[KAMPALA] Malaria vaccination and HIV treatment are among numerous health programmes at risk in Uganda as the country’s science research centres suffer the impact of a US freeze on overseas aid.

Makerere University, one of Uganda’s leading research institutions, has laid off 200 staff members and suspended multiple research programmes, according to the vice-chancellor, while more than 2,000 health workers have reported losing their jobs.

The disruption threatens to unravel decades of scientific progress in East Africa, health leaders warn.

The US government abruptly halted almost all foreign assistance delivered through USAID and the State Department last month, pending a 90-day review to ensure aid programmes align to its “America First” agenda.

USAID delivered an annual budget of US$950 million to Uganda, according to figures on its website, which has now been taken offline.

The funding freeze has led to widespread programme closures across Makarere University, including the School of Public Health, College of Health Sciences, and Infectious Diseases Institute.

The university’s vice-chancellor, Barnabas Nawangwe, said the suspension had paralysed numerous research and health initiatives.

“The Trump order is very serious for Makerere because we get a lot of financial support from institutions of the US government,” Nawangwe said in a briefing last week (3 February).

“The order is affecting a lot of our activities, especially related to health.”

Nawangwe said the Infectious Diseases Institute supports 20 per cent of all the patients in Uganda who need antiretroviral therapy (ART), a treatment for HIV. Stopping its activities threatens critical treatment programmes for thousands of patients.

“The information I have received from the units that are affected is that they had to suspend some activities and to halt some staff for the 90 days,” said Nawangwe, who also said 200 employees on USAID-funded contracts had been laid off.

A US directive issued last week stated that all USAID direct-hire personnel would be placed on administrative leave from Friday night (8 February), except those on “mission-critical functions, core leadership and specially designated programs”.

The agency will arrange return travel to the United States within 30 days for personnel posted overseas and terminate contracts not deemed essential.

The impact of closures at Makerere University extends throughout Uganda’s healthcare system.

Robert Kalyesubula, a senior lecturer, nephrologist and head of the physiology department at Makerere University, told SciDev.Net that crucial immunization programmes may be at risk.

Of particular concern, he says, is the planned malaria vaccination programme.

“The 3 million doses we are going to start within the malaria vaccination in April this year were donated by USAID,” said Kalyesubula.

“Will the Ugandan government be able to carry on with this?”

He said the vaccine was due to be introduced into the national immunisation schedule and ending the programme would mean “1.5 million children born every year are not safe”.

Programmes such as the Uganda National Expanded Program on Immunisation are heavily dependent on US funding. US support has helped reduce malaria prevalence in children under five by more than 75 per cent, according to official figures.

Kalyesubula warns that diseases long controlled could resurface as a result of the funding freeze. He says the impact also extends to education programmes, affecting scholarships and capacity building for Ugandan experts.

Simon Peter Singo, medical director at Mengo Hospital, a teaching hospital in Kampala, warns of an impending health crisis, particularly in HIV/AIDS treatment and prevention.

“The donor money has been used to pay salaries of the HIV staff team [at Mengo Hospital] where 50 have been employed to run the programmes,” Singo said.

At Mukono Church of Uganda Hospital, more than 60 health workers have been laid off.

Joyce Nannozi, the hospital’s medical superintendent, told SciDev.Net: “We can no longer give HIV/ART services to patients promptly because we are not in position to take on the dropped staff.”

Kyomukama Flavia, executive director of the National Forum of People Living with HIV Networks Uganda, says the suspension has caused turmoil.

“The past two weeks have been incredibly difficult,” Flavia said at a civil society event last week (3 February), in Kampala.

“Cutting off this support is essentially a death sentence for the 1.3 million people currently on antiretroviral treatment.”

USAID support in Uganda has been substantial. In 2024, the US provided more than US$471 million in health and development assistance, including programmes for HIV/AIDS, malaria, and tuberculosis, plus nearly US$182 million in humanitarian assistance, according to the US Bureau of African Affairs.

A USAID report for Uganda says US support has also helped improve literacy rates for five million Ugandan children.

The funding pause comes at a critical time for Uganda’s health sector, which relies heavily on external support, especially from USAID and the President’s Emergency Plan For AIDS Relief (PEPFAR).

Herbert Luswata, president of Uganda Medical Association, told SciDev.Net that USAID had been injecting millions of dollars into the country. He believes the 90-day freeze has profound consequences for all those directly and indirectly benefiting from aid programmes.

“As we speak now, over 2,000 health workers have notified us about their loss of jobs,” he said.

Luswata warns that unless the Ugandan government reconsiders its budget allocations, hard-fought gains, in areas such as child mortality and HIV, will be lost. He cites as examples the resuscitation of nearly 10,000 newborns in US-supported facilities and nearly 1.4 million Ugandans who receive lifesaving antiretrovirals through PEPFAR.

“Unfortunately, what we see online creates fear whether if even after 90 days, it will re-instated,” he added.

This piece was produced by SciDev.Net’s Sub-Saharan Africa English desk.