National Public Health Institutes in Africa, 2010–2025: pathways, governance, and outcomes, a scoping review

Abstract

Background

National Public Health Institutes (NPHIs) are government-anchored, science-driven institutions that consolidate essential public health functions, including surveillance, laboratories, workforce development, and emergency preparedness. In Africa, NPHIs are central to the Africa Centers for Disease Control (CDC) New Public Health Order, yet progress remains uneven, with fewer than half of Member States having established functional institutes by 2023. Fragmented evidence on establishment pathways, governance models, and operational maturity limits comparative learning and policy guidance.

Methods

We conducted a scoping review following the Joanna Briggs Institute (JBI) methodology and reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist. Peer-reviewed and grey literature published between 2010 and 2025 were systematically searched across PubMed (U.S. National Library of Medicine), Scopus, Web of Science, Embase, CINAHL (Cumulative Index to Nursing and Allied Health Literature), WHO repositories, Africa CDC publications, and International Association of National Public Health Institutes (IANPHI) reports. Eligible sources included case studies, institutional reports, policy analyses, and commentaries describing NPHI establishment, governance, functions, challenges, enablers, or outcomes. Data were charted and synthesised thematically into five domains: institutional establishment, governance and structure, resources and capacity, implementation factors, and outcomes and impact.

Results

Twenty-one studies were included, spanning country case studies (Nigeria, Liberia, DRC, South Sudan, Uganda, South Africa, Burkina Faso) and multi-country evaluations, continental surveys, and conceptual frameworks. Establishment pathways varied from Acts of Parliament and Presidential decrees to ministerial directives, and institutional models included autonomous/semi-autonomous, ministry-based, and networked/hybrid arrangements. Governance was consistently emphasised, with NPHIs positioned as science-based authorities coordinating surveillance, laboratories, and emergency response. Resources and capacity were shaped by donor support, Field Epidemiology Training Programs, and infrastructure investments, though underfunding and sustainability gaps persisted. Implementation enablers included political will, Africa CDC and IANPHI frameworks, and peer mentorship; challenges included fragmented functions, weak legal frameworks, and donor dependence. Reported outcomes included improved outbreak detection and response, expanded laboratory and surveillance systems, strengthened IHR core capacities, and enhanced institutional resilience.

Conclusions

NPHIs are critical anchors of health security in Africa, but their development remains uneven. Legal frameworks, sustainable financing, and integration into continental networks are essential for maturation. This review provides the first consolidated evidence map of NPHI establishment and models in Africa, highlighting best practices, recurrent challenges, and priorities for future research and policy action.

Supplementary information

The online version contains supplementary material available at 10.1186/s12913-026-14473-7.

Background

National Public Health Institutes (NPHIs) are government-anchored, science-driven institutions that consolidate and coordinate essential public health functions, including surveillance, laboratory systems, workforce development, emergency preparedness, and research [1]. Globally, NPHIs have been recognised as critical platforms for advancing the Global Health Security Agenda (GHSA) and ensuring compliance with the International Health Regulations (IHR, 2005) [2, 3]. By serving as technical “homes” for IHR core capacities, NPHIs provide centralised mechanisms for countries to strengthen readiness, accelerate detection and response to health threats, and generate evidence to guide policy decisions within ministries of health [4, 5].

In Africa, the establishment and expansion of NPHIs are central to the Africa CDC’s New Public Health Order, which emphasises stronger national institutions, regional collaboration, and reduced dependency on external actors for epidemic preparedness and response [6, 7]. The Africa Health Security and Sovereignty (AHSS) Agenda complements this vision by elevating health sovereignty, regional solidarity, locally led manufacturing, and interoperable digital systems, priorities that require strong, legally empowered NPHIs.

Africa CDC has prioritised NPHIs as a cornerstone of continental health security, aiming for every African Union (AU) Member State to establish a functional institute empowered with legal frameworks, sustainable financing, and technical capacity [8]. By linking national capacities to Regional Integrated Surveillance and Laboratory Networks (RISLNETs), NPHIs foster cross-border collaboration, harmonise standards, and strengthen accountability for resilient health systems. Despite this momentum, progress remains uneven: as of 2023, only 23 of 55 AU Member States had fully established NPHIs, with many lacking comprehensive legal mandates, strategic plans, or adequate resources [9].

In this review we use Africa CDC’s definition of a fully established National Public Health Institute, referring to a legally mandated single public health entity authorized through an Act of Parliament, Presidential decree, or Ministerial directive, and responsible for coordinating at minimum the core functions of disease surveillance, laboratory systems, emergency preparedness and response, public health research, and workforce development. This is the operational standard used in recent Africa CDC continental mappings [10].

Beyond Southern Africa, countries illustrate diverse pathways. In West Africa, Nigeria enacted the Nigeria Centre for Disease Control and Prevention (NCDC) Act (2016), Liberia legislated the National Public Health Institute of Liberia (NPHIL) (2016/2017), and Burkina Faso created the Institut National de Santé Publique (INSP) by Decree No. 2018 − 0618. In Central Africa, the DRC established the INSP by Presidential Decree 22/16 (2020), reinforced by Ordinance-Law 23/006 (2021).

In the East/Horn, Uganda’s staged UNIPH has accelerated detection-to-response while advancing an Act; Ethiopia’s Ethiopian Public Health Institute (EPHI) is grounded in Regulation 301/2013; Rwanda’s Biomedical Centre (RBC) operates under Law 13/2019; and South Sudan moved from a 2019 ministerial order to the NPHI Act (2021). In North Africa, Morocco’s long-standing Institut National d’Hygiène functions as the national reference institute under the Ministry of Health. Collectively, these examples are consistent with Africa CDC mappings that show variable models and uneven maturation across AU Member States.

At the country level, experiences in Southern Africa illustrate both opportunities and challenges. Zimbabwe consolidated surveillance and laboratory functions under the Ministry of Health and Child Care and, in 2025, launched the Public Health Institute of Zimbabwe (PHIZ) and inaugurated a Steering Committee to guide operationalization, supported by EU/WHO funding; earlier, Statutory Instrument 154 of 2020 provided a regulatory basis under the Research Act [11]. We therefore describe Zimbabwe as in the operationalization phase, with legal and institutional arrangements being consolidated.

Zambia has advanced efforts to formalise its NPHI in line with Africa CDC’s technical guidance, while Malawi remains in earlier stages of institutional development, with fragmented public health functions spread across multiple directorates [12]. These variations highlight the heterogeneity of establishment pathways, governance models, and operational maturity across the region [13]. Understanding these differences is essential for identifying best practices, common challenges, and opportunities for harmonisation within the African context.

Despite their strategic importance, the evidence based on NPHIs in Africa remains fragmented and dispersed across case studies, policy briefs, institutional reports, and commentaries [6]. Without a consolidated synthesis, policymakers and technical partners lack a clear roadmap for establishing and strengthening NPHIs across diverse contexts [14–16]. This scoping review addresses this gap by systematically mapping the available evidence on NPHI establishment, models, governance, challenges, enablers, and outcomes in Africa.

Methods

Study design

A scoping review was conducted to identify and synthesise evidence on the establishment, governance, models, challenges, enablers, and outcomes of NPHIs in Africa. The review followed the Joanna Briggs Institute (JBI) methodology for scoping reviews and was reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA‑ScR) checklist [17]. This approach ensured methodological rigour, transparency, and reproducibility.

Search strategy

Following JBI guidance (three-step approach) and reported per PRISMA‑ScR, we searched four bibliographic databases: PubMed (U.S. National Library of Medicine), Embase (Elsevier), CINAHL (Cumulative Index to Nursing and Allied Health Literature; EBSCO), and HINARI (Research4Life), for records from January 1, 2010, to September 30, 2025. We supplemented this with targeted searches of WHO IRIS, Africa CDC, IANPHI, and Ministry of Health/agency websites (grey literature), and we hand-searched reference lists of included studies.

Search concepts combined Population/Concept/Context terms for national public health institutes, governance/establishment, and Africa (including all AU Member States). The full electronic strategies (complete Boolean strings per database, search dates, and any limits) are provided in Supplementary 1. Search Strategy to enable replication.

Inclusion criteria

Eligible sources included peer-reviewed articles, institutional reports, policy briefs, and commentaries published in English between January 2010 and October 2025. Studies were included if they described NPHIs or equivalent national public health agencies in African Union Member States, focusing on establishment processes, governance arrangements, institutional models, mandates, challenges, enablers, or outcomes. Sources not specific to Africa, not addressing NPHIs, or lacking empirical or descriptive detail were excluded.

Global or multi-country sources were retained only when they informed NPHI establishment, models, or governance in Africa, or when African countries formed part of the study sample; in such cases, references to non-African NPHIs functioned solely as conceptual comparators and were not synthesized as standalone cases.

Types of evidence

The review incorporated diverse study designs, including case studies, descriptive analyses, comparative policy reviews, editorials, and institutional reports. Both empirical and conceptual contributions were considered to capture the breadth of evidence on NPHIs.

Source selection

All identified citations were imported into Mendeley for deduplication. Screening was conducted in two stages: (1) title and abstract screening against eligibility criteria, and (2) full-text screening of potentially relevant sources. Two independent reviewers conducted all screening steps, with discrepancies resolved by consensus. The study selection process was documented using a PRISMA‑ScR flow diagram.

Data extraction and analysis

A standardised data charting form was used to extract information on country, year of establishment, institutional model, governance and legal framework, core functions, funding mechanisms, reported challenges, enabling factors, and outcomes (Table 1). Data were synthesised thematically into five domains: institutional establishment, governance and structure, resources and capacity, implementation factors, and outcomes and impact. Descriptive mapping was used to summarise study characteristics, while thematic synthesis identified recurring patterns and gaps across the evidence base.

Table 1.

Summary of articles and initiatives that were reviewed

Author(s)	Year	Study design	Study Identification	Study Characteristics	Institutional Establishment	Governance and Structure	Resources and Capacity	Implementation Factors	Outcomes and Impact
Zuber et al. [20]	2023	Analytical / policy analysis (conceptual framework with illustrative case examples)	Multi-country (Burkina Faso, Colombia, Georgia, Korea, Nigeria, Norway, USA, UK, Italy, Germany, Vietnam, Haiti, Angola, etc.)	Conceptual essay with case illustrations. Data sources: literature review, consultation with NPHI leaders and experts. Provides typology of “linkages” (functional, multifunctional, multisectoral, multilevel, international) and enabling factors.	Not applicable (conceptual analysis; no single NPHI establishment described)	NPHIs are described as ministry-based, semi-autonomous, or parastatal. Emphasises the role of policies, agreements, and legislation as enablers of linkages. Mandate includes surveillance, labs, workforce development, research, outbreak response, and emergency management.	Notes the importance of dedicated/shared funding to support collaboration. Workforce development (e.g., rapid response teams, training programs) is highlighted as a linkage enabler.	Enablers: supportive policies, legislation, infrastructure (labs, IT, PHEOCs), leadership, trust, and collaboration history. Challenges: fragmentation, siloed programs, unclear roles between NPHIs and MoHs, and political influence.	Improved outbreak detection and response, faster coordination, integration of vertical programs, and cost/resource efficiencies. Long-term impact: strengthened health security, enhanced multisectoral collaboration (e.g., One Health, AMR), improved international cooperation (e.g., REDISSE in West Africa).
Hien et al. [21]	2025	Cross-sectional qualitative study	Burkina Faso	Case study of NPHI operationalisation. Data sources: document review (strategic plan, decree, statutes) + 15 key informant interviews. Focused on operationalisation phase (2018–2023); inclusive, participatory, adaptive process.	Established in 2018 via Decree nº2018 (Council of Ministers, July 19, 2018). Model: Public Health Establishment (EPS) with legal personality; semi-autonomous but under MoH oversight.	Governance: Statutes adopted; oversight by the MoH and the Ministry of Economy. Structure: 6 technical directorates (MURAZ Centre, Nouna Health Research Centre, Malaria Research Centre), Scientific Department, General Secretariat. Mandate: health monitoring, research, training, reference laboratory, and emergency response.	Funding: Annual government allocation + donor support (CDC, IANPHI, WHO, UNICEF, World Bank, EU, WAHO). Workforce: ~250 permanent staff + ~ 120 contractual/expatriates; supplemented by MoH staff. Infrastructure: merged reseacentresters, labs, IT systems, emergency operations centre, observatory.	Enablers: strong political will, MoH leadership, roadmap, institutional strategic plan, international partnerships, and continuous communication for visibility. Challenges: not explicitly detailed (authors avoided discouraging policymakers).	Short-term: Effective outbreak response (Yirgou crisis 2019, COVID-19 2020); improved coordination. Long-term: Strengthened labs and surveillance; integration into national health planning recognised by Africa CDC as a fully established NPHI.
Woldetsadik et al. [22]	2022	Qualitative study (directed content analysis of semi-structured interviews)	Cambodia, Colombia, Liberia, Mozambique, Nigeria, Rwanda, Zambia	Multi-country qualitative evaluation of NPHI development and operations. Data sources: 96 semi-structured interviews with NPHI staff, non-NPHI government staff, NGOs, and international partners. Provided rich cross-country perspectives on enabling factors and barriers.	Varies: Liberia & Zambia (< 5 years at study time); Cambodia, Nigeria, Rwanda (6–25 years); Mozambique & Colombia (40 + years). Pathways: mixed (Acts of Parliament, decrees, MoH directives). Models: autonomous, semi-autonomous, or ministry-based.	Some NPHIs are backed by law (e.g., Zambia bill in progress); othare semi-autonomousmous unthe der MoH. Structures typically included divisions for labs, surveillance, emergency operations, workand force development. Mandates: surveillance, labs, workforce development, emergency preparedness/response, research, and coordination.	Funding: heavy reliance on donors; limited domestic government allocations; some exploring self-generated income. Workforce: staff capacity building emphasised; challenges with attrition and turnover. Infrastructure: labs, surveillance systems, EOCs; capacity varied by maturity of NPHI.	Enablers: strong leadership, political commitment, financial autonomy, staff training, strategic partnerships. Challenges: donor dependence, leadership changes tied to politics, staff attrition, and inadequate government funding.	Short term: improved coordination of public health functions, enhanced credibility and trust. Long term: strengthened health security functions, improved integration of surveillance and labs, potential for sustainability if enablare ers addressed.
Woldetsadik et al. [23]	2021 (published; available 2022)	Qualitative semi-structured interviews, content analysis)	Cambodia, Colombia, Liberia, Mozambique, Nigeria, Rwanda, Zambia	Multi-country qualitative evaluation of CDC’s contributions to NPHI development. Data sources: 96 semi-structured interviews with NPHI staff, non-NPHI government staff, NGOs, and international partners. Focused specifically on CDC’s role in workforce development, labs, and governance.	Varies by country (Liberia & Zambia < 5 years; others longer established). Pathways: mixed (Acts of Parliament, decrees, MoH directives). Models: autonomous, semi-autonomous, or ministry-based.	Governance: NPHIs generally have legal mandates; CDC support emphasised strengthening governance and autonomy. Structure: divisions for labs, surveillance, emergency operations, and workforce development. Mandate: surveillance, outbreak investigation, labs, workforce training (esp. via FETP), emergency preparedness.	Funding: government allocations (often inadequate); CDC funding directed to country-defined priorities; donor earmarks. Workforce: strong emphasis on FETP graduates as backbone of NPHI workforce; CDC supported training in labs, surveillance, and emergency response. Infrastructure: strengthened labs (e.g., influenza molecular diagnostics), surveillance systems, EOCs.	Enablers: CDC support (technical assistance, flexible funding, tools like the Staged Development Tool), workforce development, and identification of national priorities. Challenges: constrained government funding, reliance on donor earmarks, and sustainability concerns.	Short term: improved surveillance reporting, epidemic response, real-time reporting, and enhanced lab capacity. Long term: strengthened national and sub-national workforce, improved coordination of public health functions, and contribution to IHR core capacities.
Angendu et al. [24]	2024–2025	Descriptive review/case study (lessons learned)	Democratic Republic of Congo	Descriptive report of the establishment process. Data sources: policy/legal documents, stakeholder engagement, outbreak response experiences. Focused on lessons learned during establishment and early operations.	Established April 2022 by Presidential Decree nº22/16; reinforced by Ordinance Law nº23/006 (March 2023). Model: Government-led, centralised institute; semi-autonomous with Board of Directors.	Governance: Oversight by the Ministry of Health and Presthe idency. Structure: Board of Directors, Director General, Public Health Emergency Operations Centre (PHEOC), integrated General Directorate of Disease Control (GDDC). Departments for labs, surveillance, research, workforand ce, health promotion. Mandate: surveillance, outbreak investigation/response, research, workforce development, health promotion, lab science, policy analysis, One Health.	Funding: Government budget (limited) + partner support (US CDC, WHO, Africa CDC, UNICEF, UNFPA, BMGF, PATH, others). Exploring public–private partnerships. Workforce: Transitioned staff from GDDC; capacity-building for midwives and perinatal care providers; training and mentorship programs. Infrastructure: PHEOC established; integrated labs and sample transport networks; improved surveillance systems.	Enablers: strong political will (Presidency & MoH), inclusive stakeholder engagement, legal frameworks, international support (CDC, WHO, Africa CDC, IANPHI), learning from other NPHIs (Liberia, Nigeria, Burkina Faso). Challenges: resistance to change, insufficient communication, lack of transition plan for HR/infrastructure, funding gaps, and partner coordination difficulties.	Short-term: improved outbreak response (Mpox, cholera, measles), operational incident management system, and centralised coordination. Long-term: strengthened surveillance and lab systems, enhanced multisectoral collaboration, contributions to Universal Health Coverage (UHC) (e.g., free maternity/newborn care program), alignment with IHR (2005).
Carnevale et al. [25]	2023	Policy analysis informed by qualitative interviews	Cambodia, Colombia, Liberia, Mozambique, Nigeria, Rwanda, Zambia	Multi-country policy analysis using Tea Collins’s health policy framework. Data sources: 96 semi-structured interviews with NPHI staff, non-NPHI government staff, NGOs, and international partners. Compared policy options for NPHI consolidation (status quo vs. partial vs. full).	Varies by country (not the focus; analysis of existing NPHIs at different stages). Pathways: country-specific (decrees, MoH restructuring, autonomous parastatals). Models: mixed (ministry-based, semi-autonomous, autonomous parastatal).	Governance: Emphasised the importance of legal authority, clarity of mandate, and political viability. Structure: compared consolidated vs. fragmented models (e.g., Nigeria CDC, Rwanda Biomedical Centre, Mozambique INS). Mandate: surveillance, labs, workforce development, emergency preparedness/response, research, health promotion.	Funding: consolidation can improve efficiency and accountability; NPHIs are sometimes better positioned to apply for grants or generate income. Workforce: FETPs often housed in NPHIs; consolidation supports training, rapid response teams, and staff retention. Infrastructure: centralised labs, incident management systems, shared data platforms; co-location improves coordination.	Enablers: strong leadership, political will, clarity of roles, trust with MoH, adequate resources, legal frameworks, stakeholder networks. Challenges: role duplication with MoH, political resistance, lack of co-location, assumptions of greater resources than available, and partner misalignment.	Short term: improved outbreak detection and response, better coordination, cost/resource efficiencies. Long term: stronger data-driven decision making, enhanced national recognition of public health, improved multisectoral collaboration, and strengthened IHR compliance.
Ihekweazu et al. [26]	2015	Descriptive case study of institutional collaboration	United Kingdom (Public Health England/HPA) and South Africa (NICD)	Case study/policy analysis of bilateral collaboration. Data sources: documentation of collaboration activities, staff secondments, joint projects, and institutional reports. Focused on the mutual benefits and challenges of North–South NPHI partnership.	NICD (South Africa) was established earlier; PHE was created in 2013 (successor to HPA). Pathways: NICD under MoH; PHE statutory creation in the UK (2013). Models: NICD, centralized communicable disease institute; PHE national public health agency.	Governance: South Africa enacted the National Public Health Institute of South Africa Act (Act 1 of 2020), which legally establishes NAPHISA; however, the Act has not yet come into force, and NAPHISA is therefore not operational. Mandates: surveillance, outbreak investigation, reference labs, workforce training, research, and IHR implementation.	Funding: UK Department of Health grant (£1.9 m over 5 years) supported collaboration. Workforce: long-term secondment of senior epidemiologist (2011–2013); 35 staff exchanges (2 weeks–3 months). Infrastructure: NICD BSL 4 lab; PHE regional labs; exchanges enhance diagnostic and epidemiological capacity.	Enablers: strong leadership, steering committee oversight, dedicated international office, trust and mutual respect, alignment with WHO IHR and UK “Health is Global” strategy. Challenges: balancing institutional priorities, covering staff duties during exchanges, and sustaining collaboration after donor funding ended.	Short term: strengthened TB surveillance, new diagnostic methods at NICD, enhanced outbreak investigation capacity, improved epidemiology training (SAFELTP). Long term: enhanced South Africa’s outbreak response capacity, UK gained preparedness for rare diseases, model for future North–South NPHI collaborations, strengthened global health security networks.
Desta et al. [27]	2022	Cross-sectional survey (policy mapping)	Africa (55 AU Member States surveyed; 40 responses)	Multi-country survey and policy mapping exercise. Data source: online semi-structured questionnaire administered by Africa CDC (July 2021–May 2022). Provides a continental overview of NPHI status, models, and legal frameworks.	Varies by country. Pathways: 12 via Act of Parliament, 12 via Presidential decree, 5 via Ministerial decree. Models: 17 autonomous, 4 networks of institutions, 8 departments undethe r MoH.	Gunder the legal frameworks include Acts of Parliament, Presidential/Prime Ministerial decrees, and Ministerial decrees. Structure: autonomous institutes, networks, or MoH departments. Mandates most commonly included research, surveillance & disease intelligence, epidemic preparedness & response, workforce development, public health informatics, and health promotion.	Funding: governments covered ~ 40% of budgets on average (range 1–95%); the remainder from partners. Workforce: Workforce development is cited as a core function in 19 NPHIs. Infrastructure: many share labs and office infrastructure; some lack full surveillance or lab systems.	Enablers: Africa CDC frameworks and advocacy, IANPHI support, peer networking, and political commitment in some states. Challenges: 5 countries reported no plan to establish an NPHI; limited autonomy in MoH-based models; underfunding; definitional inconsistencies.	Short term: 12 fully established NPHIs, 17 at the advanced stage, 6 starting the process, 5 with no plan. Long term: NPare HIs are seen as critical for IHR implementation, outbreak response, and stronger health systems; highlighthe ted urgent need for advocacy and investment.
Frieden & Koplan [28]	2010	Commentary/policy analysis	Global perspective (not country specific)	Conceptual analysis of NPHI roles and functions. Data sources: literature, global policy frameworks, WHO International Health Regulations (200and examplesples of NPHI functions. Influential in framing global discourse on NPHIs.	Not applicable (conceptual analysis; no single NPHI establishment described). Notes that many NPHIs are created after major events (e.g., SARS outbreak).	Goemphasises the need for legal mandates and authority to coordinate national public health functions. Structure: NPHIs may consolidate multiple functions (labs, surveillance, research, workforce, emergency preparedness). Mandates: surveillance, reference labs, outbreak detection/response, imimmunisationcommunicable & non-communicable disease control, injury prevention, occupational & environmental health, workforce training, emergency preparedness, health communication, policy leadership.	Resources: not detailed empirically. Capacity: highlights multidisciplinary teams (infectious disease, chemical hazards, engineering, risk communication). Infrastructure: reference laboratories, surveillance systems, emergency operations, data platforms.	Enablers: strong legal frameworks, multidisciplinary expertise, integration of functions, international collaboration. Challenges: fragmentation across multiple institutions, lack of coordination, political and structural barriers.	Short term: improved outbreak detection, response, and prevention when NPHIs are established. Long term: strengthened national and global health security, cost savings, improved population health outcomes.
Tong et al. [29]	2025	Descriptive review/case study	South Sudan	Case study of institutional establishment. Data sources: policy/legal documents, stakeholder consultations, technical working group reports, benchmarkingand sit to Ethiopia. Proa vides detailed timeline (2019–2024) and highlights phased legal and operational milestones.	Established February 2019 by Ministerial Order No. 004/2019; reinforced by NPHI Act (2,023) passed by Parliament and assented to by the President. Model: autonomous entity with legal personality, Board of Directors, Executive Director, two main directorates (Technical; Administration & Finance).	Governance: Ministerial Order (2019) and NPHI Act (2023) provlegala al framework. Structure: Technical Directorate (surveillance, EPR, research, labs, workforce, NCDs); Administration & Finance Directorate (HR, finance, procurement, ICT). Mandate: surveillance & disease intelligence, emergency preparedness & response, laboratory services, workforce development, NCDs & injuries, research & ethics.	Funding: initial donor support (US CDC, Africa CDC, WHO, IntraHealth, African Field Epidemiology Network (AFENET), Global Fund/UNDP); later domestic budget al.location (FY 2024–2025). Workforce: fellowship programs (Data Management, Leadership & Governance, FETP frontline & intermediate); 42 graduates (DM & LMG), 66 frontline epidemiologists trained. Infrastructure: Emergency Operations Centre, ICT systems, official website (https://phi.gov.ss), integration of MoH units into NPHI.	Enablers: strong political will, Africa CDC framework, donor/partner support, benchmarking visit to Ethiopia, high level advocacy meetings. Challenges: need for change management, transition of MoH departments, funding sustainability, and stakeholder coordination.	Short term: legal establishment, strategic plan (2022–2026), budget integration, fellowship training programs, and operational website. Long term: strengthened surveillance and workforce, institutionalised outbreak response capacity, improved governance and coordination of public health in South Sudan.
Cui et al. [30]	2023	Exploratory qualitative study	Cambodia, Colombia, Liberia, Mozambique, Nigeria, Rwanda, Zambia	Multi-country qualitative evaluation of the role of Field Epidemiology Training Programs (FETPs) within NPHIs. Data sources: 96 semi-structured interviews with NPHI staff, non-NPHI government staff, NGOs, and international partners. Focused specifically on FETP’s contribution to strengthening essential public health functions.	Varies by country (not the focus of this study). Pathways: not applicable (study examined integration of FETPs into existing NPHIs). Models: NPHIs with embedded FETPs (Frontline, Intermediate, Advanced tiers).	Governance: FETPs are often housed within NPHIs or MoHs; some challenges with academic accreditation and institutionalisation. Structure: FETPs integrated into NPHIs’ surveillance, outbreak response, and workforce development units. Mandates: surveillance, outbreak investigation/response, workforce development, scientific communication.	Funding: supported by the US CDC and partners; sustainability concerns noted. Workforce: FETPs trained frontline, intermediate, and advanced epidemiologists; graduates often hold leadership roles in outbreak response and NPHIs. Infrastructure: integration with Emergency Operations Centers (e.g., Zambia); strengthened data management and analysis systems.	Enablers: strong integration into NPHIs, donor/partner support, tiered training model, demonstrated outbreak response leadership. Challenges: lack of academic accreditation, difficulties in institutionalising FETP, limited career incentives and low salaries, and underutilization in some contexts.	Short term: improved surveillance systems, enhanced outbreak detection and reporting, stronger feedback loops between district and national levels. Long term: strengthened national workforce capacity, embedded outbreak response leadership, improved pandemic preparedness, and evidence for integrating FETP into NPHIs.
Ario et al. [31]	2022	Descriptive case study (review of establishment process and experiences)	Uganda	Case study of staged institutional development. Data sources: policy documents, stakeholder consultations, IANPHI Staged Development Tool, regulatory impact assessment, and programmatic reports. Strong example of incremental NPHI development; emphasises multisectoral collaboration and political leadership.	Initiated in 2013 (MoH vision). Presidential directive for autonomous status in 2019; legal Act pending as of 2021. Pathway: MoH task force (2013) → White Paper (2016) → Presidential directive (2019) → RIA & Bill drafting (2021). Model: networked model under MoH, moving toward autonomous parastatal.	Governance: supported by IANPHI and Africa CDC frameworks; awaiting the Act of Parliament for full autonomy. Structure: proposed 8 directorates (Epidemiology & Surveillance, PHEOC, Zoonotic/Environmental Health, Health Information, National Labs, Workforce Development, Research, Finance/Admin). Mandate: surveillance, outbreak response, labs, workforce development, research, health information, and emergency preparedness.	Funding: initiated donor-supported (CDC, IANPHI, Resolve to Save Lives, AFENET); plan for a dedicated government budget line once autonomous. Workforce: hosts Uganda Public Health Fellowship Program; trained epidemiologists and rapid response teams; strong lab workforce. Infrastructure: National Health Laboratories (launched 2016), PHEOC, integrated surveillance and sample transport networks.	Enablers: strong political leadership, IANPHI Staged Development Tool, multisectoral task force, donor/partner support. Challenges: lack of legal status, fragmented functions, reliance on donor funding, and need for stronger coordination.	Short term: faster outbreak detection (within 48 h), response within 24–48 hoursreal-time surveillancece, improved coordination. Long term: strengthened IHR core capacities, improved epidemic preparedness, cost savings through shared resources, enhanced multisectoral collaboration.
Binder et al. [32]	2021	Qualitative descriptive study (listening sessions + literature review)	Burkina Faso, Côte d’Ivoire, Ethiopia, Mozambique, Nigeria, Rwanda, South Africa, Togo, Uganda, Zimbabwe	Listening sessions with NPHI leaders (Nov 2020) + literature review. Data sources: semi-structured listening sessions with NPHI directors; PubMed/Google Scholar/grey literature review. Focused on COVID 19 response innovations and systemic changes; highlighted both immediate adaptations anlong-termrm capacity gains.	Varies by country (not the focus of this study). Pathways: not applicable (study focused on pandemic response, not creation). Models: NPHIs as government or semi-autonomous agencies aligned with MoHs.	Governance: NPHIs provided scientific advice, coordinated national responses, and engaged with the private sector and communities. Structural-level institutes with expanded labs, surveillance, EOCs, and communications units. Mandates: surveillance, outbreak response, labs, health communication, workforce training, emergency preparedness.	Funding: mix of government, donor, and private sector support (e.g., Nigeria’s CACOVID coalition). Workforce: expanded through FETPs, rapid training via virtual platforms, and redeployment of staff. Infrastructure: massive expansion of labs (e.g., Nigeria from 4 to all states); adoption of digital surveillance tools (Go.Data, SORMAS, DHIS2); use of drones, robots, SMS, WhatsApp, and ccentresters.	Enablers: public-private partnerships, innovative use of technology, Africa CDC and IANPHI support, and strong leadership visibility. Challenges: supply chain shortages, misinformation (“infodemic”), inequities in access, gaps in genomics/bioinformatics, strain on non-COVID services.	Short term: increased lab capacity, modernised surveillance, stronger subnational capacity, improved coordination. Long term: elevated visibility of NPHIs, strengthened partnerships, long-term improvements in lab and surveillance systems, highlighted the need for sustainable investment.
Verrecchia et al. [33]	2019	Policy/analytical essay (conceptual, programmatic perspective)	Global, with emphasis on Africa and low and middle-income countries	Conceptual essay highlighting the role of NPHIs and networks (e.g., IANPHI, Africa CDC) in strengthening public health systems. Draws on case examples and programmatic experiences. Advocates for peer-to-peer support and institutional networking as critical for capacity building.	Not applicable (conceptual analysis; no single NPHI establishment described). Notes that many NPHIs in LMICs were created with donor and peer support.	Governance: emphasises NPHIs as science-based, legally mandated institutions. Structure: NPHIs are positioned as central hubs coordinating surveillance, labs, workforce, and emergency response. Mandate: surveillance, outbreak response, workforce development, research, and policy advice.	Resources: highlight hts importance of donor leverage peer-to-peer support. Workforce: stresses the role of FETPs and international mentorship. Infrastructure: NPHIs benefit from shared labs, surveillance platforms, and emergency operations centers.	Enablers: international networks (IANPHI, Africa CDC), donor support, peer-to-peer mentorship, and political commitment. Challenges: sustainability of donor funding, fragmentation, and lack of legal frameworks in some countries.	Short term: strengthened outbreak response capacity, improved governance, enhanced credibility of NPHIs. Long term: institutionalised peer-to-peer support, stronger global health security, and sustainable capacity building through networks.
Meda et al. [34]	2016	Policy advocacy/correspondence	West Africa Economic Community of West African States (ECOWAS region)	Short correspondence advocating for the establishment of a West African network of NPHIs under ECOWAS/WAHO- West African Health Organisation. Draws lessons from the Ebola outbreak (2014–2016), emphasises regional coordination.	Not applicable (advocacy piece; no single NPHI established). Proposal: regional NPHI network coordinated by ECOWAS/WAHO.	Governance: proposed supranational governance under ECOWAS/WAHO, linking national NPHIs into a regional network. Structure: envisioned as a hub and spoke model with WAHO as the coordinating body. Mandate: surveillance, outbreak response, workforce development, research, and policy harmonisation among member states.	Resources: not empirically detailed; calls for leveraging donor support and regional resources. Workforce: emphasises the need for regional training and capacity building. Infrastructure: proposed shared labs, surveillance platforms, and emergency operations across member states.	Enablers: political momentum post Ebola, ECOWAS/WAHO institutional framework, IANPHI support, donor interest. Challenges: weak national NPHIs in some countries, limited funding, political fragmentation, and sovereignty concerns.	Short term: raised visibility of NPHIs and regional collaboration in West Africa. Long term: proposed model for a West African NPHI network to strengthen epidemic preparedness, harmonise policies, and improve IHR compliance across the region.
Tweed et al. [35]	2023	Perspective / conceptual analysis	Global, with case illustrations (Ukraine, Somalia, others)	Perspective piece highlighting the role of NPHIs in responding to syndemic crises (conflict, pandemics, climate change). Draws on case examples (Ukraine, Somalia) and global NPHI experiences. Advocates for NPHIs as system leaders in fragile and crisis-affected contexts.	Not applicable (conceptual analysis; no single NPHI establishment described). Uses case examples to illustrate resilience and adaptation.	Governance: NPHIs are positioned as national system leaders, coordinating across ministries and sectors. Structure: emphasises integration of surveillance, labs, workforce, and emergency response under one roof. Mandate: beyond outbreak response — includes climate change, conflict, migration, and broader determinants of health.	Resources: highlights the need for flexible, crisis-responsive funding. Workforce: stresses training in interdisciplinary skills (epidemiology, risk communication, humanitarian response). Infrastructure: calls for resilient labs, surveillance systems, and emergency operations that can function in fragile settings.	Enablers: international solidarity, IANPHI’s Stockholm Statement, peer-to-peer support, and political recognition of NPHIs as essential. Challenges: fragile states’ weak institutions, conflict disruption, limited funding, and competing priorities in crisis settings.	Short term: NPHIs provided continuity of surveillance and outbreak response during crises (e.g., Ukraine war, Somalia conflict). Long term: positioned NPHIs as anchors of resilience, integrating health security with humanitarian and development agendas, advancing the concept of “syndemic preparedness.”
Barzilay et al. [36]	2018	Methodological tool development + pilot testing	Global, with pilot applications in Colombia, Nigeria, and others	Development of the Staged Development Tool (SDT) to guide NPHI establishment and strengthening. Data sources: expert consensus, iterative tool design, pilot testing in multiple countries. The tool covers 28 domains of NPHI functions and organisational capacity.	Not applicable (tool, not a single NPHI establishment). Applied in countries at different stages of NPHI development (e.g., Colombia, Nigeria).	Governance: SDT provides a structured framework for assessing governance, legal authority, anorganisationalal maturity. Structure: tool assesses domains including surveillance, labs, workforce, emergency response, research, and policy. Mandate: supports countries in clarifying and strengthening NPHI mandates.	Resources: a tool helps identify funding gaps and resource needs. Workforce: assesses workforce development and training capacity. Infrastructure: evaluates labs, surveillance systems, EOCs, and IT platforms.	Enablerspeer-to-peerer support, country ownership of assessment, complementarity with the WHO Joint External Evaluation (JEE). Challenges: requires political commitment to act on findings, potential overlap with other assessment tooand ls, sustainabifollow-upollow up.	Short term: provided self-assessment for NPHIs, identified priority gaps, and informed strategic planning. Long term: supported incremental institutional strengthening, improved alignment with IHR (200and 5), enhanced reproducibility of NPHI development across countries.
Taame et al. [37]	2023	Editorial/policy perspective	Africa-wide (55 AU Member States)	Editorial in Lancet Global Health outlining the status of NPHIs across Africa. Advocates for the accelerated establishment and strengthening of NPHIs as part of Africa CDC’s continental strategy. Provides a high-level overview of progress and gaps.	Not applicable (editorial, not a single NPHI establishment). Summarises continental progress: 22/55 AU Member States with established NPHIs; 18 functional.	Governance: identifies three models of NPHIs in Africa — (1) autonomous/semi-autonomous institutes, (2) networks of institutions, (3) departments within MoHs. Structure: emphasises the need for legal frameworks and clear mandates. Mandate: surveillance, outbreak response, workforce development, labs, health promotion, policy advice.	Resources: highlights underfunding as a major barrier; calls for increased domestic financing. Workforce: stresses the need for training and retention of skilled epidemiologists and lab scientists. Infrastructure: emphasises the importance of labs, surveillance systems, and emergency operations centres.	Enablers: Africa CDC frameworks, IANPHI peer support, political momentum post COVID-19. Challenges: lack of legal frameworks in some countries, underfunding, limited autonomy for MoH-based models, and uneven progress across regions.	Short term: 22 NPHIs established, 18 functional, growing momentum for continental coordination. Long term: NPare HIs positioned as anchors of resilient health systems, critical for IHR compliance, epidemic preparedness, and continental health security.
Clemente et al. [38]	2020	Comparative policy analysis (secondary data review)	11 African countries (Burkina Faso, Cameroon, Côte d’Ivoire, DRC, Ethiopia, Liberia, Nigeria, Rwanda, Sierra Leone, Tanzania, Uganda)	Analysis of Joint External Evaluation (JEE) reports and NPHI status across 11 African countries. Data sources: WHO JEE reports, national policy documents, and secondary literature. Focused on how NPHIs contribute to IHR core capacities.	Varies by country. Pathways: Acts of Parliament (e.g., Nigeria CDC), Presidential decrees (e.g., Liberia), MoH directives (e.g., Rwanda Biomedical Centre). Models: autonomous institutes, MoH departments, or networks.	Governance: NPHIs provided legal authority and coordination for IHR implementation. Structure: varied — some centralised (Nigeria CDC), others integrated within MoH (Rwanda, Ethiopia). Mandates: surveillance, outbreak response, workforce development, labs, research, and emergency preparedness.	Funding: mixed — government allocations plus donor support. Workforce: FETPs embedded in most NPHIs; critical for outbreak response. Infrastructure: national labs, EOCs, surveillance platforms; uneven across countries.	Enablers: political will, donor/partner support, Africa CDC/IANPHI frameworks, lessons from Ebola. Challenges: fragmented systems, weak legal frameworks in some countries, underfunding, and reliance on external partners.	Short term: improved outbreak detection and response, better coordination of surveillance and labs. Long term: strengthened IHR core institutional functions, progress toward resilient health systems.
Erondu et al. [39]	2012 (updated in later reports)	Descriptive historical review	South Africa (National Institute for Communicable Diseases – NICD)	Historical review of NICD’s evolution from the National Institute for Virology (NIV) and other specialised units. Data sources: institutional records, outbreak reports, peer reviewed publications. Focused on NICD’s role as a national reference centre and its integration into the National Health Laboratory Service (NHLS).	Established in 2002 through the merger of the National Institute for Virology and other specialised units, under the NHLS Act. Model: semi-autonomous institute within the NHLS, reporting to the Ministry of Health.	Governance: NICD is a division of the NHLS, with oversight from the Ministry of Health. Structure: multiple centres (e.g., Centre for Respiratory Diseases and Meningitis, Centre for Emerging Zoonotic Diseases, Centre for Tuberculosis, Centre for HIV/STIs, Centre for Vaccines and Immunology, Centre for Healthcare Associated Infections, Antimicrobial Resistance & Mycoses). Mandate: national reference laboratory, surveillance, outbreak investigation, research, training, policy advice.	Funding: government allocations via NHLS, supplemented by donor and research grants. Workforce: highly specialised scientists, epidemiologists, and lab staff; training hub for FETP South Africa. Infrastructure: BSL 4 laboratory, national reference labs, surveillance systems, genomic sequencing capacity.	Enablers: strong legal foundation (NHLS Act), integration of labs and surveillance, international collaborations, donor support for research. Challenges: resource constraints in the public health sector, high burden of HIV/TB, and need for sustained investment in lab infrastructure.	Short term: rapid outbreak detection and response (e.g., listeriosis, influenza, COVID 19). Long term: established as a continental leader in lab science and surveillance, strengthened South Africa’s IHR compliance, and contributed to global health security through training, research, and reference services.

We drew the five analytic domains from the Africa CDC NPHI Development Framework and IANPHI Core Functions guidance, which outline the foundational, organizational, operational, and performance dimensions of NPHIs. We defined each domain as follows:

• I.Institutional establishment: The legal and political pathway through which an NPHI is created (e.g., Act of Parliament, Presidential/Ministerial decree), including its authorization process and structural model (autonomous, semi-autonomous, ministry-based, or networked). This domain focuses on how an NPHI comes into existence [10].
• II.Governance and structure: The NPHI’s mandate, oversight arrangements, internal organizational design (directorates, centers, divisions), and coordination mechanisms. Whereas institutional establishment concerns how an NPHI is created, governance concerns how it operates, is led, and is held accountable [18].
• III.Resources and capacity: the financial, human, and infrastructural assets enabling NPHI functioning. This includes domestic and partner financing; laboratory, surveillance, and emergency operations infrastructure; workforce size and competencies; digital and data systems; and logistical capacity [10].
• IV.Implementation factors: the enablers and barriers affecting operationalization of NPHI functions, including political commitment, partner support, legal clarity, change-management challenges, intersectoral coordination, and absorptive capacity.
• V.Outcomes and impact: reported results such as improvements in outbreak detection, response timelines, laboratory and surveillance performance, IHR core capacities, workforce strengthening, and other system-level or public-health gains. These domain definitions were applied consistently across included studies and guided the thematic synthesis.

Although the domains are analytically distinct, some conceptual overlap is inherent, particularly between institutional establishment and governance, and between resources and implementation, because NPHI development involves interdependent processes that evolve simultaneously.

Institutional establishment captures how an NPHI is legally created and configured, governance reflects how it is led and held accountable, resources refer to the financial, human, and infrastructural inputs enabling functionality, and implementation factors capture contextual enablers and barriers that influence operationalization. In applying these definitions, reviewers ensured consistent and non-duplicative coding across sources.

To visually characterize variation in how included studies addressed the five analytic domains, we developed a simple emphasis-mapping tool that applied an ordinal scale (0, 1, 2, 3) to each domain for every study. This scoring system was not a quality assessment; rather, it served as a descriptive visualization of reporting emphasis across heterogeneous sources. The scoring criteria were defined a priori as follows: 0 = not addressed, 1 = briefly mentioned, 2 = described with moderate detail, and 3 = emphasized or discussed as a central feature of the study. Two reviewers independently assigned scores to each study based on these criteria. Discrepancies were resolved through discussion to reach a consensus. This approach provided a transparent, reproducible method for summarizing emphasis patterns while acknowledging that some degree of subjectivity is inherent in narrative synthesis.

Methodological quality appraisal

Consistent with JBI guidance for scoping reviews, no formal risk of bias assessment was undertaken, as the purpose of this review was to map the breadth and characteristics of available evidence rather than to exclude studies based on quality [19]. However, the credibility of sources was considered during synthesis, distinguishing between peer-reviewed publications, institutional reports, and conceptual commentaries. This approach ensured transparency while acknowledging the heterogeneity of the evidence base.

Results

Selection of studies

The search across PubMed, HINARI, and Embase, supplemented by grey literature and handsearching, yielded 421 records after duplicates were removed. Following title and abstract screening, 373 records were excluded. 48 full-text articles were assessed for eligibility, of which 20 studies met the inclusion criteria and were synthesised.

The PRISMA-ScR flow diagram summarising the selection process is presented in Fig. 1.

Fig. 1.

Prisma-ScR flowchart: National Public Health Institutes in Africa, 2010–2025: pathways, governance, and outcomes — a scoping review

Characteristics of included studies

The 20 included studies spanned the period 2010–2025 and comprised four broad categories:

• i.Country case studies: Nigeria [20], Liberia [22], Burkina Faso [21], the Democratic Republic of Congo [24], South Sudan [29], Uganda [31], and South Africa [39, 40]. These studies documented national experiences of establishing or strengthening NPHIs through legislation, presidential or ministerial decrees, and institutional reforms.
• ii.Multi-country evaluations: US CDC–supported assessments of NPHI development and operations, conducted through the U.S. Centers for Disease Control and Prevention’s Division of Global Health Protection [23], FETP integration studies [30], Joint External Evaluation (JEE) analyses across 11 African member states [36], policy analyses on consolidation and linkages [25, 32], and other global commentaries [28]. These studies provided comparative insights into NPHI functions, integration, and system performance. In interpreting JEE-related findings, we used them strictly as contextual indicators of system capacities relevant to NPHI functions and not as evidence of NPHI establishment or institutional performance.
• iii.Continental surveys and editorials: Africa CDC mapping survey of 40 member states [27], listening sessions across 10 African member states during COVID-19 [26], BMJ Global Health conceptual essay [33], Lancet perspectives [37], and additional Africa-focused editorials [38]. These contributions highlighted continental trends, institutional challenges, and regional perspectives.
• iv.Conceptual or methodological contributions: ECOWAS/WAHO proposal for a regional NPHI [34], pilots of the Staged Development Tool [30], and pandemic preparedness perspectives [35]. These works advanced frameworks and methodological tools for NPHI development and resilience.

The evidence base was heterogeneous, drawing on peer-reviewed articles, institutional reports, policy briefs, and commentaries. This diversity reflects both the practical experiences of countries and the conceptual or methodological contributions shaping NPHI discourse.

Where global or mixed-country papers cited examples from outside Africa (e.g., China, the UK, Cambodia, Colombia), these served contextual and typological purposes only; all findings and narrative synthesis are derived from African evidence.

The emphasis scores below reflect the degree of reporting attention within each study rather than methodological quality or importance of the domain.

Fig. 2 presents the matrix of emphasis across five thematic domains.

Fig. 2.

Emphasis scores (0–3) across five thematic domains for 20 studies on National Public Health Institutes (NPHIs), 2010–2025. Darker shading indicates stronger emphasis

Across the 20 included studies, emphasis varied by domain. Governance and Outcomes show the highest emphasis across most studies. At the same time, Institutional Establishment is moderate-to-high, driven by country case studies that report legal instruments and establishment pathways (e.g., Acts, decrees, ministerial orders). Resources and Capacity receive comparatively lower emphasis overall, and Implementation Factors fall between these patterns. These findings, as depicted in Fig. 2, indicate that authors more often describe how institutes are authorized and governed, and the results they report, than they do the depth of resourcing.

As a scoping review, these domain patterns should be interpreted as reporting emphasis across sources, not as evidence of institutional performance or effectiveness.

Case-oriented papers, such as those on Burkina Faso and South Sudan, report formal legal instruments, organizational arrangements, resourcing, implementation enablers, and outcomes, and therefore score higher across multiple domains. By contrast, conceptual or perspective papers (e.g., global commentaries and “syndemic preparedness” perspectives) primarily present frameworks or lessons and provide little detail on authorization pathways or resourcing; accordingly, they score lower on Institutional Establishment and Resources & Capacity. This pattern is visible in Fig. 2 and consistent with the study types summarized in Table 1.

The heatmap (Fig. 2) illustrates these patterns at the study level, showing darker shading for governance and outcomes across most rows, while lighter shading is evident for establishment and resources in several studies. The domain-level bar chart (Fig. 3) further summarises these trends, with governance and outcomes achieving the highest average scores, followed by implementation, while establishment and resources lagged.

Fig. 3.

Average emphasis scores across five thematic domains for 20 studies on NPHIs, showing overall strengths and gaps

Together, these findings indicate greater emphasis in the literature on governance arrangements and reported outcomes, alongside less detailed reporting on institutional establishment and resourcing. The visualizations therefore, synthesize where discussion is densest across studies and where reporting is sparser, rather than implying comparative performance.

Thematic synthesis

Institutional establishment

Pathways varied across countries. Legal instruments included Acts of Parliament, for example, Nigeria’s Nigeria Centre for Disease Control and Prevention (Establishment) Act, 2018; in Liberia, the NPHI was created by an Act passed in December 2016 and signed in January 2017. Presidential decrees were used in the DRC (Décret No. 22/16 of 9 April 2022), subsequently reinforced by Ordinance-Law No. 23/006 of 3 March 2023 that amended the public health law [14]. Ministerial or executive orders/decrees also feature, for instance, South Sudan’s Ministerial Order No. 004/2019 (followed by the National Public Health Institute Act, 2023) and Mozambique’s Council of Ministers Decree 57/2017, strengthening the INS’s autonomy.

Some countries have ministry-based configurations, such as Rwanda’s Rwanda Biomedical Centre (Law No. 13/2019) and Ethiopia’s Ethiopian Public Health Institute (Council of Ministers Regulation No. 301/2013), both accountable to their Ministries of Health. Regional proposals, e.g., calls for a West African network of NPHIs under ECOWAS/WAHO, underscore the role of supranational coordination. Consistent with Africa CDC guidance and continental mappings, we treat networked/hybrid arrangements as governance/structure models (organizational configurations) rather than establishment pathways. Continental mappings also show uneven progress across Member States, reflecting political and legal variation.

Governance and structure

Governance was consistently emphasised. NPHIs were described as legally mandated, science-based authorities coordinating surveillance, laboratories, workforce development, and emergency preparedness. Three dominant models emerged:

1. Autonomous/semi-autonomous institutes (Nigeria CDC, South Africa NICD).

2. Ministry-based departments (Rwanda Biomedical Centre).

3. Networked or hybrid models (ECOWAS proposal).

Resources and capacity

Funding was often donor-driven (CDC, IANPHI, Africa CDC, Global Fund), with sustainability concerns recurring. Workforce development was strongly linked to Field Epidemiology Training Programs (FETPs). Infrastructure investments included national reference laboratories, emergency operations centres, digital surveillance platforms (SORMAS, Go. Data, DHIS2), and genomic sequencing facilities.

Across studies, staffing constraints extend beyond financing. Multicountry evaluations describe gaps in staffing numbers, skill-mix, and retention, with turnover driven by salary differentials, short-term donor contracts, and limited civil-service career ladders for epidemiology, laboratory science, and emergency operations (e.g., PHEOCs). Workforce development is cited as both an enabler (through FETP and partner-supported training) and a vulnerability when programs are not fully embedded in NPHIs and public-sector HR systems. These patterns appear alongside continental mapping that lists workforce as a core NPHI function but also reports partial domestic financing, underscoring exposure to external-funding cycles.

Implementation factors

Enablers included political commitment, legal frameworks, peer mentorship (IANPHI, Africa CDC), and donor support. Regional solidarity post-Ebola also facilitated progress. Challenges included underfunding, donor dependence, fragmented functions, weak legal authority, and difficulties in institutional consolidation. Transitioning MoH departments into new NPHIs required significant change management.

Outcomes and impact

All studies reported outcomes. Short-term impacts included faster outbreak detection (Uganda’s 24–48-hour response), rapid laboratory expansion during COVID-19 (Nigeria’s scale-up from 4 labs to nationwide coverage), and improved coordination of surveillance. Long-term impacts included strengthened IHR capacities, institutional resilience, cost savings, and enhanced credibility of NPHIs as national technical authorities. Mature institutes (South Africa NICD) demonstrated continental/global leadership, while newer institutes (South Sudan, DRC) illustrated the importance of legal frameworks and donor partnerships.

In South Africa, although the National Public Health Institute of South Africa Act (Act 1 of 2020) provides the legal mandate for establishing NAPHISA, the Act has not yet commenced; therefore, NAPHISA is not operational. As a result, the National Institute for Communicable Diseases (NICD), housed within the National Health Laboratory Service, continues to serve as the country’s de facto NPHI and remains the national hub for surveillance, diagnostics, and outbreak response [41].

Across cases, the linkage between NPHI development and outcomes is most visible in operational indicators that the studies report, such as shorter detection-to-response intervals (Uganda’s 24–48-hour window), rapid expansion of national laboratory networks during COVID-19 (Nigeria’s scale-up from a handful of labs to nationwide coverage), and documented improvements in IHR/core capacities. These metrics are consistent with the functions NPHIs are designed to coordinate and therefore provide plausible, proximal signals of impact, even as longer-term population effects remain underreported.

Evidence gaps

Few studies systematically assessed financing sustainability, performance metrics, or intersectoral integration. Limited evidence exists on long-term population health outcomes beyond outbreak response. Comparative evaluations of institutional models (autonomous vs. ministry-based) remain scarce. These gaps highlight priorities for future research and policy development.

Discussion

This scoping review provides a consolidated evidence map of the establishment, models, governance, challenges, and outcomes of National Public Health Institutes (NPHIs) in Africa between 2010 and 2025. The findings highlight both the promise and the persistent fragilities of NPHIs as anchors of health security under Africa CDC’s New Public Health Order. Several key themes emerged, including heterogeneity of establishment pathways, the centrality of governance, donor-driven resource patterns, recurrent implementation challenges, and uneven yet tangible outcomes.

Policy implications and conclusions are drawn exclusively from the African body of evidence; non-African examples in mixed-country or conceptual papers were used only to contextualize NPHI models.

Establishment pathways: political windows and legal anchoring

The review shows that NPHIs in Africa have been established through diverse legal and political instruments, including Acts of Parliament (Nigeria, DRC, South Africa), Presidential decrees (Liberia, Uganda), and ministerial directives (South Sudan, Mozambique) [42, 43]. This heterogeneity reflects broader global patterns: Binder and Adigun (2006) noted that NPHIs often emerge during “policy windows” created by crises such as epidemics, when political will is heightened. Similarly, Heymann (2006) emphasised that NPHIs thrive when they are legally mandated and insulated from political turnover. Our synthesis confirms that countries with strong legal frameworks (e.g., Nigeria CDC, South Africa NICD) have achieved greater institutional stability, while those relying on executive orders or temporary decrees remain vulnerable to political shifts and resource volatility.

By situating NPHIs within the Africa CDC’s New Public Health Order, this review underscores their critical role in strengthening national and continental health security. In November 2025, Africa CDC launched the Africa Health Security and Sovereignty (AHSS) Agenda, a continental strategy that builds on the New Public Health Order and emphasises country-led health security, sustainable domestic financing, expanded manufacturing, and digital transformation, further underscoring the central role of NPHIs in achieving resilient, sovereign health systems across the African continent.

Findings highlight the need for legal frameworks, sustainable financing, and integration into continental networks to ensure maturation and resilience. The evidence provides actionable insights for policymakers, ministries of health, Africa CDC, IANPHI, and global partners to accelerate NPHI development, harmonise governance, and advance compliance with the International Health Regulations.

Governance and structure: convergence and divergence

Governance was the most consistently emphasised domain across studies. Three dominant models emerged: autonomous/semi-autonomous institutes (Nigeria CDC, South Africa NICD), ministry-based departments (Rwanda Biomedical Centre), and networked or hybrid models (ECOWAS proposal). This mirrors global arrangements: the U.S. CDC functions as an operating division of the Department of Health and Human Services (HHS); the China CDC sits under the National Disease Control and Prevention Administration within the national health portfolio; and many European NPHIs are public agencies embedded within or supervised by ministries of health (e.g., Germany’s Robert Koch Institute, Italy’s Istituto Superiore di Sanità, France’s Santé publique France). Africa’s diversity likewise reflects administrative traditions and the influence of external financing.

Africa’s diversity reflects both political traditions and donor influence. Importantly, governance arrangements shape credibility: autonomous institutes often enjoy greater visibility and authority, but ministry-based models may integrate more seamlessly with national health systems [44]. Comparative evaluations of these models remain scarce, representing a critical evidence gap.

Resources and capacity: donor dependence and sustainability risks

Resource mobilisation emerged as a double-edged sword. Donor support (CDC, IANPHI, Global Fund, Africa CDC) has been pivotal in establishing laboratories, surveillance platforms, and workforce training programs. Field Epidemiology Training Programs (FETPs) were repeatedly identified as the backbone of NPHI workforce capacity, echoing findings from global evaluations that FETPs are “the single most important investment in sustainable epidemiologic capacity” [45]. However, sustainability remains a major concern. Experience from electronic health record (EHR) adoption in sub-Saharan Africa shows that donor-driven initiatives can fragment systems and are vulnerable to collapse when external funding wanes [46].

The parallel is striking, just as EHR systems falter without reliable infrastructure and financing, NPHIs struggle to maintain core functions without domestic budget lines. This underscores the need for governments to progressively transition from donor reliance to sustainable domestic financing.

Implementation factors: enablers and persistent barriers

Implementation enablers included political commitment, Africa CDC and IANPHI frameworks, peer-to-peer mentorship, and regional solidarity post-Ebola. These align with the “peer learning and staged development” approach advocated by IANPHI, which has been shown to accelerate institutional maturation [47]. However, challenges were equally prominent: underfunding, donor dependence, fragmented functions, weak legal authority, and difficulties in consolidating disparate units into a single institute. Taken together, the evidence suggests a structural HR gap, not only budgetary shortfalls but also insufficient headcount, uneven skill-mix, weak retention/career pathways, and incomplete institutionalization of training pipelines (e.g., FETP) within NPHIs.

These findings echo WHO’s 2021 IHR progress report, which highlighted that many African countries remain “partially functional” in core capacities due to fragmented institutional arrangements [48]. The parallels with digital health adoption are again instructive: as EHR studies in sub-Saharan Africa (SSA) revealed [49, 50] infrastructure gaps, workforce resistance, and interoperability challenges undermine sustainability. For NPHIs, the equivalent barriers are legal ambiguity, siloed functions, and fragile financing.

Outcomes and impact: tangible gains, uneven depth

Linking NPHI development to outcomes can be clarified by distinguishing proximate operational outputs from intermediate system effects and distal population outcomes. Proximate outputs, such as faster incident detection and response, activation and performance of PHEOCs, and expanded national lab coverage, are the most consistently reported and align directly with NPHI mandates. Intermediate effects include improved data integration and decision-making for IHR core capacities and multisector coordination. Distal outcomes (e.g., reductions in epidemic size or mortality) are rarely quantified in the included literature, reflecting the well-known attribution challenge in complex systems where many actors contribute.

Despite these challenges, outcomes were consistently reported. Short-term impacts included faster outbreak detection and response (e.g., Uganda’s 24–48-hour response window), rapid laboratory expansion duringCOVID-199 (Nigeria’s scale-up from 4 labs to nationwide coverage), and improved coordination of surveillance. Long-term impacts included strengthened IHR core capacities, institutional resilience, and enhanced credibility of NPHIs as national technical authorities. Mature institutes such as South Africa’s NICD demonstrated continental and global leadership, while newer institutes (South Sudan, DRC) illustrated the importance of legal frameworks and donor partnerships in early phases. These findings resonate with global literature: the US CDC’s role in polio eradication and China CDC’s role in SARS response demonstrate how NPHIs can become global leaders when adequately resourced and empowered [51].

In practical terms, studies most often used the following indicators to evidence NPHI-related outcomes:

• Timeliness indicators (detection-to-notification; notification-to-response);

• laboratory network coverage and throughput (number of functional sites; turnaround time; EQA performance);

• EPR performance (PHEOC activation and incident management);

• IHR/core capacity scores linked to surveillance, laboratories, and workforce; and.

• Workforce pipeline outputs (FETP tiers and deployment to responses). These are consistent with Africa CDC’s capacity assessments of fully established NPHIs [18].

While these indicators strengthen the plausibility link between NPHI functions and observed outcomes, they do not by themselves prove causality. Future evaluations could apply quasi-experimental designs such as interrupted time series around legal establishment, difference-in-differences using comparable countries without an operational NPHI, or synthetic controls, combined with routine indicators noted above to address confounding and strengthen causal inference [10].

Notably, JEE analyses provide system-level capacity signals rather than NPHI-specific assessments; in this review, they served to triangulate functional context, not to judge NPHI establishment or effectiveness.

Evidence gaps and research priorities

The review highlights several gaps. Few studies systematically assessed financing sustainability, performance metrics, or intersectoral integration. Evidence on the long-term impact of NPHIs on population health outcomes beyond outbreak response is limited. Comparative evaluations of institutional models (autonomous vs. ministry-based) remain absent. These gaps mirror those identified in other system-strengthening domains: for example, the Electronic Health Records (EHR) scoping review in sub-Saharan Africa (SSA) [46] found limited evidence on cost-effectiveness and long-term outcomes, despite widespread pilot projects. Addressing these gaps will require longitudinal evaluations, standardised performance indicators, and comparative policy analyses.

Implications for policy and research

Policy implications

The policy actions outlined below are derived directly from the thematic findings presented in the Discussion, reflecting recurrent patterns across establishment pathways, governance models, financing arrangements, and implementation factors:

• Legal frameworks are foundational: Countries should prioritise statutory authority for NPHIs to ensure institutional stability and credibility, reducing vulnerability to political turnover. In line with our findings, countries should prioritize statutory instruments such as Acts of Parliament, Presidential decrees, or Ministerial orders, which are the legal mechanisms most commonly used to establish NPHIs across Africa. Evidence from multiple case studies indicates that Acts of Parliament provide the strongest and most durable institutional authority, while decrees and ministerial directives can serve as interim instruments during transition phases.

• Domestic financing is critical: Governments must progressively increase budget allocations to NPHIs, transitioning from donor dependence to sustainable national funding.

• Continental integration strengthens resilience: Embedding NPHIs within Africa CDC’s New Public Health Order and regional networks (e.g., RISLNETs, IANPHI peer mentorship) can accelerate institutional maturation and harmonise standards.

• Governance models should be context-specific: While autonomous institutes often enjoy greater visibility, ministry-based models may integrate more seamlessly with national health systems. Policymakers should select models aligned with political traditions and health system structures.

• Digital health integration: Linking NPHIs with electronic health records, DHIS2, and real-time surveillance platforms can enhance data use but requires interoperability safeguards and governance oversight. At the continental level, Africa CDC is operationalizing digital public health through its Digital Transformation Strategy (2021), which prioritizes interoperable platforms, digital workforce capacity, and data governance for Member States. Complementary initiatives, such as the Africa HealthTech Marketplace (launched in 2024) and RISLNET’s development of unified IT and disease-intelligence platforms, create opportunities for NPHIs to standardize analytics, accelerate event detection, and improve decision-support across borders.

• Alignment with the AHSS Agenda provides a continental framework for accelerating NPHI development, linking national institutional strengthening to broader goals in surveillance integration, domestic financing, public health workforce expansion, and digital intelligence ecosystems.

Research priorities

• Financing sustainability: Longitudinal studies are needed to assess how NPHIs transition from donor-driven to domestically financed models.

• Performance metrics: Development of standardised indicators to measure NPHI effectiveness, resilience, and impact on IHR compliance.

• Comparative evaluations: Systematic comparisons of autonomous versus ministry-based models to identify strengths, weaknesses, and contextual suitability.

• Population health outcomes: Evidence on the long-term impact of NPHIs beyond outbreak response, such as chronic disease surveillance, health promotion, and research capacity, remains limited.

• Intersectoral integration: Future studies should examine how NPHIs collaborate with other sectors (e.g., agriculture, environment, digital innovation) to address syndemics across border threats.

Strengths and limitations

This review’s strength lies in its comprehensive mapping of diverse evidence sources, including peer-reviewed grey literature, across 20 studies synthesising findings into five thematic domains. It provides a structured framework for understanding NPHI development in Africa. However, limitations include heterogeneity of study designs, uneven reporting across countries, and reliance on descriptive rather than evaluative studies. As with other scoping reviews [52], the aim was breadth rather than depth, and no formal risk of bias assessment was undertaken. Lastly, while JEEs do not directly evaluate NPHI’s legal status or internal operations, any JJEE-linked findings in our synthesis were used only to contextualize (e.g., surveillance, laboratories, IHR coordination) and were not interpreted as evidence of NPHI establishment or performance.

Conclusion

This scoping review mapped and synthesised evidence on the establishment, models, governance arrangements, resources, implementation factors, and outcomes of National Public Health Institutes (NPHIs) in Africa between 2010 and 2025. The findings demonstrate that while NPHIs are increasingly recognised as indispensable anchors of national and continental health security, their development remains uneven and fragile. Countries with strong legal frameworks and autonomous governance models have achieved greater institutional stability and credibility, whereas those relying on temporary directives or donor-driven arrangements remain vulnerable to political and financial volatility.

Despite tangible gains, such as faster outbreak detection, expanded laboratory networks, and strengthened International Health Regulations (IHR) capacities, persistent challenges in financing sustainability, workforce development, and institutional consolidation continue to hinder progress. Evidence gaps remain particularly in comparative evaluations of governance models, long-term health outcomes, and intersectoral integration. Addressing these gaps is critical for guiding future policy and investment.

The implications are clear: NPHIs must be legally empowered, sustainably financed, and embedded within continental peer networks to mature into resilient institutions capable of safeguarding public health. Africa CDC’s New Public Health Order provides a strategic framework, but its success will depend on national governments committing to statutory authority, domestic financing, and systematic evaluation. By consolidating fragmented evidence into a coherent map, this review offers policymakers, researchers, and technical partners a foundation for accelerating NPHI development and harmonising governance across Africa.

Supplementary Information

Below is the link to the electronic supplementary material.

Author contributions

Conceptualisation and protocol development: HN, TT, HDM. Search strategy and data extraction: HN, HDM, TT. Analysis and synthesis: HDM, HN, TF. Drafting of manuscript: HDM, HN, TT. Critical revisions: HN, HDM, TH. Final approval of manuscript: All authors.

Funding

This study did not receive direct funding. The work was supported indirectly through institutional affiliations with the University of Lusaka, the University of Zimbabwe, and Africa CDC. Where applicable, authors acknowledge support from the Global Fund and other technical partners for strengthening national public health systems.

Data availability

All data used in this review were derived from publicly available peer-reviewed publications, institutional reports, and grey literature. No primary data were collected. The full search strategies and data extraction instruments are available as supplementary material.

Declarations

Ethical approval

This study was conducted in accordance with the ethical principles outlined in the Declaration of Helsinki. As a scoping review of published and grey literature, it did not involve human participants or primary data collection; therefore, ethics approval and informed consent were not required.

Disclosure

The authors declare no competing interests. The views expressed in this article are those of the authors and do not necessarily reflect the positions of their institutions or funding partners.

Consent for publication

Not applicable. This scoping review synthesizes data from publicly available sources and does not contain individual participant data, identifying images, or personal/clinical details.

Competing interests

The authors declare no competing interests.