Figure 1.

Study design

(A) Locations of the RCCS in eastern Africa (left) and the Rakai region of Uganda where the RCCS survey was done (right). The RCCS included an estimated 75·7% of populations in the lakeside area within 3 km of the Lake Victoria shoreline (light brown), and 16·2% of populations in the inland area of the Rakai region (light green). Areas classified as external in this study are shown in light blue. Not shown is one RCCS community northwest outside the map, in which virus sequences were not obtained. (B) The phyloscanner approach for inferring directed HIV transmission networks from deep sequence phylogenies based on ancestral relationships between infecting viruses. With viral deep-sequencing, co-circulating HIV lineages within hosts are represented by many distinct sequence fragments in the data (diamonds, size indicating frequency with which distinct virus was sequenced). In the corresponding phylogenies, sequences from the same individual tend to form subtrees (colours, one for each of the six individuals shown). The ordering of subtrees provides evidence of the direction of transmission. (C) Scale of in-migration into the cohort. For this purpose, RCCS participants were classified as in-migrants if they in-migrated into the cohort in the 2 years before their first visit in the observation period, and otherwise as residents. The panel shows the proportion of in-migrants and residents as well as the size of the population infected with HIV. (D) Key study outcomes including participation, sequencing, and linkage rates. RCCS=Rakai Community Cohort Study.