Across Africa, US-funded health programmes are moving onto government budgets and systems. Funding can change hands in a budget cycle. The patient records behind those programmes take more care to move.
For two decades, international funding has built some of the most sophisticated patient data systems in African health. HIV programmes in particular have tracked millions of patients over many years, often through systems supported by implementing partners rather than run directly by ministries.
That model is changing. Under new bilateral agreements, US-funded programmes are moving toward government budgets, government systems and government oversight. Much of the public discussion has been about money, commodities and health workers. Less has been said about the patient data.
This guide looks at what the transition means for programme records, why data governance has become part of the conversation, and what ministries and partners can do to make sure patient history arrives intact. It draws on our experience at Jonda Health, where our work is turning health records from many different sources into structured, standardised information that clinicians and systems can actually use.
The America First Global Health Strategy, released in September 2025, moves US health assistance toward five-year bilateral agreements with partner governments. Support is shifting from contractor-based delivery toward government-to-government transfers and direct provision of commodities to government systems, with partner countries committing to year-by-year increases in their own health spending. Most of the countries involved are expected to be fully self-reliant by the end of the agreement period, and US contracts with many previous implementing partners have ended (Brookings).
By September 2026, more than 30 countries had signed agreements, most covering 2026 to 2030, among them Nigeria, Kenya, Ethiopia, Rwanda, Mozambique, Tanzania, Uganda, Botswana and Malawi, with a combined value of at least US$24.2 billion. Detailed implementation plans were expected by the end of March 2026, and some countries planned limited-period contracts with existing partners during the handover (Think Global Health; KFF).
Figure 1. The first year of the transition.
Behind every programme is a body of patient data: who is on treatment, which regimens they have taken, their laboratory results over time, missed appointments and transfers between facilities. In many countries this sits in electronic patient tracking systems, laboratory systems and reporting databases, some hosted or supported by partners, and often alongside paper registers.
Some of this work is well advanced. In Mozambique, for example, the HIV programme's electronic patient tracking system has been centralised at provincial level, with a phase to integrate a master patient index and reduce duplicate entries (C-Saúde). Elsewhere, records are more fragmented, split across partners, districts and systems that were never designed to meet.
At the same time, many of the same countries are building national systems of their own: health information exchanges, shared health records and national patient registries, which we cover in our articles on Kenya, Nigeria, Rwanda, Ethiopia and Mozambique. Programme records are one of the richest sources of longitudinal patient history those systems could draw on, if they arrive in usable form.
The agreements also cover data. Kenya's agreement, signed on 4 December 2025, provides for sharing programmatic and outcome data for US-supported programmes, states that Kenya retains ownership of the data, and says individual-level information should not be shared to the maximum extent practical (Health and Human Rights Journal). A petition raised concerns about its consistency with Kenya's Data Protection Act and Digital Health Act, and the High Court suspended the data-sharing provisions in December 2025 and, on 19 December, extended the suspension to the wider agreement (Carnegie Endowment). On 12 May 2026, the Court of Appeal stayed those orders, allowing implementation to proceed while the appeal continues, with a ruling on the stay expected on 30 October 2026 (Capital FM).
Commentators note that similar questions have been raised in other countries, and that most signatories also have data protection laws of their own (Carnegie Endowment). Views differ on how the agreements balance data sharing and protection, and we take no position on that here. The practical point for anyone handling programme records is simpler: ownership, hosting, access and reporting need to be clear, documented and consistent with national law before records move.
Moving a programme is not only a contract change. For patients on long-term treatment, their history has to arrive in the new system complete, correctly matched and usable by the clinician who sees them next.
Figure 2. What has to move when a programme moves.
In the records we work with across Africa and Asia, the same patterns appear again and again.
AI can do much of the heavy lifting at speed, and we use it extensively ourselves, but it needs clinical review and quality checks behind it. That is why we argue that healthcare AI will not work without trusted data infrastructure. Where records are shared or reused beyond direct care, the right protections matter, which we explain in this guide.
At Jonda Health, we have spent years working with health records across formats, languages and health systems in Africa and Asia, and we know how much of this work only becomes visible once real data starts to move. Depending on where your organisation is in the transition, there are three ways we can help.
It is the United States government's global health strategy, released in September 2025. It moves US health assistance toward five-year bilateral agreements with partner governments, with support delivered increasingly through government systems and partner countries committing to raise their own health spending over time.
Public trackers reported more than 30 countries with signed agreements by September 2026, most of them in Africa and most covering 2026 to 2030. Think Global Health put their combined value at at least US$24.2 billion.
Many programme records, such as HIV treatment histories, laboratory results and patient tracking, have been held in systems supported by implementing partners. As programmes move to government, those records need to be identified, matched, checked and moved into systems the ministry owns and runs, without losing patient history.
Kenya signed its agreement on 4 December 2025. Following a petition raising data protection concerns, the High Court suspended its data-sharing provisions and later the wider agreement. On 12 May 2026 the Court of Appeal stayed those orders, allowing implementation to proceed while the appeal continues, with a ruling on the stay expected on 30 October 2026.
With an inventory: which systems hold programme patient data, who hosts and supports them, how patients are identified, and which records are needed for continuity of care. From there, agree ownership and hosting under national law, and plan how records will be matched, cleaned and moved.
Sources: Brookings (7 August 2026); Think Global Health (updated September 2026); KFF (September 2026); C-Saúde (24 July 2024); Health and Human Rights Journal (17 December 2025); Carnegie Endowment for International Peace (March 2026); Capital FM (12 May 2026). This article is for general information, is not legal advice, and takes no position on the policy or the litigation described.
