Understanding the US Funding Cuts and Their Origins

South Africa's research ecosystem, particularly in health sciences, has long been a global leader, thanks in large part to substantial investments from the United States. Institutions like the University of the Witwatersrand (Wits), University of Cape Town (UCT), and Stellenbosch University have pioneered breakthroughs in HIV prevention, tuberculosis diagnostics, and vaccine development. However, starting in early 2025, policies from the Trump administration dramatically altered this landscape. A 90-day freeze on international aid in January 2025 halted funding for projects classified as aid, followed by targeted cuts to South Africa in February, citing local policies and disinformation campaigns. By May 2025, the National Institutes of Health (NIH) prohibited foreign sub-awardees, including South African partners, from new or renewing grants, forcing independent applications—a process fraught with barriers.

These moves dismantled collaborative networks built over decades. Direct NIH grants to South Africa dropped from US$44 million across 102 awards in 2024 to US$34 million across 73 in 2025, and just US$5.9 million across seven as of April 2026. Broader impacts from PEPFAR (President's Emergency Plan for AIDS Relief) and USAID compounded the crisis, with estimates of R1.85 billion lost at Wits alone and over R437 million at UCT in the first year. The chaos peaked with labs shuttering, trials pausing, and thousands of jobs—clinic staff, data analysts, counselors—at risk across universities.

The Ripple Effects on South African Universities

Universities bore the brunt, as US funding supported core infrastructure: labs equipped for clinical trials, data platforms for epidemiology, and skilled personnel driving innovation. At Wits, the Desmond Tutu HIV Centre saw projects grind to a halt, threatening 27 HIV trials and 20 TB studies nationwide. UCT reported a projected R1.67 billion shortfall over 2025-2027, forcing reallocations from teaching to salvage research. Stellenbosch's research units, pivotal in lenacaprivir (injectable PrEP) trials, faced similar fates, with community testing and linkage to care programs collapsing.

Job losses rippled through higher education: peer educators, lab technicians, and postdocs were let go, eroding talent pipelines. Data backlogs emerged, blinding policymakers to HIV incidence trends among adolescent girls and sex workers—key populations where SA excels in targeted interventions. Non-HIV work suffered too; newborn health studies and non-communicable disease platforms faltered, straining university clinics already overburdened.

The economic toll is stark: billions wasted globally on built infrastructure, per Physicians for Human Rights (PHR), as US firms lose trial data benefiting drug development. In SA, universities scrambled, raising internal funds to retain staff while projects teetered.

Trump Administration Policies: A Triple Blow Explained

Executive Order 14204 in February 2025 banned aid to South Africa over unverified claims, collapsing diplomatic channels for health MOUs. The 'America First Global Health Strategy' prioritized US interests, sidelining equitable partnerships. NIH's sub-award ban, despite a June 2025 carve-out for ongoing trials, created uncertainty—applications withdrawn or rejected amid flux. PEPFAR dismantling hit 17% of SA's HIV response directly, but ecosystem-wide effects amplified damage.

Step-by-step, the process unfolded: aid freeze (Jan), targeted halt (Feb), policy shift (May), partial relief (June), yet overall flows plummeted. Universities navigated this by lobbying for direct grants, but low success rates persist. Cultural context: SA's high disease burden made it ideal for trials, yielding global goods like Xpert MTB/RIF TB test—now jeopardized.

SAMRC's Swift Rescue: R600 Million Lifeline Deployed

Enter the South African Medical Research Council (SAMRC), statutory body under the National Health Act. In August 2025, SAMRC announced 'Support for the South African National Health Research Enterprise in Response to USA Funding Withdrawals'—R600 million over three years. Sourced from National Treasury (R400m), Gates Foundation (R100m), Wellcome Trust (R100m), and ELMA (R14.4m), funds targeted continuity: sustaining projects, staff, ethical wind-downs.

Two calls for applications (July/December 2025) yielded 102 submissions; 28 withdrawn post-reinstatement, 59 of 74 eligible approved (15 rejected, mostly unstarted multi-year). R115 million disbursed in 2025/26, remainder phased. Allocation: TB (40%), HIV (29%), child health (12%), NCDs (9%), others (10%). Universities supplemented with own funds, preserving ecosystems.

Specific Projects and Universities Saved by Rescue Grants

While recipients aren't fully public, patterns emerge: Wits HIV foundational research, UCT's pediatric diagnostics, Stellenbosch TB platforms gained bridge funding. Emthonjeni Counseling halted STI testing but pivoted partially. A UCT-led newborn health study continued, averting data loss. Wits' genomics for drug resistance persisted, vital for global pipelines.

Case study: Desmond Tutu Centre at Stellenbosch bridged injectable PrEP trials, retaining counselors for key populations. UCT's Desmond Tutu HIV Foundation sustained community linkage, preventing incidence spikes. These saved not just projects but university reputations as trial hubs, with 39 sites nationwide stabilized.

Stakeholder Perspectives: Voices from the Frontlines

Prof. Ntobeko Ntusi, SAMRC President: "Catastrophic if unchecked—28% of our budget from US sources." Dr. Michelle Mulder, SAMRC: "We've built infrastructure over years; can't let it collapse." Candice Roux: "Uncertainty drove dual calls; we adapted in chaos."

University leaders: Wits VC decried R1.85b loss as 'setback with global implications'; UCT navigated R437m hit via pivots. PHR warns of wasted billions, looming HIV surges. Optimism tempers: direct NIH apps rising, though slow.

Challenges Persist: Uncertainty and Long-Term Risks

Rescue is bridge, not cure. Multi-year projects rejected if unstarted; data lags hinder incidence tracking. Staff retention strains university budgets amid SA's fiscal woes. Broader risks: brain drain, trial site closures erode SA's edge—second only to US in NIH grants pre-cuts.

Regional context: High HIV/TB burden demands sustained research; cuts risk resurgence, overburdening public health.

Solutions and Path Forward: Building Resilience

SAMRC's flagship programme looms—legacy sustaining capacity. Universities diversify: EU, UK, China partnerships; domestic levies eyed. Direct NIH strategy: independent apps yielding early wins. Policy advocacy: transparent MOUs, equity safeguards.

Actionable insights: Unis bolster internal grants; researchers pivot to African-led trials; gov ring-fence health R&D.

Implications for South African Higher Education

Beyond health, cuts signal vulnerability. Unis rethink dependencies, invest in sovereignty: NRF chairs expand (41 new for HDIs). Student impacts: fewer postdocs mean talent gaps. Positively, crisis spurs innovation—SAMRC model replicable.

Global Lessons and Future Outlook

SA's resilience shines: R600m mobilized swiftly, projects saved. Yet, Trump policies waste billions, per PHR—US loses trial data too. Outlook: Stabilizing 2026, with SAMRC flagship ensuring legacy. Unis emerge stronger, diversified, African-led.

For researchers: Explore SAMRC calls, diversify funders. Higher ed: Prioritize sustainability amid geopolitics.

Photo by Francesco Ungaro on Unsplash