What the end of PEPFAR funding could mean for South Africa’s HIV response
Last month, the U.S. State Department announced plans to phase out South Africa’s support from PEPFAR (the U.S. President’s Emergency Plan for AIDS Relief), the landmark HIV/AIDS initiative credited with saving an estimated 26 million lives in more than 50 countries since its launch in 2003. In South Africa—which has the world’s largest HIV epidemic—most PEPFAR-funded programs are scheduled to end by Sept. 30, with support for critical personnel continuing through March 31, 2027.
Roger Shapiro, professor of immunology and infectious diseases at Harvard T.H. Chan School of Public Health, has worked on HIV/AIDS prevention and treatment in Botswana for more than 25 years. He recently discussed what the end of PEPFAR funding in South Africa could mean for the country’s HIV response.
Q: South Africa’s PEPFAR funding had already been significantly reduced as a result of the Trump administration’s 2025 foreign aid cuts. What has been the impact?
A: PEPFAR supported about 17% of South Africa’s HIV program, excluding antiretroviral purchases. If this moves from the category of temporary disruption to long-term structural loss, there will be aspects of the program that will be very hard hit.
HIV testing and PrEP [medication to prevent HIV infection] services appear to have been already hit hard by cuts, especially community-based prevention services. Specialized HIV clinics serving key populations, including sex workers and other marginalized groups, were also heavily affected: 12 such clinics closed, and more than 60,000 patients who had been receiving care through those clinics have needed to be registered at state health facilities. This shift risks pushing vulnerable patients into already stretched public clinics where stigma, long waits, and weaker follow-up may reduce access and retention in care.
Q: What do you predict will be the impact of the loss of remaining PEPFAR support through the formal phased drawdown of aid?
A: The South African government announced a $45 million emergency fund last year, but the annual losses after aid ceases will be closer to $400 million. Maintaining the treatment program will certainly be prioritized, as it should, but there will likely be gaps in diagnostics, prevention, and targeted outreach to the highest-risk populations.
A sudden nationwide antiretroviral stockout [facilities running out of medication] is not the most likely scenario. The bigger risk is a deterioration in the HIV care cascade: fewer tests, later diagnosis, fewer people starting treatment, more missed viral load monitoring, less re-engagement after default, and weaker PrEP uptake.
Q: Two years ago, you were cautiously optimistic about the anti-HIV drug lenacapavir. How will PEPFAR’s shutdown impact people’s ability to access the drug in South Africa?
A: Lenacapavir is still a major opportunity, but the loss of PEPFAR makes it harder to roll out. South Africa formally launched lenacapavir for PrEP in June 2026, and the first phase stocks it free at about 360 public clinics in six provinces. That is promising, but lenacapavir delivery requires demand creation, HIV testing before initiation, counseling, follow-up every six months, adverse-event systems, and targeting to people at highest risk. Those are exactly the functions damaged by the PEPFAR and USAID cuts.
Q: How quickly could the funding drawdown translate into increased HIV infections or AIDS-related deaths?
A: If it isn’t addressed, this loss of funding will lead to a gradual reversal of the gains that have been made over years, and an uptick in HIV-related deaths. It is hard to predict the future, but there is modeling that suggests over a million additional infections could occur over the next 20 years if funding is not restored, because of declines in testing, PrEP, linkage to care, retention in care, and viral load monitoring. In the shorter term, the South African government’s own modeling projects 56,000–65,000 additional AIDS-related deaths in the country between 2025–2028 under a “no-replacement” scenario. But I hope we see a different scenario, where replacement funding and new long-acting treatment and PrEP options help maintain the progress that has been made in the past two decades.
Q: What broader impact do you expect to see on South Africa’s health system following the drawdown?
A: The broader impact is likely to be a less resilient, more congested, less data-driven system of HIV treatment and prevention. In addition, HIV research programs will suffer. Without PEPFAR, there will be far less ability to monitor the implementation of HIV services across the country, and to coordinate the response. To make matters worse, South Africa is facing major challenges receiving NIH [U.S. National Institutes of Health] funding at the moment, threatening many core trials and programs working to control and ultimately end HIV.
Q: What is the current status of your own work on pediatric HIV/AIDS in Botswana?
A: Our pediatric HIV cure program in Botswana is doing really well, and we have presented exciting scientific results this year. Some very generous donations kept us going during the difficult months in 2025 when Harvard lost all NIH grant funding [which was restored later that fall], and because of this, our clinical trial was not interrupted. This allowed us to show that specialized antibodies directed at HIV, called broadly neutralizing antibodies, could maintain viral suppression in almost all children, even when we stopped their standard antiretroviral treatment. The next phase of the study is testing whether these antibodies can lead to true HIV remission, where some children remain without detectable virus off all treatment.
