Currently the PANGEA database holds over 18,000 NGS sequence files from sub-Saharan Africa with basic epidemiological metadata associated with them. For some cohorts, extensive metadata is available; contact us for more information. We currently obtain full genomes from ~ 90% of high-quality samples, with many of the less-complete sequences originating from participants who are likely to be virally suppressed. See the resource section for sequencing protocols used.
Last updated December 2018
*Sequences from PopART Phylogenetics will become available to accredited researchers in spring 2020.
This section gives an overview of each of the cohorts and trial populations that data was collected from.
Botswana Harvard AIDS Institute Partnership
The Botswana-Harvard AIDS Institute Partnership (BHP) is a collaborative research and training initiative established in 1996 between the Government of Botswana and the Harvard School of Public Health AIDS Initiative. The primary goal of the BHP is to help end the AIDS epidemic in Africa by conducting basic and clinical research relevant to southern Africa and by building capacity within Botswana. The research at BHP focuses on epidemiology, virology, molecular biology, immunology, genetics, clinical treatment, and social and behavioral issues relevant to the epidemic in Botswana and southern Africa.
BHP has contributed sampled from two studies to PANGEA, the Mochudi Prevention Project and the Botswana Combination Provention Project / Ya Tsie trial. The Mochudi Prevention Project (Mochudi study) implemented a comprehensive package of behavioral and biomedical interventions to 16-64-year-olds in Mochudi, a village in the south of Botswana about 37 km (23 mi) northeast of the national capital, Gaborone. The Botswana Combination Prevention Project (BCPP) is designed to test the hypothesis that implementing an enhanced combination prevention package which includes provision of ART as prevention for HIV-infected individuals with HIV-1 RNA ≥10,000 copies/ml will impact the HIV/AIDS epidemic by significantly reducing population-level, cumulative HIV incidence in a defined geographic area over a period of three years and will be cost-effective. The main results of the trial have just been published in the New England Journal of Medicine.
PARTNERS in prevention / ICRC
The International Clinical Research Center (ICRC) was established at the University in Washington in September 2007 to expand clinical research trial capacity for infectious disease interventions of public health importance. The ICRC facilitates collaborations, improves observational cohort studies and clinical trial operations; and provides repositories of biologic specimens and reagents for future scientific investigations for pathogenesis and prevention research related to HIV and other infectious diseases.
Africa Health Research Institute
In 2016, the KwaZulu-Natal Research Institute for TB-HIV and Africa Centre for Population Health joined to form an exciting new interdisciplinary research institute, the Africa Health Research Institute (AHRI). AHRI is a multidisciplinary, independent research institute based across two sites in the province of KwaZulu-Natal, South Africa. AHRI's goal is to become a source of fundamental discoveries into the susceptibility, transmission and cure of HIV, TB and related diseases. The insitute also seek ways to improve diagnosis, prevention and treatment. To achieve this, AHRI brings together leading researchers from different fields, use cutting edge science to improve people’s health, and help to train the next generation of African scientists.
AHRI has contibuted samples from the Treatment as Prevention (TasP) trial to PANGEA, and is currently contributing samples from the Vukuzazi study. TasP is a cluster-randomised trial which compared the impact of immediate ART initiation versus recommendations from the South Africa Department of Health guidelines on ART initiation. The results were published in the Lancet HIV in 2018.
The MRC/UVRI and LSHTM Uganda Research Unit
The Unit was established in 1988 to improve the understanding and control of the HIV epidemic in Uganda and globally, and in 2018 joined the London School of Hygiene and Tropical Medicine (LSHTM) to become The MRC/UVRI and LSHTM Uganda Research Unit. The unit's vision is to contribute to the control of the HIV epidemic, of other infectious diseases, and of non-communicable diseases, in Uganda, the region and the world, by conducting research and contributing to the translation of research findings into policy and practice, and by building capacity for research in Africa.
MRC Uganda has contributed samples from three projects / cohorts: The Fisherfolk cohorts, the MRC General Population Cohort and the MRC God Health for Women Project. The Fisherfolk cohorts are high-risk HIV cohorts amonh the fishing communities around Lake Vistoria. The MRC General Population Cohort in Kyamulibwa in southwest Uganda has been followed since 1989. It is an open cohort designed to document trends in the prevalence and incidence of HIV infection and their determinants (behavioural and epidemiological) through annual demographic, socio-medical and serological surveys. The MRC Good Health for Women Project is an ongoing cohort of high-risk women established in Kampala 2008. The rationale for the cohort was the curious lack of data on HIV epidemiology among women involved in high-risk sexual behaviour in Uganda. This cohort has since been opened up to enrol a larger number of women who are also encouraged to invite their regular male partners to enrol into the cohort.
Rakai Health Sciences Program
The Rakai Health Sciences Program (RHSP) grew out of a small cohort study initiated in 1987 into a collaborative not-for-profit health research and service organization with a focus on community-based research, treatment and prevention of HIV and other communicable diseases with just under 400 staff. The RHSP conducts the Rakai Community Cohort Study (RCCS) which is one of the largest, ongoing population-based cohort studies of HIV incidence in Africa. RHSP's mission is to conduct innovative and relevant health research in infectious diseases, communicable and noncommunicable diseases, and reproductive health and to provide health related services in order to improve public health and inform policy.
RHSP contributes samples from the Rakai Community Cohort Study to PANGEA. is an open, population-based cohort of persons 15 to 49 years of age across multiple community clusters in and near Rakai District. Agrarian and trading community boundaries were established in 1994 as part of a community-randomized trial. In 2011, the four largest Lake Victoria fishing communities in the Rakai region were added to the RCCS based upon their proximity and access to Rakai District’s non-fishing community populations. There are currently 40 communities surveyed by the RCCS; however, the total number of communities ever included in the RCCS exceeds this number. Thirty communities have been continuously surveyed since 1999 and 28 communities since 2004. There have been a total of 18 RCCS surveys conducted. RCCS Survey Round 19 is currently ongoing.
HPTN 071-2 (PopART) Phylogenetics ANciallary study
The HPTN 071 study, also known as PopART (Population Effects of Antiretroviral Therapy to Reduce HIV Transmission), is a large community-randomized trial which took place in South Africa and Zambia from 2013 to 2018 to evaluate the impact of a universal test-and-treat intervention on population-level HIV incidence. Almost 50,000 people out of a population of over a million were followed over four years. The trial is was carried out by a multi-national research consortium, led by the London School of Hygiene and Tropical Medicine in collaboration with the following institutions: Imperial College London, Desmond Tutu TB Centre, University of Stellenbosch, South Africa, ZAMBART, Zambia, the HIV Prevention Trials Network (HPTN) including the Leadership and Operations Center at FHI360, the Laboratory Center at Johns Hopkins University and the Statistical and Data Management Center at the Fred Hutchinson Cancer Research Center.
The HPTN 071-2 PopART Phylogenetics Anciallary study contributes samples from seroconverters in the PopART population cohort in the Zambian, but not the South African trial communities. In addition, PoPART phylogenetics contributes HIV-positve samples from health clinics in nine of the twelve Zambian PopART communities.