Inside the Pepfar waiver letters: What’s in and out

Pepfar-funded projects in South Africa have received waiver letters in which they’ve been asked to review which of their activities fall within the scope of the Trump administration’s rules for projects that can temporarily restart until the US government has decided if it will continue to fund them.  

But the national health department, which receives Pepfar funding that makes up 17% of the department’s HIV budget, has not received a waiver letter, says spokesperson Foster Mohale. “We are, however, aware of the communication on the waiver which was received by their partners,” he says. 

Pepfar, the US President’s Emergency Plan for Aids, was launched in 2003 to help fight Aids in countries with high HIV infection rates such as South Africa. The country has since received about $8bn, of which $439,537,828 was for the current US financial year, which stretches from October 1 2024 to September 30 2025.

But the new Trump administration froze funding globally for all US-funded aid projects on January 24. It then announced a limited waiver for some projects on February 1. On February 7, however, President Donald Trump signed an executive order that cancelled all funding from his government for South Africa for what he labels as “unjust and immoral practices” of South Africa that “harm our nation [the US]”. 

But on Monday, the US embassy and consulate in South Africa announced that Pepfar-funded projects could still apply for waivers. 

What can — and can’t — projects do? 

Approved activities have to directly relate to “the delivery of lifesaving HIV care and treatment services”, which, according to the Trump administration, don’t include HIV prevention services, unless they are for pregnant or breastfeeding women. 

Programmes that were therefore funded to hand out anti-HIV medication such as the daily HIV prevention pill, or Pepfar-supported implementation studies such as the Catalyst trial, which looks at the best ways to roll out the pill, a monthly preventive vaginal ring or a two-monthly anti-HIV injection, have therefore had to stop. The Catalyst study, which had six sites in South Africa — two in Joburg and four in the Free State — was run by the Wits Reproductive Health Institute.  

According to a health department spokesperson, Pepfar was going to fund the rollout of 520,123 anti-HIV pill “initiations” (people starting on the pill) this year — though the government paid for the pills, Pepfar funded the salaries of health workers, employed by NGOs, who administered the tablets from within state or mobile clinics. The fund also helped to cover the cost of data collectors and outreach campaigns to raise awareness of the medication. 

Anti-HIV medication can dramatically reduce someone’s chances of contracting HIV through sex and therefore helps to slow down the spread of new infections. Almost 40% of the world’s HIV prevention pill users live in South Africa. 

No-one knows what happens after the waivers 

Projects with Pepfar funds channelled through the Centers for Disease Control & Prevention (CDC) have been told to submit work plans and adjusted budgets up to April 19 and those that are funded through the US Agency for International Aid (USAID) were instructed to submit a plan and budget for 30 days. 

Bhekisisa has seen the waiver letters of organisations funded through both agencies.

The letters make clear that no project can restart work until their USAID or CDC project officer has reviewed and approved their new work plans and budgets in writing. 

“But the reality check is that I don’t think any of the organisations can actually restart, whatever the instruction is, until they receive the funds in the bank,” one of the founders of an affected organisation, who doesn’t want to be named out of fear of losing funds, tells Bhekisisa. “Everyone has exhausted their reserves.” 

What happens once the waivers have expired is unclear; projects only know that the US government would have decided their fate by the end of April.  

In order to financially survive, many organisations have closed down facilities or temporarily laid off staff. 

No equity, no ‘gender ideology’

In addition to work plans and adjusted budgets, organisations have to provide monthly written confirmation, on an official letterhead, that they will only continue with activities that qualify for the waiver and not roll out any “related to abortion services, family planning, conferences, administrative costs outside the scope of the limited waiver, gender ideology or diversity, equity and inclusion programmes [DEI], transgender surgeries or other forms of nonlifesaving assistance”. 

Some projects which, for instance, run transgender HIV treatment clinics, or projects for gay and bisexual men, are confused as to whether they qualify for the waiver — even though the waiver guidelines say treatment at “mobile clinics or drop-in centres for provision of services to persons at high risk for or living with HIV” is covered. “The confusion arises because DEI is not defined in any executive order, and there are vague terms like ‘gender ideology’. We have no real confirmation of that until someone actually gives approval,” one project leader says. 

Waiver letters also specify that funds that would have been used for activities that are now not allowed can’t be used for approved activities; that money belongs to the US government. 

Organisations are, however, allowed to submit incurred costs before January 24 (the date on which Trump froze foreign aid), as well as “incurred costs associated with the stop-work order”. 

Costs linked to “suspension of activities and stoppage of work” to comply with local labour laws or “existing contractual obligations that cannot be legally paused” as well as payments “associated with the security of assets” can also be claimed. 

HIV testing rules 

Frequently asked questions (FAQs) about the waiver, issued on February 10, explain that Pepfar will only fund HIV testing for pregnant and breastfeeding women and their babies, and to find out if someone needs treatment. No HIV testing that is done before someone gets medically circumcised (medical circumcision reduces an HIV-negative man’s chances of contracting HIV) or testing to establish if someone is HIV negative before putting them on preventive anti-HIV medication, is allowed. 

Social and behavioural change communication activities, such as treatment literacy and adherence campaigns, are also not covered by the waiver.

The FAQs document also says Pepfar officials may, at this stage, only discuss “high-level talking points” to be provided by the department of state, with civil society organisations, and that “talking points and press guidance are under development”. 

To the court

Meanwhile, New York-based HIV advocacy organisation Avac, along with the Journalism Development Network, filed a lawsuit against the Trump administration on Monday, arguing that it froze foreign funding “illegally and unconscionably”.

Avac receives Pepfar funding via USAID and runs HIV projects in East and Southern Africa. 

“We don’t expect to see our funding renewed any time soon, if ever,” executive director Mitchell Warren tells Bhekisisa. “But we filed the case to make the point that the actions of this new administration defy logic, defy science and actually defy the US legal system. 

“We know that foreign assistance is going to change. We know that Pepfar is going to change. We know that all programmes should be reviewed and re-evaluated, but they need to be done with clarity, with a strategy and clear metrics.” 

Warren concludes: “What we’re trying to do is to get the freeze on foreign assistance stopped, and then let’s all talk together, implementers, governments, the US administration, about what the future can look like, not only for Pepfar and the Aids response, but for global health and development.

“There is much riding on this; it can’t be dictated by executive orders.”

This story was produced by the Bhekisisa Centre for Health Journalism. Sign up for the newsletter.