The Shock of US Funding Cuts

South Africa's medical research landscape, long a global leader in HIV and tuberculosis studies, faced a seismic shift starting in early 2025. The Trump administration's executive orders froze international aid, targeting South Africa over policy disagreements including its Expropriation Act and stance on international issues. This led to a cascade of cuts from key US agencies like the National Institutes of Health (NIH), President's Emergency Plan for AIDS Relief (PEPFAR), Centers for Disease Control and Prevention (CDC), and USAID. Universities, which host much of the nation's clinical research, bore the brunt as sub-awards— the primary mechanism for funding—were halted or not renewed.

NIH data reveals the scale: South African groups received US$44 million across 102 grants in 2024, dropping to US$34 million over 73 grants in 2025, and just US$5.9 million across seven grants by April 2026. For the South African Medical Research Council (SAMRC), US sources accounted for 28% of its roughly R2 billion annual budget, amplifying the crisis across affiliated university programs.

Universities on the Frontline

Higher education institutions in South Africa, particularly research-intensive ones, saw immediate disruptions. The University of Cape Town (UCT) reported potential losses of R172 million across 22 projects, including TB treatment trials in Khayelitsha where experimental regimens for 52 participants were abruptly stopped, forcing transitions to standard care. At the University of the Witwatersrand (Wits), the Perinatal HIV Research Unit grappled with gaps in mother-to-infant transmission studies. Stellenbosch University's Centre for Tuberculosis Research Innovation faced shortfalls in aerosol transmission modeling, while the University of KwaZulu-Natal's (UKZN) Centre for the AIDS Programme of Research in KwaZulu-Natal (CAPRISA) risked halting Phase III trial follow-ups.

At least 35 programs across 11 universities were hit early, threatening jobs for over 110 staff at SAMRC sites alone, postgraduate training for PhD students and postdocs, and critical infrastructure like biobanks and cohort studies. Early-career researchers, many on their first NIH awards, faced career derailment, with universities dipping into reserves to retain talent.

SAMRC's Swift Mobilization

The South African Medical Research Council (SAMRC), a statutory body under the National Health Act promoting health research, responded decisively. In August 2025, it announced a R600 million rescue package titled "Support for the South African National Health Research Enterprise in Response to USA Funding Withdrawals." Funding sources included R400 million from National Treasury, R100 million each from the Bill & Melinda Gates Foundation and Wellcome Trust, and R14.4 million from the ELMA Foundation.

Two Requests for Applications (RFAs) were launched in July and December 2025, attracting 102 submissions from public universities and research entities. Twenty-eight were withdrawn after partial US restorations, leaving 74 for review. Ultimately, 59 projects were approved, prioritizing project costs (e.g., participant care, lab supplies) while institutions matched for staff salaries.

Breakdown of Rescue Allocations

By the 2025/2026 financial year, R115 million had been disbursed, with R485 million remaining over two years. Allocation by focus: tuberculosis (40%), HIV (29%), newborn and child health (12%), non-communicable diseases (9%), and other infectious diseases (10%). This preserved 39 TB and HIV clinical sites, 27 HIV trials, and 20 TB trials.

• TB research: Sustained aerosol modeling at Stellenbosch and site operations nationwide.
• HIV: Bridged genomic analysis at UCT's Desmond Tutu HIV Centre and perinatal studies at Wits.
• Child health: Protected vulnerable cohort follow-ups at UKZN.

Universities like UCT, Wits, Stellenbosch, and UKZN received support, enabling PhD completions and postdoc continuity. No major trials were abandoned, averting ethical dilemmas in patient care transitions.

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Preserving Talent and Infrastructure

Beyond immediate survival, the grants safeguarded human capital. Postgraduate traineeships for PhDs and postdocs were prioritized, preventing a brain drain among emerging clinician-scientists. At Stellenbosch, postdocs credited SAMRC for enabling thesis defenses; UKZN students emphasized sustained pathways for clinician-researchers.

Infrastructure like biobanks and data platforms was maintained, crucial for future studies. Universities supplemented with internal funds, but SAMRC's intervention prevented mass layoffs and project collapses, preserving South Africa's reputation as a research hub.

Challenges Amid Recovery

Recovery wasn't seamless. Chaotic US implementation—pauses, terminations, partial restorations—created uncertainty, with some grants reinstated mid-RFA. Ethical concerns arose in winding down trials, ensuring participant care without experimental drugs. Staff positions required university matching, straining budgets already hit by national austerity.

Professor Ntobeko Ntusi, SAMRC President, called the cuts "catastrophic," highlighting risks to decades-built capacity. Dr. Michelle Mulder, SAMRC's grants director, stressed preserving "infrastructure, people, projects, and platforms." UCT's Deputy Vice-Chancellor warned of long-term erosion.

Implications for South African Higher Education

These cuts exposed overreliance on foreign funding in South African universities' medical faculties. Research-intensive institutions like UCT, Wits, and Stellenbosch, which host SAMRC extramural units, faced shortfalls threatening core missions. Student training suffered, with clinician-scientist pipelines at risk, potentially widening skills gaps in public health.

However, the crisis spurred diversification. Universities pursued EU partnerships (e.g., EDCTP), Korean collaborations, and private philanthropy. National Treasury's R400 million match signals government commitment, though experts urge doubling SAMRC's budget to R4 billion annually.

Towards Sustainable Research Independence

SAMRC envisions a flagship grant program as a legacy of the crisis, fostering self-reliance. Calls grow for increased domestic investment, leveraging SA's clean audits and global impact—e.g., contributions to HIV vaccines and TB diagnostics. Universities advocate diversified portfolios, blending local, philanthropic, and international sources.

Stakeholders like USAf emphasize lobbying for sustained funding. With R485 million left, the focus shifts to long-term resilience, positioning SA universities as independent leaders in global health research.

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Stakeholder Perspectives and Lessons Learned

University leaders praise SAMRC's agility but warn of fragility. Wits researchers note bridged gaps allowed new grant pursuits; UKZN students push for permanent local funding. Lessons: Ethical trial management, rapid contingency planning, and diversified funding are vital.

The episode underscores universities' role in national health security, urging policy reforms for stable research ecosystems.