In 2005, AIDS claimed the lives of 900 people in South Africa every day. Despite an overwhelming consensus within the biomedical community, Thabo Mbeki, President of South Africa at the time and his health ministry maintained their denialist stance.
A domestic history of epidemics being used as a tool of racial segregation, combined with conspiracies that HIV was a weapon aimed at eradicating the black population, and widespread distrust of Western medicine only further supported this stance. Doctor Francois Venter, a clinician researcher at the University of Witwatersrand recalled his country’s struggle, stating, “We were smuggling drugs into the country from the US, Australia and Europe … but our President was saying HIV didn’t even exist.”
In the midst of the growing death toll of the HIV/AIDS epidemic, the United States President’s Emergency Plan for AIDS Relief (PEPFAR) was established. Launched in 2003 under the Bush Administration, it partnered with non-profit organisations across the country, facilitating the distribution of antiretroviral treatment (ART).
One such organisation was the Anova Health Institute. By managing programs to strengthen government systems, prioritising efforts to prevent mother-to-child transmission, and making services accessible for gay men and adolescent girls, it, among other nonprofits, became essential to South Africa’s HIV response.
PEPFAR partnerships and funding were primarily instituted through USAID, which began to be dismantled on January 20, 2025, after Trump issued an executive order halting all foreign aid programs following a 90-day review. PEPFAR, deemed a life-saving service, was granted a waiver that moved its operations to the State Department. Even under its new remit, the program has been scaled back significantly and non-profit collaborations have continued to be terminated. These cuts to the PEPFAR program threaten to undo much of the progress it achieved in combatting the HIV epidemic.
Kate Rees, a public health specialist who has worked for over 9 years at Anova, explained the impact of these cuts, stating, “When the termination notices came through, all of our US funding was terminated. So in February and April, we had to retrench and let go of 3,000 workers — healthcare workers, data capturers, nurses. We haven’t hired any of them back. Some of them are unemployed, some of them have gotten other jobs, but our programs are not going to restart.”
PEPFAR’s HIV Relief Infrastructure
PEPFAR was initially launched in 2003 to combat the growing HIV/AIDS epidemic in developing nations. Doctor Anne Neilan, an Associate Professor at Harvard Medical School and Mass General Research Institute, explained that PEPFAR has changed the trajectory of the global HIV epidemic by saving upwards of 20 million lives, whether that be through providing HIV PrEP (pre-exposure prophylaxis for HIV prevention), conducting large-scale HIV testing, or making ART accessible. In South Africa, she specified, PEPFAR has contributed more than $8 billion to HIV/AIDS relief since its inception and accounted for 18 percent of the country’s total HIV budget in 2022.
PEPFAR’s role varied across countries, depending on the capacity of local healthcare systems. In places like Malawi and Mozambique, PEPFAR provided the vast majority of relief funding. Consequently, the human cost of termination has proven devastating. “It’s exactly the horror you’d expect,” said Venter.
South Africa is a different story. Being a relatively richer nation, it has developed its primary healthcare system and as a result reduced its reliance on PEPFAR. In 2019, globally, the South African government contributed more towards funding for drugs than both the Global Fund and PEPFAR itself. What then was the role of the program in South Africa? It served two crucial purposes.
The first was investing heavily in prevention. Venter explained, “What PEPFAR did incredibly well was that it funded detections in South Africa with laser-like efficiency. It’s also important to understand that we don’t do that anywhere in the world for other diseases. We don’t do it for diabetes, we don’t do it for cancer, and we don’t do it for mental health issues.” PEPFAR programs diagnosed people before they presented symptoms, preventing the disease from progressing. The system was efficient: people would be started on treatment the same day of detection, ensuring that they would not get lost within the system. This not only reduced mortality but also aided prevention efforts by making sure that more people did not unintentionally transmit the virus.
The second role PEPFAR undertook was setting up programs for disenfranchised populations. Venter found this strange, given that American politics itself tends to be increasingly polarizing in its discussion of these populations, but he explained that a crucial function of PEPFAR was catering to groups normally considered “unmentionable.” PEPFAR provided services to members of the LGBTQ+ community, drug users, and sex workers––all populations disproportionately affected by HIV.
When discussing which of Anova’s programs have been most affected, Kate Rees echoed this dimension of PEPFAR. Critical care provided by the organization in the form of prevention, family planning, and specific services for adolescent girls and young women have been shut down. The supply of PrEP and antiretrovirals has not been disrupted, as they are purchased by the government, but people can no longer seek personalized services and find it significantly harder to get medication in the absence of free clinics.
Care Without Continuity
Elna Schutz, a health journalist in South Africa who has written extensively about the HIV funding cuts, said “PEPFAR had a huge impact on our continued and strong fight against HIV and AIDS … but to have it pulled at such short notice on such a large scale really seemed like the end of the world for some people in this space.” She continued, “One researcher described it to me as a train ripped off its tracks in the sense that you can’t just press a button and start it all again, even if we had funding again tomorrow. It’s really been derailed in the long term. I cried. People cried.”
To assess the damage of cuts to PEPFAR funding, many experts have attempted to quantify and predict the impact of HIV transmission in South Africa. Dr Neilan, in one such study, modeled the entire adult population in South Africa and then projected clinical outcomes if PEPFAR funding was eliminated. They found that, over the next ten years in South Africa, cuts to PEPFAR are likely to lead to 565,000 new HIV infections and 601,000 HIV-related deaths.
This translates to a terrifying on-ground reality. Doctor Lyle Murray, an infectious disease specialist at the University of Witwatersrand, explained, “It’s easy to listen to the South African government saying we’ve managed to initiate 500,000 people on antiretroviral drugs over the last six months and to not really look at what’s actually happening to particular projects. We’ve got an NGO called Engage in the middle of Hillbrow, which is focused on men’s health for men who have sex with men, a particularly vulnerable group of patients who live with HIV. They had 4,000 patients on PrEP, one and a half thousand patients on ARVs, and then their doors closed, suddenly.” The future of PEPFAR partner organizations without support remains bleak.
For patients, safe medication is now available only at government hospitals. However, the criminalization of sex work in South Africa almost entirely prevents sex workers from attending healthcare facilities to access these medications out of fear of being reported. Even when they decide to seek care despite this threat, they get turned away. Sex workers have been told they need a transfer letter from their previous clinic––many of which have abruptly shut down––despite the referral not being a requirement. Further, transgender women, globally 49 times more likely to be affected with HIV, have been denied medication because hospitals limit PrEP to only those in a relationship with someone HIV-positive and trying to conceive. This has forced the most vulnerable to turn to the private or black market. Prices there have only increased with increased demand (now $25 a bottle) and one can never verify the quality of what they are purchasing.
Innovation Paused
HIV relief in South Africa has been severely undermined, not only because of cuts to services but also cuts to research efforts. Dr Venter explained that about 70 percent of research in Sub-Saharan Africa, including South Africa, was funded by the United States. The country’s sophisticated laboratory systems and scaled trials were dependent on US funding. When USAID shut down and NIH budgets were slashed, projects were stopped mid-study, proving devastating not only for the future of innovation but also for the patients already enrolled in trials.
For instance, CAPRISA (Centre for the AIDS Programme of Research in South Africa) was created through an NIH grant in 2002. While the organization has diversified its sources of revenue since then, it was still largely dependent on the US government, with US funding accounting for 51 percent of their budget.
Doctor Salim Abdool Karim, director of CAPRISA and a global health professor at Columbia University, stated, “When they made those cuts [to USAID], we just received an email, no warning, to stop all work. I mean literally, it was a stop work order, and it didn’t say stop work tomorrow; it was immediate.”
Karim, and many other researchers, were at the time investigating a novel vaginal intervention and had 17 women enrolled in the experimental trial, with one even planning to come in that very day they were let go. While they stopped using US money, they couldn’t shut down the study without a planned closure and safety assessments. As Karim explained, “We couldn’t accept an unethical request, an instruction that is devoid of its moral context. These are young black African women who volunteered and are participating in the study. We can’t just walk away.”
Research studies abruptly shutting down reflected the immediate and far-reaching nature of funding cuts. While CAPRISA had the capacity to continue its study until it could assure participant safety through its non-US sources of revenue, clinics throughout the country much more reliant on USAID funding were left with no alternative but to leave their work stranded.
Finding Alternatives
The status quo across the continent is one of uncertainty. It seems unlikely that governments themselves will be able to sustain current programs. Individual organizations are looking for alternative sources to continue running their services. As Karim told us for CAPRISA, “At the end of February, we decided to write new grant proposals. We wrote nearly 40 grants … it’s an existential problem for us if we lose half our money.”
Similarly, Rees thinks that Anova needs to pivot to new ways of working. PEPFAR enabled unique levels of NGO participation in the healthcare system, and despite the government trying to match funding or collaborate with the private sector, it seems unlikely that NGOs will be able to retain their previous role.
Beyond the decline of NGO-provided services, there’s also the upstream question of whether governments even have the capacity to replace the quality of care that came through the US. Across the continent, given the scale of funding that was provided by PEPFAR, many experts are not optimistic about the future of HIV relief.
When asked if African countries might be able to fill the funding gap through domestic financing or finding alternative sources, Dr Venter said, “The short answer is no … the amount of money is astronomical. People keep talking about the Gates Foundation. The Gates Foundation could throw its entire endowment at Kenya alone, and they’d spend it in a year.”
Specifically for South Africa, he explains that even if the government can supplement funding given a comparatively lower reliance on US funding, two issues persist. The first is one of efficiency. The PEPFAR model for early detection involved complex modelling to predict the number of people with HIV in a particular area, followed by testing efforts that would require workers to meet weekly testing targets. The vigilance of this process is not easy to replicate, especially if it is subsumed into government bureaucracy or even taken over by private companies.
Doctor Allyala Nandakumar, Senior Adviser at the State Department Global Health and Security Office explained that, “[PEPFAR] was one of the few programs I knew that collected a lot of data and used that to drive decisions. And it was really, really focused on outcomes, regardless of what it cost to get there.”
The second issue, beyond funding, is one of political capital. HIV disproportionately affects sex workers and drug users who are heavily stigmatized. Both groups are considered ‘criminals’ under South African law, making it incredibly unpopular for governments to launch services tailored to them. This is harmful, given that key population programmes are currently the most optimal way to target the spread of HIV.
Dr Nandkumar argues that when PEPFAR initially began, HIV relief was viewed as a public health response; therefore, what was most important was building up primary healthcare infrastructure. Today, however, HIV has transformed into a chronic health disease. If diagnosed quickly and started on treatment, anyone with HIV is perfectly capable of leading a long and healthy life. Therefore, for countries that have achieved or are close to achieving epidemic control, the only meaningful way to fight back against HIV is to run targeted programs for communities where infection rates tend to be the highest.
With limited resources, another key trade-off that the government will have to consider is one between prevention and treatment. Schutz thinks that while government priorities are inevitably subjective, HIV prevention is close to seeing significant breakthroughs. In particular, she highlighted how crucial the rollout of Lenacapavir could be for prevention: “It’s a twice-a-year injection which bypasses so many issues of access and social stigma – you don’t have to tell your partner, have pills in the house, or access it every month.” Its adoption, however, might be undermined by the reduced capacity that NGOs now have. Even if government healthcare systems can procure Lenacapavir, individuals historically excluded by traditional institutions will face significant challenges in its access.
The Way Forward
The cuts to funding have left many disillusioned about the future of international aid. Venter told us, “I came back from a recent HIV conference in Rwanda, and there were government figures giving talks and all of my American and European colleagues saying, ‘Yeah, Africans are so resilient. They’re so amazing. They’re already building systems to try and replace PEPFAR.’ That’s a complete bloody lie. They can’t magic out tablets. There’s no wise magic helping nurses when they’ve got absolutely nothing. It’s like this romanticized rubbish.”
There is, however, some reason to be optimistic. Nandakumar points out that the latest update to American global health policy released on September 18, 2025 (the America First Global Health Strategy) has guaranteed that, for at least another year and a half, PEPFAR will ensure the same level of funding for drugs and frontline workers. While this won’t sustain programmes targeted at key populations, it is an attempt to retain the most fundamental infrastructure of countries’ HIV response.
Regardless of the update, with organizations losing trust in international aid and in the US, both Murray and Rees affirm that there’s a greater push than ever on the South African government to be self-reliant in their HIV response. This push is substantiated further when one considers the reasons behind funding cuts in the first place. Nandakumar highlighted that scaling down PEPFAR wasn’t necessarily prompted by a concern over the program’s efficiency. Rather, they were borne out of fears that the United States wasn’t prioritizing its self-interest in the region and the politicization of USAID as a whole. This precarious nature of US funding encourages skepticism and a focus on domestic financing.
Going forward, countries have a critical decision to make. With South Africa’s health minister denying reports that their HIV programme has been hurt and failing to outline a plan to replace the 8,000 healthcare workers supported by the US, many are worried about the country falling back into patterns of denialism. The country needs to build the organizational structure that PEPFAR once provided, despite its substantial economic and political cost.
While programs get reimagined, millions will remain without access to services that once sustained their life, caught in the crossroads of broken promises and government inaction.