Phylogenetics And Networks for Generalised HIV Epidemics in Africa


Rakai Cohort

Rakai images

Since 1994 the Rakai Health Sciences Program (RHSP) has conducted the Rakai Community Cohort Study (RCCS).  The RCCS is an open population-based cohort which enrolls all consenting residents aged 15-49 in ~50 communities distributed throughout the district.  Participants respond to a detailed sociodemographic, behavioral, sexual network, mobility, health and service utilization interview, and provide a blood sample for HIV testing. Approximately 18,000 individuals participate in the RCCS; the response rate among age eligible persons is over 90%, and annual follow up is approximately 75%, with losses due primarily to out-migration and aging beyond 49.  (The latter is balanced by annual in-migration and aging into the cohort.)  HIV prevalence ranges from ~12% in smaller rural trading villages, to ~20% in larger trading centers with serve as local and regional transport hubs, and to ~42% in high risk fishing communities on Lake Victoria.   HIV incidence ranges from ~0.9/100 person years in the more rural communities to ~3.5-4/100 PY in the fishing villages.  The HIV epidemic in Rakai is composed of subtypes A, and D, plus recombinants:  in adults, almost all transmission occurs through heterosexual intercourse.   All RCCS communities have been mapped by GPS.

The RHSP is providing the Pangea collaboration with samples from all prevalent HIV+ persons who are not yet on ART from the 2012-13 RCCS survey round (n ~ 2,000).   Sera from new HIV seroconverters from the 2013-2014 survey round (~200) will also be made available.

Given both the duration of the HIV epidemic in the District, and Rakai’s  road and lake connections with other Ugandan and African regions, the data from these full length sequences will contribute to the overall Pangea goals of better defining the HIV epidemic within Southern and Eastern Africa. The data will also provide additional insights into transmission patterns in Rakai, within and between rural communities, transport hubs and fishing communities, within the context of a long-term, generalized and well characterized HIV epidemic.  

Rakai images