Critical South African-led HIV research, the outcome of which could affect millions of people worldwide, has been stopped in its tracks at a vital point, thanks to the abrupt withdrawal of financial support from the United States.
Lab technician Nozipho Mlotshwa was waiting in a Wits University lab for the test results for a potential HIV vaccine, which has eluded scientists for decades, when the order came from USAID to stop work.
The first round of vaccines she and her colleagues made in Johannesburg had produced an immune response in rabbits, which was promising but not conclusive, so they tweaked the formula and sent off four new versions for pre-clinical tests.
“This was exciting. We were getting good results,” Mlotshwa, told Reuters in the lab in the Antiviral Gene Therapy Research Unit at the University of the Witwatersrand.
Now the animal blood samples containing their results are sitting untouched in a freezer.
A trial of an earlier, separate vaccine candidate, which was about to be tested on humans in South Africa, Kenya and Uganda, is also on ice, reports TimesLIVE.
Both trials are among the casualties of President Donald Trump’s decision to dismantle the US Agency for International Development (USAID).
They are part of a wider South African-led HIV vaccine development scheme known as Brilliant, which is funded by a $45m grant from USAID. It is unclear if or when the project could resume.
“It feels as if you’re building something and you could really make a huge difference,” Nigel Garrett, chief scientific officer at the Desmond Tutu Health Foundation, a partner in the project, said. “And then it’s wiped away.”
The project is one of many research efforts worldwide to be hit by Trump's actions. Others include halting efforts to protect food crops from pests and diseases and blocking publication of a paper on the mpox outbreak.
HIV’s ability to mutate quickly has confounded efforts to create a vaccine since it was first identified in 1983.
The researchers in Johannesburg are using the mRNA technology that created some Covid-19 vaccines. Several other mRNA-based HIV vaccine candidates worldwide have reached clinical trials. Brilliant is unique in being Africa-led, aiming to develop capacity for producing vaccines in Africa.
For the past year the team had been working with genetic sequences from two South African patients who have HIV but whose bodies produce a rare type of antibody that neutralises the virus. They are trying to simulate that immune response.
“We were gaining momentum,” said Patrick Arbuthnot, director of the research unit, adding, “an HIV vaccine is the holy grail of the field.”
Garrett said the shot that was ready for testing on humans was a mix of two vaccine substances developed in the US and The Netherlands, which have shown promise but never been tested together.
They are now in storage.
“We had a huge opportunity, good funding. It’s difficult for other funders to fill that gap,” he said.
The US foreign aid freeze has affected programmes across the globe, stranding shipments of life-saving medical supplies, including HIV drugs, and leaving disaster response teams unable to deploy. Waivers for “life-saving humanitarian assistance” have been hampered.
Because South Africa has the world’s largest population of people living with HIV, more than 8m, it is a hub for research on the virus.
“Most of the landmark and ground-breaking studies have been conducted in this country, but these have been good for the whole world,” said Ntobeko Ntusi, CEO of the South African Medical Research Council, which is spearheading the HIV vaccine search.
Ntusi said he did not expect funding for projects such as Brilliant to resume, given the executive order on aid to South Africa. The council gets about a third of its funding from US federal sources, for research that is mostly on HIV and TB but covers other areas including maternal and infant mortality and antimicrobial resistance, he said.
“But the consequences will be catastrophic if funding is stopped… for science that is important for the whole world,” he added.
South Africa plays a critical role in advancing HIV science, Ntusi said. “Many of the major trials that have advanced our understanding of both the effective strategies for HIV management, as well as understanding the mechanisms of disease, emanated from South Africa.”
Spotlight reports that Americans, for example, are now able to access long-acting HIV prevention shots, largely because of research that was conducted in South Africa and Uganda. Research conducted in this country has also been critical to validating new tuberculosis treatments that are currently the standard of care worldwide.
The SAMRC’s research on infectious diseases, gender-based violence, health systems strengthening, as well as disease burden monitoring, are also affected by the funding cuts.
“In addition to support for HIV research, we have significant CDC grant funding in our burden of disease research unit, which publishes weekly statistics on morbidity and mortality in South Africa,” said Ntusi.
Along with programmes being hard-hit by the halting of USAID and CDC funding, Ntusi said there would also be major staffing ramifications at the SAMRC as well as at universities.
“There will be huge fallout… we just wouldn’t be able to cover the hundreds of staff employed through the NIH granting process.”
The SAMRC’s combined annual income from US grants (NIH, CDC and USAID) is 28% of its total earnings (including both the disbursement from the SA government as well as all external contracts) for the 2025/2026 financial year, according to Ntusi.
“So, this is substantial – effectively a third of our income is from US federal agencies,” he said.
Looking beyond health, Ntusi told Spotlight the executive order halting aid to South Africa would be felt across a range of different development initiatives, such as water and sanitation, and climate change.
‘Going to be tough’
Professor Salim Abdool-Karim, Director of the Centre for the Aids Programme Research in South Africa (CAPRISA), said the impact of the funding withdrawal was hugely significant, and affected all parts of society.
“The irony, of course, is that the research we’re working on in South Africa is actually aiming to produce benefits that will benefit the US as much as every other country.”
However, he told SABC News, this country had made significant strides in the treatment of HIV and Aids patients, and hoped to continue with certain clinical trials without the assistance of the United States, albeit this would be difficult to do without the additional funding.
“I think we can continue the Aids control programme and Aids treatment functions without the need for Pepfar, anyway, but what we will see is a programme that will now not have certain data … or some of the circumcision programmes or some of the condom programmes. We will see some of those disappearing, but the core of the Aids treatment programme, which treats around 6m people in South Africa, that will stay intact.”
In fact, offering state HIV patients – who qualify – a six-month supply of ARVs at a time is one of the Health Department’s plans to cope with the crisis.
This would mean HIV patients only have to return to clinics or community pick-up points twice annually to collect their medication, reducing workloads for health workers, according to a strategy sent to provincial health departments and facilities on 11 February.
Bhekisisa’s Mia Malan writes that the contingency plan circular says patients who qualify for a supply of six months of treatment at a time must have a suppressed viral load for “two consecutive periods”.
Viral load testing is usually done once a year if the treatment works well for them, so patients would need to have been on ARVs for at least two years to be considered for six-monthly supplies.
The plan also says only people who already get a three-month supply at a time can be considered for a six months’ supply – and that’s only if the clinic the person visits has enough stock of the entry-level three-in-one pill, TLD, to hand out.
Currently, the longest period for which government patients receive ARVs at once is three months, acting Deputy DG for HIV Ramphelane Morewane said.
Of the 5.8m South Africans on ARVs, 5.417m are state patients. Of these, 1.6m – or around 30% – get their medicine for three months at a time.
ARVs from community points
The Health Department’s plan also says clients older than six months should, during this crisis period, get an ARV supply of at least three months if they don’t have complications with their treatment.
All HIV-negative people who would like to use the daily anti-HIV pill should also get a three-month supply, along with HIV self-tests to ensure they’re still HIV negative before continuing with the treatment for another three months, but that’s mostly already been happening, said a department spokesperson.
Another “coping strategy” that the plan includes is allowing people who collect their treatment from community pick-up points – churches, mosques, private pharmacies or adherence clubs – a 28-day grace period to fetch it.
They could then still qualify for an automatic script renewal, without having to return to a health facility for a new script.
Around 2.7m ARV patients received their medication outside a health facility by the end of 2024, and the goal is to increase this to 3.2m by the end of March, but, said Morewane, the sudden withdrawal of Pepfar “could slow us down on this”.
“But it won’t cause a total disruption, because we don’t exclusively depend on Pepfar.”
Pepfar only pays for resources in about 27 of South Africa’s 52 health districts. In those 27 districts, the Health department has 271 606 staff working for its HIV programmes, of whom 15 154, or 5.6%, are funded through Pepfar (they are paid by non-profits); the department pays for the salaries of the remaining 94.4%.
Impact on PrEP
The effect of the freeze on preventive treatment – pre-exposure prophylaxis, or PrEP – or of waivers for individual projects that haven’t yet been approved, is likely to be worse, especially regarding getting daily anti-HIV pills to groups like teen girls and young women, sex workers, gay and bisexual men and transgender women, who all have a higher chance of contracting the virus.
It was with high-risk groups that Pepfar particularly assisted by helping to pay for mobile clinics or drop-in centres, catering for their specific needs.
The department’s goal is to get around 700 000 new HIV-negative people to use the anti-HIV pill at least once, a department spokesperson said. Pepfar, through the CDC and USAID, supported about 520 000 of these “initiations”.
Provincial Health Departments, however, pay for the medication, so although salaries of some of the staff who dispense the drugs were paid for by Pepfar, it doesn’t mean the medicine won’t be unavailable – just harder to get, because queues will be longer as there will be fewer health workers to help people.
Research sites
South Africa has 16 research sites testing the best ways to roll out different forms of PrEP, which includes the pill, the monthly vaginal ring, and the two-monthly injection cabotegravir.
Six of those sites – two in Johannesburg and four in Lejweleputswa in the Free State – which are part of a study called Catalyst, were funded by Pepfar via USAID.
Those sites, a department spokesperson confirmed, have closed down.
The two Johannesburg clinics, a sex worker and transgender clinic, have physically closed; the Free State sites were run from government facilities, so those facilities, but not the studies, continue to run, and trial participants who chose the ring and injection are now being offered the pill.
Francois Venter, an HIV researcher who heads up the organisation Ezintsha at Wits University, and which doesn’t receive Pepfar funding, said: “Stopping such studies so abruptly is unethical, a huge waste of time and resources, and a violation of trust. It’s extremely complicated – and expensive – to restart them.”
Waiver chaos
Devex reports that even in cases in countries where waivers have been approved, the Trump administration hasn’t made the funds for those activities available (the online payment system was disabled or the remaining USAID staff had been locked out of their emails, leaving them unable to respond to questions of organisations whose grants they managed).
In the meantime, a court ruling late last week instructed Trump’s administration to temporarily unfreeze all foreign assistance funding, including Pepfar funds.
That judgment effectively cancelled the waivers and allowed for projects to revert to their original grants.
But in practise, it means very little, at least for now.
“The finding itself does not restart foreign assistance,” said Mitchell Warren, who heads up the New York-based advocacy organisation, Avac, one of the organisations that brought the case against the Trump administration.
“Sadly, these programmes don’t have on-off switches, and even if they did, the legal order telling the government to turn the switch back on does not yet come with formal approval from USAID to begin work again.”
Meanwhile, Pepfar projects funded through the CDC restarted last week after a federal judge enforced a temporary restraining order blocking Trump’s administration from freezing federal grants.
In South Africa, those projects have been able to access their funds and have sent dismissed employees letters, asking them to return to work.
But even in these cases, the transition has been anything but seamless.
“A major challenge has been the absence of clear leadership, not just from the national Health department, but also from Pepfar,” said a manager at one organisation, who spoke to Bhekisisa on condition of anonymity.
“Instead of a structured, co-ordinated approach, implementation partners have been left to navigate an uncertain landscape with little direction, forced to answer difficult questions from provincial health officials; questions that, in many cases, simply have no clear answers.”
The organisation Right to Care, which has been allowed to restart its voluntary medical male circumcision programme (VMMC) in all 27 Pepfar-supported districts, distributed a guidance document to its workers and provincial health departments on how to behave.
Throughout, it warns workers to keep a low profile – and to effectively self-sensor.
Spotlight article – SA health research facing catastrophic financing cuts (Creative Commons Licence)
SABC News article – Withdrawal of USAID already impacting HIV research: Abdool-Karim (Open access)
Bhekisisa article – How the health department will deal with Pepfar’s near collapse
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