in the bottom plot. The plot shows the inferred timing of Markov jumps representing transmission between two locations for the geographic history shown in the top plot. Vertical lines represent a geographic transition between two locations, while horizontal lines indicate times during which the ‘lineage’ remains in the same location, i.e. the reward times. Greater density of lines indicates greater certainty of inferred transmission events around a given date, while sparsity of lines indicates lower certainty.