The Center for Global Health and Pandemic Intelligence breaks down the Implications for Health Security, Data Governance, and Global Health Architecture

Dr. Mark Nanyingi, (December 13, 2025, Nairobi-Kenya)

Over the past month, the United States has entered into a series of bilateral health cooperation agreements with African countries, so far  Kenya (2.5 B USD), Uganda (2.3 B USD), Lesotho (364 M USD), and Rwanda (228 M USD), close to 50 African Countries are expected to sign this framework. These agreements go beyond traditional aid commitments. They establish long-term, government-to-government (G2G) cooperation frameworks focused on strengthening national health systems, public health institutions, surveillance, laboratories, workforce capacity, and data governance. At a time when health risks spread rapidly across borders, these agreements are reshaping how countries invest in preparedness, manage health data, and share responsibility for global health security. Understanding what these agreements mean and how they are implemented matters for both Africa’s health systems and shared global safety.

From Projects to Long-Term Cooperation Frameworks
Unlike short-term, project-based health assistance, the new bilateral agreements are designed as multi-year cooperation frameworks. They align external support with national priorities, embed implementation within government institutions, and include explicit plans for progressive domestic ownership. This structure signals a shift from fragmented delivery models toward system-level strengthening anchored in national institutions. Using the Kenya–US Cooperation Framework on Health as an illustrative example, these agreements span:

• Disease prevention and control (HIV, TB, malaria, and epidemic-prone diseases)
• National surveillance and outbreak response
• Laboratory systems and diagnostics
• Health workforce development
• Digital health and data governance
• Supply chains and commodities

National Public Health Institutes as Centers of Excellence
A defining feature of these agreements is the central role given to National Public Health Institutes (NPHIs). In practical terms, this means that decisions during outbreaks are made earlier and closer to the source, rather than waiting for external direction. For African countries, this strengthens institutional authority. For the global community, it reduces the risk that outbreaks escalate undetected. In Kenya, for example, the framework positions the National Public Health Institute (KNPHI) as the lead authority for Disease surveillance, outbreaks, and Epidemic detection, One Health, Emergency response coordination, workforce capacity building, and Pandemic preparedness. This includes:

• Real-time digitial disease surveillance and laboratory diagnosis
• Rapid notification of public health events (PHE)
• Coordinated response through Emergency Operations Centres (EOC)
• Early, Intra and After Action Reviews with Performance benchmarks aligned with the 7-1-7 framework

Surveillance as Decision Support: From reporting to Pandemic Intelligence
A central element of the US bilateral health cooperation agreements is the repositioning of surveillance from routine disease reporting to a core pandemic intelligence function. Rather than focusing solely on notifiable diseases, the agreements support integrated surveillance systems that combine routine indicator-based reporting with event-based detection of unusual health signals arising from communities, laboratories, and other non-traditional sources. This approach increases the likelihood that emerging or unexpected outbreaks are identified early, before they escalate into national or regional emergencies. The agreements place strong emphasis on timeliness and real-time data flow, strengthening digital reporting platforms that link sub-national and national levels and reduce delays between detection, notification, and response. Surveillance data is explicitly connected to national risk assessment and decision-making processes, enabling proportionate and targeted public health actions, including the activation of emergency operations centres and escalation pathways. This enables countries to respond decisively while minimizing unnecessary social and economic disruption.

Laboratory systems are tightly integrated into surveillance functions, ensuring that diagnostic confirmation, pathogen characterization, antimicrobial resistance monitoring, and, where available, genomic data feed directly into situational awareness. This integration allows public health authorities to understand not only where outbreaks are occurring, but also the nature and evolution of the threats involved. Surveillance strengthening under these agreements is anchored within National Public Health Institutes, supported by sustained investment in epidemiologists, surveillance officers, and data analysts. This institutionalization ensures continuity of surveillance capacity beyond individual projects or funding cycles. At the same time, the agreements recognize that effective surveillance depends on robust data governance, with clear rules governing data ownership, access, storage, and information sharing. By balancing timely data exchange with national data sovereignty, the agreements seek to build trust and enable sustained cooperation.

These surveillance investments enhance countries’ ability to detect outbreaks early, assess risk accurately, and act quickly. In doing so, they strengthen national preparedness while contributing to shared global pandemic intelligence—reducing the likelihood that localized events escalate into global crises. Surveillance is framed not as a reporting obligation, but as a decision-support function. This approach overal improves: Speed of detection, Quality of risk assessment and Timeliness of response

Laboratory Systems for All-Hazards Preparedness
Laboratory strengthening is a core pillar of the cooperation agreements. Strong laboratories are essential not only for diagnosing diseases, but for understanding what threats are emerging and how dangerous they are. These capacities underpin preparedness for pandemic-prone pathogens, antimicrobial resistance, and zoonotic spillovers, while also supporting global biosecurity objectives. Investments focus on:

• National and sub-national human and animal laboratory networks
• Biosafety and biosecurity
• Quality management and accreditation
• Integrated laboratory information systems (LIMS)

Health Workforce Capacity building
A persistent weakness in pandemic preparedness has been the loss of skilled public-health personnel when donor-funded projects end. Epidemiologists, laboratorians, surveillance officers, and data analysts are often recruited on short-term contracts tied to specific programmes, only to exit the system once funding cycles close. This erodes institutional memory, weakens surge capacity during emergencies, and repeatedly forces countries to rely on external deployments during crises.

The bilateral health cooperation agreements aim to reverse this pattern by embedding workforce capacity within permanent public institutions rather than temporary projects. They provide sustained support for frontline epidemiologists conducting outbreak investigations, surveillance officers managing routine and event-based reporting, laboratorians operating national reference laboratories, and data analysts translating surveillance signals into decision-ready intelligence. These roles are treated as core functions of national health security systems, anchored within Ministries of Health and National Public Health Institutes.

Critically, the agreements include planned transition pathways for salaries, benefits, and employment terms, enabling governments to progressively absorb these positions into the public service. This reduces abrupt workforce attrition and helps retain experienced professionals with deep knowledge of local systems and response protocols. The impact on preparedness is substantial. Countries with a stable, institutionalized workforce can scale operations rapidly during emergencies, staff Emergency Operations Centres immediately, launch field investigations quickly, and generate internal risk assessments. Beyond crises, workforce stabilization supports continuous preparedness through routine surveillance, simulations, and system improvement—transforming health security from a reactive activity into a sustained national capability.

HIV, TB, and Malaria as System Anchors
HIV, tuberculosis, and malaria remain priority areas within the US bilateral health cooperation agreements, reflecting their continued public health importance and the scale of long-standing investments. However, a key shift introduced by these agreements is the integration of these programmes into national health systems, rather than treating them as isolated, disease-specific verticals. This approach protects hard-won disease gains while strengthening the broader systems needed for future outbreak preparedness. In practice, HIV, TB, and malaria programmes are increasingly linked to national surveillance and laboratory platforms, ensuring that case detection, diagnostics, and reporting feed into unified systems used for epidemic-prone diseases. Laboratory networks strengthened for TB or malaria diagnostics also support outbreak investigation, antimicrobial resistance monitoring, and detection of emerging pathogens, improving overall situational awareness.

The agreements also prioritize strengthening national procurement and supply chains, gradually transitioning from donor-managed systems to government-led forecasting, warehousing, and distribution. This safeguards treatment continuity while building supply chain resilience that can be mobilized during health emergencies. By reducing parallel delivery structures over time, the agreements improve coordination, accountability, and sustainability. HIV, TB, and malaria programmes thus serve not only as life-saving interventions, but as foundational pillars of stronger health systems and pandemic preparedness

Data Governance and Security: The Sovereignty dilemma
Perhaps the most sensitive and consequential issue raised by this agreement is Data governance. At the heart of this debate lies a fundamental question of sovereignty: Who controls public health data, Where that data is stored, Who can access it, and for What purposes it is ultimately used?. These questions matter because public health data particularly surveillance, laboratory, and genomic data are not merely technical inputs; they are strategic national assets that shape decision-making, risk perception, and global responses during health emergencies.

Strong data governance frameworks can significantly enhance national decision-making autonomy. When countries retain ownership of their digital health systems and data architectures, they are able to conduct in-country analysis, generate context-specific risk assessments, and make timely policy decisions without over-reliance on external interpretation. Weak or poorly defined governance, however, carries clear risks. Without explicit rules on data ownership, hosting, access, and secondary use, bilateral cooperation can unintentionally reinforce asymmetric data flows, where raw data moves outward while analytic value, insights, and strategic advantage accrue elsewhere.

Importantly, data sovereignty in this context is not about restricting data sharing or disengaging from global systems. On the contrary, effective pandemic preparedness depends on timely and transparent information exchange. The challenge is to ensure that data sharing is secure, equitable, and purpose-driven, aligned with national laws, public health objectives, and agreed international norms. This requires clarity on how data may be used for surveillance, research, policy, or commercial purposes, and safeguards against unauthorized or unintended secondary use.

The cooperation frameworks seek to address this balance by emphasizing national ownership of digital health systems, ensuring that surveillance platforms, laboratory information systems, and analytic tools remain embedded within national institutions. They also promote interoperability across platforms, enabling data to move efficiently between surveillance, laboratory, logistics, and clinical systems without fragmenting control. Finally, they rely on controlled data sharing through negotiated agreements, particularly for cross-border exchange and international reporting, rather than automatic or undefined data flows. If implemented with strong governance, these provisions can strengthen sovereignty while supporting global solidarity, enabling countries to share critical information confidently and responsibly.

Strengthening Health Supply Chains and Essential Commodities
A critical but often underemphasized pillar of bilateral health cooperation is the strengthening of national health supply chains and the reliable availability of essential health commodities. Surveillance, laboratories, and emergency operations can only function effectively if vaccines, diagnostics, therapeutics, personal protective equipment, and medical supplies are consistently available at the point of care. Recent global shocks—from COVID-19 to climate-driven emergencies—have underscored how fragile and fragmented supply chains can undermine otherwise robust preparedness investments.

Bilateral cooperation agreements create an opportunity to modernize supply-chain governance, digitization, and resilience at national and regional levels. In Kenya, the Kenya Medical Supplies Authority (KEMSA) provides a functional platform of how such partnerships can add value. Targeted technical assistance and financing can support reforms in demand forecasting, end-to-end logistics visibility, warehousing standards, last-mile distribution, and emergency surge mechanisms. Integration of supply-chain data with surveillance and early-warning systems enables anticipatory procurement and pre-positioning of commodities before outbreaks escalate.
At a regional scale, harmonized regulatory standards, pooled procurement, and cross-border logistics coordination supported through bilateral and multilateral cooperation can reduce costs, minimize stock-outs, and enhance equity in access to life-saving commodities. By embedding supply-chain strengthening within broader health security cooperation, countries move beyond reactive responses toward resilient systems capable of sustaining preparedness, response, and recovery across future public-health emergencies.

Pandemic Agreement and PABS alignment
These bilateral agreements intersect with ongoing negotiations on the WHO Pandemic Agreement and the Pathogen Access and Benefit Sharing (PABS) mechanism.Both seek to address long-standing imbalances in global health governance, where pathogens and data often move rapidly from low- and middle-income countries, while benefits return slowly or unevenly. Poor alignment, however, risks creating parallel and fragmented systems that weaken global coherence.When aligned with PABS principles, bilateral agreements can:

• Strengthen countries’ capacity to meet global obligations
• Improve transparency and trust in data sharing
• Translate surveillance investments into equitable access to countermeasures

Global Health Governance and Architecture
The cooperation agreements do not replace the roles of WHO or Africa CDC. Instead, they operationalise global norms at country level. WHO continues to set standards and provide normative guidance, while Africa CDC plays a critical role in regional surveillance and cross-border coordination. The effectiveness of bilateral agreements depends on intentional alignment with these institutions, ensuring that national investments reinforce rather than fragment the global health security architecture.

Shared Global Health Security benefits for the US and the World
Beyond national systems strengthening, these agreements generate broader global benefits:

• Earlier outbreak detection reduces international spread
• Improved biosecurity lowers risks of accidental or deliberate misuse
• Enhanced laboratory networks support AMR surveillance
• Stronger supply chains stabilise global markets
• Domestic co-investment supports long-term sustainability

For the United States, these investments function as upstream risk reduction, lowering the likelihood of costly global health emergencies.

Implications for One Health and Pandemic Preparedness
When implemented with strong governance, these bilateral health cooperation agreements can materially strengthen pandemic preparedness by:

• Enabling earlier detection of outbreaks and faster, coordinated response actions
• Expanding laboratory readiness for all-hazards threats, including novel pathogens and antimicrobial resistance
• Improving continuity and surge capacity of the public-health workforce during health emergencies
• Anchoring preparedness functions within permanent national institutions, reducing reliance on ad-hoc emergency mechanisms

However, these preparedness gains are not automatic. Their realization depends on:

• Clear leadership and coordination by National Public Health Institutes (NPHIs)
• Robust data governance and security frameworks that protect national interests while enabling timely data sharing
• Alignment with national, regional, and global preparedness frameworks, including IHR, NAPHS, and Africa CDC strategies
• Integrated One Health implementation, linking human, animal, and environmental surveillance and response systems

The US bilateral health cooperation agreements represent important cooperation frameworks with the potential to strengthen Africa’s health systems and advance shared global health security. Their impact will depend less on funding levels, and more on how institutions are empowered, data is governed, and national priorities are aligned with regional and global commitments. When implemented well, these agreements can support stronger sovereignty, greater trust, and a more resilient global health security landscape.