Makerere's contribution to the development of a high impact HIV research population-based cohort in the Rakai Region, Uganda

Longitudinal population-based cohort studies can provide critical insights on temporal, spatial and sociodemographic changes in health status and health determinants that are not obtained by other study designs. However, establishing and maintaining such a cohort study can be challenging and expensive. Here, we describe the role of Makerere University in the development and conduct of such a cohort. We chronicle the first academia-led reports of HIV in East Africa; how this led to initiation of the Rakai Community Cohort Study in 1988, the first and oldest HIV cohort in sub-Saharan Africa; its impact on HIV prevention, care and treatment; how the cohort has been maintained; and opportunities, challenges, and future directions including non-communicable diseases.


Uganda
A war between Uganda and Tanzania ended in 1979 with disputed elections in 1980 and the eventual outbreak of the Uganda civil war of 1980-1986. By 1982, reports began emerging of cases of an unknown disease in Rakai, a Ugandan district bordering Northern Tanzania and neighboring Masaka district. The information was passed on to the Uganda Ministry of Health which dispatched a team of senior doctors to investigate. They reported that these cases were likely to be usual diseases such as tuberculosis presenting with gastrointestinal manifestations. Nonetheless, Dr. Anthony Lwegaba, a young Medical Ofcolleagues at Mulago Hospital, Makerere Medical School. Subsequently, a medical research team travelled to Rakai and Masaka districts. The team was comprised of Nelson K. Sewankambo, David M. Serwadda and Roy D. Muger-well and Ann C. Bailey, senior British doctors working in Mulago Hospital and the University of Zambia in Lusaka, respectively (Ann C. Bailey had been working on Kaposi sarcoma). Nelson, David, and Roy wanted to better understand the disease. They secured donations of a few syringes, gloves and test tubes from Mulago Hospital, the Uganda Cancer Institute, and the Uganda Virus Research Institute (the civil war was still in progress, and basic sup-British embassy to lend them a Land Rover. Thus, without any formal research support, they headed south-west to Masaka Hospital and rural Rakai District. The patients in Rakai and Masaka had intermittent fevers and moderate to severe diarrhea, an irritating skin rash, and were weak and extremely wasted. Local attendants were at a loss -they were having to resort to using mpombo (steamed soft banana leaves) as nappies for the patients with diarrhea. There were many fresh graves around households, and multiple afternoon burial processions were a common sight every day. The local people called the condition "slim disease" because of the extreme weight loss that patients manifested. They suggested that cross-border movements by military personnel during the earlier Uganda-Tanzania war, as well as traders involved in illicit trade brought this disease from Tanzania to Uganda. Uganda was undergoing severe economic hardship because of the repeated wars and smuggling from Tanzania was rampant across Lake Victoria and along dilapidated roads. Because many of the early patients were traders who frequently crossed the borders, Rakai residents theorized that the former engaged in commercial sex in Tanzania and were bewitched or cursed by medicine men in that country. In addition, some people thought the disease was a punishment from God for the illicit trade. symptoms at Kalisizo Health Center and Masaka Hospital and visited the homes of some of these individuals. The team took medical histories, examined in-hospital medical and surgical patients, and collected biological samples that included sputum, urine, stool, and blood. They noted similarities between these cases and those reported among homosexual men in North America at the time. The paradox was that the Uganda patients were heterosexual men and women. The cases in North America man T-cell Leukemia Virus type 3 or the Lymphadenopathy-Associated Virus (HTLV-III/LAV) 1 prevalence of up to 52.8% in some communities, as well as descriptions of the pattern of community spreadfrom main road trading centers, through intermediate trading villages, to rural agricultural villages (Figure 1) 5 . These data indicated that there was a public health emergency in the region. In the following years, additional funding from multiple funding agencies and foundations, including NIH, CDC, the World Bank, the Ugandan Ministry of Health, the Rockefeller Foundation, the Gates Foundation, the Walter Reed Army Institute of Research/Henry Jackson Foundation, and the Doris Duke Charitable Foundation enabled expansion of the Rakai project with establishment of a lab, inclusion of new communit clusters, provision of counseling services, and new HIV/STD stud-ies nested within the cohort. The cohort in its current form ( Figure 2) was reorganized and further expanded in 1994 and has since included comprehensive sociodemographic, behavioral and health interviews, and collection of biospecimens for assessment of HIV, other sexually transmitted infections (STIs), opportunistic infections, and more recently, non-communicable diseases once every 18 months. At the close of 2020, the Rakai Community Cohort Study (RCCS), included over 22,000 individuals aged 15 to 49 years old from 40 agrarian, trading, 2021 to also expand surveillance of emerging non-communicable diseases.

Impact of the Rakai cohort on HIV prevention, treatment, and care policy
The cohort has thrived over the years and has had a profound impact on our understanding of HIV epidemiology, spatial distribution, modes of prevention, treatment, and care globally. Since the early 1990s, cohort data provided numerous insights into the effects of HIV on population-level demography, modes of transmission and risk factors [6][7][8][9][10][11] . Between 1994-1998, the RHSP nested a community-randomized trial to test the effect of mass treatment of STIs on HIV incidence. Although the in-it did not reduce HIV incidence 12 . The latter negative was later replicated in multiple other international studies), the data and biospecimen repository helped generate viremia level as a main driver of HIV transmission and that viral load was highest in the early and late stages of HIV infection (Figure 3) 13,14 . In addition, a nested study for both the women and their infants from the low cost, feasible mass STI treatment used in the trial 15 . r P e e r R e v i e w renamed Human Immune deficiency Virus type-1 or HIV-1 (Coffin et al., 1986). Through Dr Robert Downing at the Uganda Ministry of Health / Uganda Virus Research Institute agreed these samples to the Public Health Laboratory in Porton Down, Salisbury, UK for testing wh samples tested positive for HTLV-III/LAV. This constituted the first report of HIV in East Afri in The Lancet, (Serwadda et al., 1985).
The Uganda civil war ended about three months later in January 1986, but the new govern double challenge -rebuilding the country's dilapidated infrastructure and economy; and g an untreatable and fatal new disease.
Establishment of the first and oldest population-based HIV cohort in Africa, since 1988. N David wrote proposals to several funding agencies including the WHO and the US Centers f Control (CDC) and received encouragement but no funding. Eventually after two years, Col University learnt of the Rakai reports and of the frantic search for funding, and asked Mari physician/ epidemiologist to travel to Uganda to check out the potential for a small HIV/AID using a m grant lef from a re health pr Initially s regardin possibilit Maria wa convince determin David an a trip to "So, proposa These data indicated that there was a public health emergency in the region. In the following years, additional funding from multiple funding agencies and foundations, including NIH, CDC, the World Bank, the Ugandan Ministry of Health, the Rockefeller Foundation, the Gates Foundation, the Walter Reed Army Institute of Research/Henry Jackson Foundation, and the Doris Duke Charitable Foundation enabled expansion of the Rakai project with establishment of a lab, inclusion of new communit clusters, provision of counseling services, and new HIV/STD stud-ies nested within the cohort. The cohort in its current form ( Figure 2) was reorganized and further expanded in 1994 and has since included comprehensive sociodemographic, behavioral and health interviews, and collection of biospecimens for assessment of HIV, other sexually transmitted infections (STIs), opportunistic infections, and more recently, non-communicable diseases once every 18 months. At the close of 2020, the Rakai Community Cohort Study (RCCS), included over 22,000 individuals aged 15 to 49 years old from 40 agrarian, trading, 2021 to also expand surveillance of emerging non-communicable diseases.

Impact of the Rakai cohort on HIV prevention, treatment, and care policy
The cohort has thrived over the years and has had a profound impact on our understanding of HIV epidemiology, spatial distribution, modes of prevention, treatment, and care globally. Since the early 1990s, cohort data provided numerous insights into the effects of HIV on population-level demography, modes of transmission and risk factors [6][7][8][9][10][11] . Between 1994-1998, the RHSP nested a community-randomized trial to test the effect of mass treatment of STIs on HIV incidence. Although the in-it did not reduce HIV incidence 12 . The latter negative was later replicated in multiple other international studies), the data and biospecimen repository helped generate viremia level as a main driver of HIV transmission and that viral load was highest in the early and late stages of HIV infection (Figure 3) 13,14 . In addition, a nested study for both the women and their infants from the low cost, feasible mass STI treatment used in the trial 15 .   (Serwadda et al., 1985).
The Uganda civil war ended about three months later in January 1986, but the new govern double challenge -rebuilding the country's dilapidated infrastructure and economy; and g an untreatable and fatal new disease.  dure was safe, acceptable and reduced the risk of male HIV acquisition by over 50%. VMMC also reduced the risk of male acquisition of other STIs 24,25 HIV-positive men 26 . The WHO and the Joint United Nations Program on HIV/AIDS (UNAIDS) recommended VMMC for HIV prevention in countries with high HIV burdens and low male circumcision prevalence 27 . It is now an integral part of HIV programs in over 14 countries in sub-Saharan Africa. Since the Rakai cohort was also the only of the threerials to include female partners, it was also able to show that VMMC was highly acceptable to men and their partners 28,29 transmission of multiple STIs to these partners 30 . Through the cohort, more attention was drawn to the need for enhanced treatment of pregnant women and prevention of mother to child transmission (PMTCT) 7 . Effective modalities of delivering antiretroviral therapy to pregnant mothers and their infants were suggested 31 posed babies was demonstrated 32 , as well as the potential for integration of contraception services in HIV care for the mothers 33 . The Rakai cohort has also provided a platform to evaluate the impact of HIV combination interventions, including VMMC and antiretroviral therapy. In 2017, the combination HIV prevention including a 42% reduction in HIV incidence within about 10 years 34 in the general population and 48% decline (within 5 years) in hyper-en- 35 . The RHSP, based on cohort has conducted multiple implementation research studies to determine how to improve the availability and acceptance of combined HIV prevention 36,37 . Since 2016, RHSP has supported a comprehensive HIV service program (beyond VMMC and ART) across 12 districts of the Masaka region (including Rakai) with funding from PEPFAR through CDC-Uganda. The program includes prevention services such as Pre-and Post-Exposure prophylaxis (PrEP and PEP), DREAMS-an HIV prevention program among adolescent girls and young women, programs to reach key and priority populations with treatment, and program to mitigate effects of intimate partner violence and to protect children. An ongoing collaboration with the PANGEA-HIV consortium, funded by the Bill and Melinda Gates Foundation, which includes multiple southern and eastern Afri-  dure was safe, acceptable and reduced the risk of male HIV acquisition by over 50%. VMMC also reduced the risk of male acquisition of other STIs 24,25 HIV-positive men 26 . The WHO and the Joint United Nations Program on HIV/AIDS (UNAIDS) recommended VMMC for HIV prevention in countries with high HIV burdens and low male circumcision prevalence 27 . It is now also able to show that VMMC was highly acceptabl men and their partners 28,29 transmission of multiple STIs to these partners 30 . Through the cohort, more attention was drawn to need for enhanced treatment of pregnant women prevention of mother to child transmission (PMTC Effective modalities of delivering antiretroviral ther to pregnant mothers and their infants were suggest posed babies was demonstrated 32 , as well as the poten for integration of contraception services in HIV care the mothers 33 . The Rakai cohort has also provided a platform to e uate the impact of HIV combination interventions, cluding VMMC and antiretroviral therapy. In 2017, combination HIV prevention including a 42% reduc in HIV incidence within about 10 years 34 in the gen population and 48% decline (within 5 years) in hyper 35 . The RHSP, based on coh has conducted multiple implementation research st ies to determine how to improve the availability and ceptance of combined HIV prevention 36,37 . Since 20 RHSP has supported a comprehensive HIV service p gram (beyond VMMC and ART) across 12 districts the Masaka region (including Rakai) with funding fr PEPFAR through CDC-Uganda. The program inclu prevention services such as Pre-and Post-Exposure p phylaxis (PrEP and PEP), DREAMS-an HIV prev tion program among adolescent girls and young wo en, programs to reach key and priority populations w treatment, and program to mitigate effects of intim partner violence and to protect children.  (Quinn et al. N Engl. J Med 2000, Wawer et al, JID, 2005 can cohorts, is assembling the most comprehensive data and analyses on HIV phylogenetics on the continent. With the Rakai cohort as the largest biospecimen contribcommunities do not spread HIV to the general populations and that "super spreaders" do not play a major role in transmission 38 . Recent epidemiologic and phylogenetic data from the Rakai cohort and other cohorts in sub-Saharan Africa show that in a generalized African epidemic "many infect few". By 2022, nearly 600 publications have come from this cohort and have been cited more than 20,000 times. The cohort is expanding to follow-up Rakai cohort participants who migrate to major urban areas in Uganda (Kampala and Masaka) to determine how such migration affects access to and use of HIV prevention and treatment, and importantly, any changes in NCD status (e.g., hypertension, asthma, and related conditions). "We owe this small community of committed researchers a debt of gratitude for all the knowledge they have given us, from their post on the front lines of this terrible scourge. Paraphrasing Sir Winston Churchill, never was so much owed by so many to so few!" Roger I Glass, Director, Fogarty International Center 39 .

Partnerships to support the cohort and science
The role of partnerships between the RHSP and its population-based cohort, Makerere University, the Ugandan MOH, and multiple international entities is evident from David and Nelson's early efforts to mobilize multidisciplinary, national, and international teams to address the HIV problem in Uganda. The strategic partnerships built over the years have been invaluable in accelerating progress and maximizing local and international impact. RHSP now has co-investigators from multiple institutions -Institute, UK. It has been designated an International Center for Excellence in Research by the National Institute of Allergy and Infectious Diseases, NIH, USA, which greatly facilitates research collaboration with NIH Intramural Scientists. It is also an Implementing Partner for the PEPFAR program through CDC in Uganda. Multiple Ugandan scientists trained and mentored through the RHSP have in turn contributed to research, research training, public health education and mentoring, laboratory sciences training and scholarship at Makerere and other Ugandan and foreign universities -including professors. Very importantly, the RHSP and the cohort provide a rich opportunity for researchers to gain higher degrees from Ugandan and international universities, using cohort data, and returning to a vibrant research environment in Uganda. With Gates Foundation and NIH was built with a state-of-the-art clinic, laboratory, data management center, secure internet support, information technology equipment, biorepository, power backup inmanagement, conference and training facilities, and limited residential facilities for visiting researchers and some trainees.
Opportunities, challenges, and the future From small beginnings, the Rakai cohort in rural South-Central Uganda has been invaluable in fostering discoveries and providing information critical for HIV control that we had not envisioned in the early years of the epidemic. When the Makerere University researchers and colleagues from its partner institutions travelled to Rakai and Masaka districts in the early 1980's to research on "Slim" disease, they never imagined that they were setting a foundation for a future vibrant research institution in rural Africa with potential for global impact and that it would be in existence for nearly 35 years later. Given the physical and human infrastructure that exists now, the future is extremely bright and there are opportunities for expansion and greater impact in the region and globally through research, service delivery, education, and research capacity building. In the absence of an HIV vaccine and a cure -which the RHSP is increasingly researching 40-43 , we are yet to close the chapter on HIV. We must remain vigilant lest the gains made be lost. The epidemic must be consistently measured in the population and its ever-changing determinants characterized. The Rakai Cohort data have been made publicly available to other researchers on a dashboard 44 . Also, as people live longer and lifestyles and the environment change, non-communicable diseases (NCDs) are starting to emerge in the population and the cohort provides the infrastructure to study the epidemiology, test interventions and evaluate the population-level impact of these interventions on NCDs.

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Longitudinal cohorts like the Rakai cohort require time would ensure a stable research human resource is an enduring problem. Equally challenging is the long-term sustenance of the research infrastructure that has been developed over the years, largely dependent on winning foreign grants. "But the future is promising. It is now more than 30 years and the cohort is still alive and well. I am optimistic it will be sustained longer," says Nelson. Going forward, the RHSP needs to establish an even stronger partnership with Makerere (and other Ugandan of each party. Ugandan institutions especially Makerere University can tap the research opportunities from the accumulated data, mentoring and potential partnerships. Local grants writing capacity needs to increase. There should be more research output from Ugandan and African students and researchers. RHSP should aim to become a stronger educational and research-training hub -hosting more doctoral, post-doctoral and visiting students and scientists with prolonged stay to increase research output and visibility. Makerere and other universities in Uganda and Africa should make efforts to acquire minds -the story of RHSP started with such inquisitive young minds. Finally, the biggest testimony of Rakai will always remain the improved lives of the local population who participate in the research and are the primary recipients of Rakai's services. "We were asked -why go to Rakai [a miserable place then], are you born there? But we came. We volunteered our time. We did the mined," concludes Nelson.