Infectious diseases pose a considerable threat to health in Africa — a threat that is compounded by an unpredictable rise in emerging and re-emerging infections, with more than 100 disease outbreaks reported annually within the continent1. In addition to the COVID-19 pandemic, Africa has grappled with three Ebola virus epidemics, a re-emergence of Marburg virus, continued antimicrobial resistance, and increased burden to health-care systems.

Effective control and monitoring of these disease threats have been successfully demonstrated in high-income countries, mainly in Europe and North America, in which next-generation sequencing (NGS) analysis of pathogens has been incorporated into disease surveillance systems, allowing for timely and in-depth pathogen characterization.

In high-income countries, prompt response to disease threats is facilitated by access to a critical mass of genomics and bioinformatics expertise, amassed over time and embedded in strong collaborative networks (Box 1). By contrast, fragmented surveillance systems in Africa required a multifaceted strategy to respond to COVID-19; notably, the mobilization of resources for 55 countries; the coordination of logistics to ensure timely deployment of equipment, supplies and reagents; and the provision of training in SARS-CoV-2 analytics to detect genetic variants and understand disease transmission.

The sustained use of genomics in Africa throughout the period 2020–2022 has been widely acknowledged. Its success can be ascribed to heightened coordination among regional bodies such as the Africa Centers for Disease Control and Prevention (Africa CDC), the World Health Organization Regional Office for Africa (WHO-AFRO), the West African Health Organization (WAHO) and others.

Local expertise was harnessed through a coordinated NGS pathogen surveillance network across Africa, supported by industry partners and funding agencies2,3. Unfortunately, the anticipated increase in NGS data has not been accompanied by adequate data management infrastructure within individual countries or across the continent. Nevertheless, the continental response to COVID-19 showed marked improvements in throughput, leading to reduced times to generate viral genome data4, which was facilitated by sustained regional-led capacity building, training and quality-assurance efforts. Evidence obtained from the African Pathogen Genomics Initiative, a project by the Africa CDC, identified data governance, including data sharing mechanisms, as a key element of a functional and real-time disease surveillance system in the continent.

Ethical data sharing

Data sharing has been recognized as essential in a public health emergencies, underpinned by core principles such as ethics, timely response, equity, accessibility, transparency, fairness and quality5. Unlike other disease outbreaks, the COVID-19 pandemic saw an unprecedented sharing of viral genome data that has shaped global public health policies6. The success of this data-sharing strategy, including that observed in low- and middle-income countries (LMICs), can be attributed to increased access to NGS technology2 and perceived trust in international data repositories7.

However, researchers have raised concerns about a lack of equitable data-sharing protocols during the pandemic7. Recently, the ethics and data-sharing working group of the Public Health Alliance for Genomic Epidemiology (PHA4GE) outlined an ethical benefit-sharing framework for human genomics research8, addressing at a practical level many of these concerns. As such frameworks mature and become embedded in genomics initiatives, other elements of the data life cycle, such as data management and data storage, must also be interrogated.

Africa has a proven track record of leading international genomics projects that harness the rich genetic diversity of the continent9. However, these initiatives do not include a centralized African archive that can stand alongside global repositories. Although data cleaning is typically conducted locally, existing protocols prioritize the archiving of data to offshore facilities. The pervasive assumption is that there is no support for an African equivalent to the International Nucleotide Sequence Database Collaboration (INSDC). However, progress is being made in federated data-sharing approaches10.

During the COVID-19 pandemic, the Africa CDC established a technical working group to lead extensive continental stakeholder engagement meetings across 37 countries. The aim was to develop a vision for a data governance platform that can accelerate data sharing during disease outbreaks. Key factors were identified that can hinder, but also aid, efforts to incorporate genomics into disease surveillance across Africa, beyond COVID-19, with data governance a key unifying motif.

Data infrastructure

Countries that have consistently invested in genomic technology and laboratory infrastructure demonstrated rapid national responses to COVID-19 (Box 1). With a few exceptions, this was not the case in Africa. A potentially game-changing pre-pandemic decision by the Africa CDC to strengthen NGS capacity across the continent was compromised by limited investment in data infrastructure. Putting this capacity in place requires a continent-wide vision that is adopted by local, regional, and international stakeholders to minimize duplication.

Data protection

A close look at Africa’s personal data protection landscape shows that there has been a concerted effort among several countries to develop legal frameworks to protect personal data11. Nevertheless, evolving data protection policies across the continent creates uncertainty and no impetus for harmonization of policy frameworks across borders, or adherence. Establishing national pathogen surveillance policy frameworks can address these gaps.

Data access

Data protection (security of data) must be disentangled from data privacy (data governance) and its associated administrative compliance processes. For transparent and trusted data storage, continental and global data management and sharing standards must be adopted by all players. The COVID-19 pandemic provided the impetus to explore solutions to these complex concerns and opened doors for suitable public–private partnerships.

Laboratory surveillance systems

The Integrated Disease Surveillance and Response (IDSR) strategy aims to improve disease surveillance and the use of data for timely detection of and response to communicable and noncommunicable diseases in African countries. In line with the IDSR, Africa has a track record of quality surveillance data monitoring of disease outbreaks such as Ebola12, mpox13 and polio14. These programs would benefit from genomics technologies to deliver an even better public health service.

Core digital platform capabilities

The continental drive for genomic surveillance of SARS-CoV-2 has re-ignited discussion on the need for a trusted African genome archive to strengthen the broader uptake of genomic technology and data governance in Africa. It is possible to imagine the INSDC as a federation across seven continents, with the genomic scientific community contributing their data to localized repositories that can interface with the rest of the world.

The ever-increasing data stream generated by NGS data analytics across Africa should support an ecosystem that informs data-driven decisions to prevent and respond to locally relevant diseases (Fig. 1). The complexity of the genomics landscape in Africa to support disease surveillance lies not only in managing volumes of data but in the ability to integrate data streams among a wide range of stakeholders.

Fig. 1: A pathogen genomics ecosystem for Africa.
figure 1

The complexity of the genomics landscape in Africa to support disease surveillance requires integrated data streams among public health practitioners, scientists, technology providers, government and health workers. NPHIs, National Public Health Institutes.

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A continental technology roadmap for a trusted data platform for routine pathogen data management in general and for immediate application to SARS-CoV-2 genome data was conceptualized through a series of stakeholder workshops during the past two years. These continental workshops gave rise to the Africa CDC-Africa Pathogen Genomics Initiative (PGI) data architecture technical working group (DTWG), who identified core digital platform capabilities as well as the associated management and support intrastructure that will realize the envisaged African pathogen genomic shared data platform (Table 1). The continental roadmap has started with an initial technical and stakeholder implementation of our data platform. It is being built in parallel with political and legal consultation to refine data-sharing agreements and support national data governance frameworks. The six pillars for such a platform would be: adoption and change management; program management; user experience; data products and data services; data management; and core infrastructure.

Table 1 Pillars of an African pathogen genomics shared data platform for disease surveillance
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Open-source technology platforms

Open-source technology platforms are key drivers of innovation and accelerate genomics discovery, as demonstrated by visualization tools15, workspace and application management systems16,17,18, data management platforms (https://www.overture.bio/documentation/) and others. There is an immediate need for a pilot data management platform to accommodate locally produced SARS-CoV-2, Ebola and Mpox genomic data, with built-in flexibility for other relevant pathogens. This platform is already being built to reduce turnaround time from sample collection to sharing, enable real-time genomic data utilization for public health decision making, and empower the overall pathogen genomic data sharing ecosystem across the continent.

Federated data management

Federated data can be made available as objects using a standardized application programming interface (API), the ‘S3 API’. This API is implemented by commercial cloud vendors such as Amazon Web Services, Microsoft Azure and Google Cloud as well as software such as Ceph Object Gateway, OpenStack Object Storage and MinIO. These implementations enable data owners in public health and the wider scientific community to decide on the best architecture for their data storage, taking into account legal, policy and technical constraints. The shared data platform will be implemented on Amazon Web Services, Microsoft Azure and Google Cloud to future-proof the shared pathogen genomics archive and ensure that it does not suffer from vendor lock-in

Pathogen analysis tools

A wide range of pathogen analytics tools15,19,20,21,22 is tailored for public health use, but few funding opportunities are available globally to develop methods or algorithms for the public health setting. Global initiatives such as the PHA4GE have attempted to break this implementation barrier by providing resources to catalyze collaborations in public health laboratories.

Helpdesk support

Core support functions for genomics and bioinformatics queries are usually handled as requests on social media, via emails, bioinformatics-specific Slack communities, or helpdesks driven by the research community23. A pan-African pathogen genomics helpdesk (https://africapgi.freshdesk.com) has already been established to leverage existing expertise within the African pathogen genomics ecosystem and beyond, and will evolve towards multi-lingual support.

Data curation

Careful curation of data submitted to a shared data platform will be essential to ensure that researchers adhere to the FAIR principles of data management24. Partnering with the international biocuration community will help to develop and nurture a cohort of curators that can support an evolving genomics archive in LMICs.

A global imperative

Data management and analytics to support data-driven decision making in public health is a global imperative, requiring continuous engagement with international disease surveillance stakeholders and technology platform developers. The response to future pandemics must be balanced against measures to tackle current disease outbreaks affecting the African continent, which place great burden on health-care systems. An African pathogen genomics shared data platform would seek to consistently implement capabilities, processes, resources, and systems for cost-effective NGS data analytics to respond to current disease outbreaks and potential future threats.