USAID exit exposes fragility of Africa's donor-funded health systems

For decades, the running of critical health programmes in Kenya and across Africa has heavily relied on donor funding.

From HIV, Tuberculosis (TB), malaria, maternal health, immunisation, disease surveillance and pandemic preparedness, billions of dollars from donors have sustained health systems that governments have struggled to finance independently.

But recent cuts in external financing, particularly the exit of USAID after stop-work orders signed by US President Donald Trump have exposed deep cracks in the continent’s health systems.

This has revealed long-standing gaps in domestic ownership, financing, sustainability and accountability.

This reality dominated discussions at the just concluded World Health Summit Regional Meeting 2026 in Nairobi, where health experts, policymakers, and development partners called on African governments to urgently take responsibility for financing their own health systems.

Experts warn that Africa’s continued dependence on foreign aid has left the continent vulnerable to shifting donor priorities and global political decisions, often disrupting critical health services whenever external funding is reduced or withdrawn.

The International President of the World Health Summit regional Meeting 2026, Prof Lukoye Atwoli observes that health systems in Africa where designed in favour of the donor.

Prof Lukoye says that the era of depending on a donor, with donor driven system is long gone.

“Health systems in the continent were designed with the idea that people are poor and cannot afford high quality care. It was poor medicine for poor people,” he says.

“The central outcome of the Summit was a strong push toward health sovereignty across the continent, emphasising the need for African countries to expand local manufacturing of health products, increase domestic health financing, build resilient systems capable of responding to shocks, and ensure that policies and legislation are driven by local priorities rather than external dependencies,” he adds.

AFIDEP Executive Director and Malawi representative Eliya Msiyaphazi Zulu, emphasises the need for Africa to build resilient health systems that respond to the needs of its people, guided by evidence.

Dr Zulu says it is the responsibility of African leaders to ensure their populations remain healthy and productive.

He points out that human capital is critical in transforming the continent, underscoring why investment in health must remain a priority.

Donor support since 1970s, has had significant focus on primary healthcare, with deliberate efforts to bring services closer to communities.

However, over time, development partners and other players entering the health sector increasingly financed programmes aligned to their own interests, with greater focus on infectious diseases.

This shift, according to Zulu, gradually weakened efforts to build integrated and sustainable health systems capable of addressing the continent’s broader health needs.

The move is not meant to benefit Africa, but prevent a spill of diseases and pandemics to their countries.

Concentration on specific diseases has been vertical, instead of holistic model.

Laxity in funding NCDs like cancer, diabetes and hypertension have been ignored, despite being emerging diseases affecting more people.

“Donors through PEPFAR and Global Fund have reduced HIV infections, but this has not build resilient and sustainable health systems in Africa, interventions must be holistic and not vertical,” says Dr Zulu.

However, the expert warns that the continent shall not achieve her health agenda, with donor dependency.

“Agenda of the West is to prevent diseases from becoming global concerns. Issues like heart diseases, diabetes are self centered and even with big disease, they will not affect Americans,” Zulu emphasises.

He warns, “If African countries do not own and drive the health agenda, the continent will not have comprehensive health system to cater for its needs,”

Zulu regrets that one year later, after exit of USAID, countries are yet to own the health agenda.

Exit of USAID gave birth to Government to Government (G2G) bilateral health deal.

The new funding model, which seeks to link health funding to access to strategic minerals and pathogen data, is however facing its stiffest test on the continent.

Ghana is the latest country to reject the deal, citing concerns over terms requiring sharing of sensitive data.

At least 32 nations have signed the U.S. bilateral health agreements.

These include Kenya, Angola, Bolivia, Botswana, Burkina Faso, Burundi, Cambodia, Cameroon, Cote D' Ivoire, Democratic Republic of Congo, Dominican Republic, El Salvador, Eswatini, Ethiopia, Guatemala and Guinea.

Other countries are Honduras, Lesotho, Liberia, Madagascar, Malawi, Mozambique, Niger, Nigeria, Panama, Papua New Guinea, Philippines, Rwanda, Senegal, Sierra Leone, Tajikistan, and Uganda.

Apart from Ghana, Zimbabwe and Zambia have also rejected the deal.

In Zambia, negotiations stalled after the US reportedly linked a billion-dollar grant to access to the country's copper and cobalt reserves.

The deal, scheduled for signing last December, hit a snag just four days before the ceremony.

"We want to leverage U.S. assistance to bring about reforms that will unleash business investment that enhances US access to critical supply chains," Caleb Orr, US Assistant Secretary of State for Economic, Energy, and Business Affairs, said while announcing the proposed minerals-for-aid swap.

In Zambia the government requested revisions to the agreement, which reportedly saw the U.S. commitment drop from $1.5 billion (Sh193.5 billion) to $1.012 billion (Sh130.5 billion).

A leaked draft also revealed demands for Zambia to share data on pandemic-potential pathogens for 25 years.

Elsewhere in Zimbabwe, it was reported that President directly ordered a halt to negotiations on a $367 million (Sh47.3 billion) deal.

In a leaked letter, Zimbabwe's Secretary for Foreign Affairs, Albert Chimbindi, instructed officials to "discontinue any negotiations with the USA," describing deal as "clearly lopsided" and an affront to the nation's sovereignty.

"Zimbabwe was being asked to share its biological resources and data over an extended period, with no corresponding guarantee of access to any medical innovation, such as vaccines, diagnostics, or treatments that might result from that shared data," said Nick Mangwana, the government's spokesman.

The official observed that accepting a bilateral arrangement that bypasses multilateral mechanisms would undermine the solidarity African nations have been advocating for on the global stage.

Kenya was the first country to sign its five-year cooperation framework, valued at $2.5 billion (Sh325 billion), but actualisation of the deal has since been contested in court.

Under the bilateral government-to-government arrangement, the US was to provide $1.6 billion (Sh206 billion), while Kenya was expected to raise $850 million (Sh109 billion) through a co-financing model.

The deal was suspended following a court case challenging the framework, citing data-sharing and national sovereignty concerns, and lack of public participation.

Petitioners, including Busia Senator Okiya Omtatah, argue the deal could expose citizens to privacy violations, stigma, and misuse of sensitive health information.

As Africans poke holes in the deal, Zulu argues that the continent has never had sovereignty over health because of donor dependency.

“If Africa put money in their systems, we do not need help from Americans. Americans are pumping in money because they have their own interest that must be fulfilled,” observes the expert.

But he warns of rejecting the deal without a quick solution, on the basis of sovereignty and data.

This therefore calls for states to negotiate, and agree with the U.S. on the bilateral deal.

“America has been funding the continent, and no one can imagine they do not have access to data. The only new thing is that they want it written in a contract,” observes the official.

Sovereignty cited by states in rejection of the deal according to him should start with “solving critical things that affect the region”.

“It is unlikely for America to fund African continent with no benefit. If you need unconditional money, use your money. You don’t demand money without conditions,” Zulu emphasises.

Africa Centres for Disease Control and Prevention (Africa CDC) Director General Jean Kaseya echoes the concerns, warning that the continent cannot claim sovereignty while basic health outcomes remain poor.

“We cannot talk about sovereignty when mothers are still dying from preventable complications,” says Dr Kaseya.

On his part President of the World Health Summit (WHS) Prof Axel Pries, notes that changes in health funding should be a wake up calls for states.

"We all have wakeup call. After wakeup call, you are awake a have senses. Looking at everything, does it fit into requirement and wherever solution must fit the bill," says Pries.

Prof Pries maintains that data is key, and it should be protected at any cost.

"Data is a currency, you have to be really careful when you have it. This data has to be fair otherwise we will get into big problem," he says.

He adds, “Knowledge is power, and data and knowledge is power,"

Stalled actualisation of the bilateral health deal is pushing states lead by Africa CDC to meet the U.S. Government to fast track a deal.

In an exclusive interview with The Standard on Saturday, Kaseya reveals to have lead the negotiation with the US government to give money directly to governments, instead of using NGOs and other partners.

However, along the way, he acknowledges that states discovered there were components on data sharing, pathogen sharing that has resulted into laxity in signing the deal.

"We need to understand more. We need to keep the evidence and stop misinformation. Now we have agreed with the US to organise a big meeting for all African ministers, and U.S. Government, African CDC to discuss this issue," says the Africa CDC boss.

Countries that have signed the deal, and those yet to shall all participate in the planned meeting.

In case of Kenya, where the deal is contested in court, the official maintains the country is democratic, with laws, and verdict of the court shall be respected.

But meeting U.S. President according to Zulu is not a solution, as he is a ‘transactional’ leader, whose radical moves have not only affected health, put political, security, agriculture and environment across the globe.

“People can go meet President Trump, but at the end of the day, the question is-shall it matter? At end of the day, American have their own interest,” emphasises Zulu.

Nevertheless, domestic health financing amid changes in financing landscape is the way to go, according to Africa CDC.

Even as African states push for domestic financing, for more than two decades, African Union member states committed under the Abuja Declaration to allocate at least 15 per cent of annual national budgets to health, only six countries have actualised the deal, namely Rwanda, Botswana, Niger, Malawi, Zambia and Burkina Faso.

In Kenya, health budget ranges between five and nine percent.

President William Ruto, who officially opened the summit, said Kenya has made strides towards sustainable health financing through the adoption of the Social Health Authority (SHA), a scheme aimed at expanding risk pooling and reducing out-of-pocket expenditure.

SHA with membership of 30.7 million, he said, is a key vehicle in Kenya’s journey towards attaining Universal Health Coverage (UHC).

Additionally, Mr Ruto said Kenya has embraced advanced digital health systems to improve accountability, transparency and efficiency in service delivery.

“There will always be resistance to reform, especially when it comes to financing and technology, but these are changes we must embrace,” said Mr Ruto.

Dr Zulu said Kenya is on the right trajectory in reforming its health financing system, but warned that the country and continent must address corruption loopholes and wastage that continue to undermine the sector.

Countries like DRC are documented to loss more resources through inefficiencies such as payments to ghost workers.

WHO Regional Director for Africa, Prof Mohamed Janabi, said investment in health should be viewed as a critical driver of economic growth rather than a cost.

The continent according to the official has endured repeated public health emergencies and pandemics for example Covid-19, mpox, Ebola and Marburg, outbreaks that have placed immense strain on already fragile health systems 

“Health is insurance for the continent’s prosperity. We must make our systems work and finance them sustainably instead of relying on donors, said Janabi.