Figure 3.

Phylogenetically highly supported transmission flows in the population-based sample, and predicted transmission flows

Viral deep-sequence phylogenetics identified 293 source–recipient pairs with strong phylogenetic support for epidemiological linkage and the direction of transmission. Transmission events were geo-located to the communities in which the phylogenetically likely sources and recipients had their households, or to the origin of recent in-migration events. (A) Phylogenetically reconstructed transmission events. 94 phylogenetically reconstructed transmissions events occurred from inland to inland communities, and six occurred from outside the Rakai area to inland communities; seven were observed from fishing to inland communities; 23 occurred from inland to fishing communities; 141 occurred from fishing to fishing communities, and 17 from outside the Rakai area to fishing communities. Not shown are two phylogenetically probable transmission events with unknown source location to inland communities, and three such events to fishing communities. (B) Predicted transmission flow ratio among populations living in inland and lakeside areas of the Rakai region, after adjusting for survey, participation, and sequence sampling bias. The predicted flow ratio of transmissions from inland to lakeside areas compared with the opposite direction was 2·50 (95% CrI 1·02–7·30).