Almost 136 000 babies are expected to be born with HIV in the next three months, mostly in Africa, because of the Trump administration’s “stop work order” on foreign assistance, according to a top research foundation.

The Andelson Office of Public Policy said children in South Africa, Mozambique and Uganda will be the most affected, and it could lead to a rise in new infections of a disease that already kills more than half a million people a year.

Trump’s directive, part of a broader freeze on foreign aid initiated last week, means organizations could have to stop disbursing HIV drugs bought with US funds from the President’s Emergency Plan for Aids Relief, known as PEPFAR.

Secretary of State Marco Rubio late Tuesday approved some waivers for “lifesaving” emergency aid, but it’s not clear yet what that entails and if PEPFAR is exempt, leaving health workers scrambling to figure out if they can reopen clinics that support the 20-million people that rely on the program.

PEPFAR provides treatment to almost 680 000 pregnant women living with HIV, in order to reduce the rate of transmission of the disease during birth. Babies infected at birth face a higher risk of death as well as a future involving lifelong treatment with anti-retroviral drugs. Without such treatment, the disease is generally fatal.

In poorer countries, PEPFAR-supported health-care workers are often the only staff who can dispense HIV medications, according to the Andelson Office of Public Policy, which is part of amfAR, the Foundation for Aids Research.

“Most smaller primary health centers will only have a single pharmacist, meaning that even if there are other staff providing clinical services, they have no legal mechanism to dispense medications during the stoppage,” the foundation said. “Likewise, the suspension of laboratory services will have systematic impacts on the entire HIV response in a country.”

While babies are among the most affected, there are 222 333 people globally taking antiretrovirals every day, and “critically, getting people back onto treatment after the stop work order is lifted will take enormous effort,” it added.

The World Health Organization expressed “deep concern” over the impact the funding pause will have on HIV programs in low-and-middle income countries.

The halt “if prolonged, could lead to rises in new infections and deaths, reversing decades of progress and potentially taking the world back to the 1980s and 1990s when millions died of HIV every year globally,” including in the US, the global agency said.

US President Donald Trump ordered a wide review of foreign aid programs on his first day in office and announced his intention to exit the World Health Organization. The US is the world’s largest donor of foreign aid and spent about $68-billion on overseas assistance in 2023. The waivers Rubio approved included for emergency food aid and some salaries.