The African continent is a hotspot for frequent disease outbreaks, with more than 160 public health events reported in 2023 alone. Coupled with the high burden of endemic diseases, malnutrition, the impact of climate change, and rising non-communicable diseases, these factors have not only strained Africa’s health systems but have also spotlighted critical gaps in our early warning surveillance, laboratory systems, and response capabilities.
The COVID-19 pandemic brutally exposed these vulnerabilities, revealing a pressing need for robust systems capable of withstanding global health threats. At the core of strengthening these systems is the advancement of molecular diagnostics and pathogen genomics sequencing—a powerful tool instrumental in rapidly detecting and responding to health threats. This capability allows for the integration of timely detection and genomic surveillance into core public health functions and enhances data-sharing mechanisms, enabling crucial evidence-based decision-making.
Collaboration remains a cornerstone of these efforts. The Africa Pathogen Genomics Initiative (Africa PGI), a public-private partnership of the Africa CDC with Bill and Melinda Gates Foundation, Illumina Inc, ASLM, and other partners, has paved the way in expanding genomics and bioinformatics capacity in the continent. Mastercard Foundation’s Saving Lives and Livelihoods initiative, further scaled up pathogen genomics labs during the pandemic and beyond. These partnerships aim to strengthen continental molecular diagnostic and pathogen genomics capacity and exemplify how public, philanthropic, and private sectors can unite to democratize cutting-edge medical technologies across Africa.
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The continent has come a long way. Sequencing capacity has expanded from 7 African Union member states in 2019 to 40 in 2023, with a further six labs opening this year – en route to the goal of reaching all 55 member states by 2025. This expansion is also supported by the Africa Pathogen Genomics Initiative, which has facilitated the diagnosis and sequencing of multiple pathogens including SARS-COV-2, Ebola virus, Mpox, Dengue, and Cholera cases and has established a robust continental genomic surveillance network and sample referral system. By integrating genomic surveillance into core public health functions and fostering enhanced data-sharing mechanisms, these initiatives are setting a new standard for evidence-based decision-making across the continent.
Training and developing a skilled workforce is foundational to these endeavors. Africa CDC’s comprehensive training programs have equipped hundreds of experts with necessary skills in laboratory technologies, genomics, bioinformatics, and data interpretation. These efforts are crucial for building long-term genomic science capacity. And they are directly supporting global health security, particularly in combating antimicrobial resistance (AMR) and other epidemic prone diseases.
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AMR presents a grave global threat, with infections caused by antimicrobial resistant pathogens claiming more lives annually than either malaria or HIV. Africa, bearing the heaviest burden, has seen a rise in drug-resistant diseases, which thrive under conditions of poverty and inequality. The continent is actively combating this silent epidemic through initiatives like the African Union Framework for Antimicrobial Resistance Control, which aims to enhance awareness, advocate for effective policies, and engage community organizations in the fight against AMR, considered one of the next major global health threats.
The Africa CDC aims to foster and advance collaboration among national public health laboratories, international partners, and academia to enhance laboratory and surveillance systems, timely data sharing, and data-driven decision-making. This collective action exemplifies the power of partnerships in optimizing and strengthening genomics and bioinformatics capabilities across the continent.
Looking ahead, the potential applications of genomics in public health are vast. The Africa CDC is poised to enhance regional and global health security by advancing the use of innovative technologies and strategies, such as wastewater surveillance. These tools are essential for strengthening early warning systems and ensuring a rapid response to infectious disease outbreaks. Global health security relies on strong data management systems, timely data sharing, and extracting meaningful insights from different data sources to inform interventions. The Equitable Pathogen Access and Benefit Sharing System, as part of the Pandemic Agreement, is critical to strengthen data capacity in Africa and ensure timely sharing.
The journey to bolster Africa’s genomics capacity is both challenging and promising. If Member States, governments and funders support expansion by continuing to invest in strategic partnerships, comprehensive training, and innovative technologies, Africa can lead the way in building resilient health systems. Such systems – and public-private partnerships are vital not only for the continent’s well-being but also for the global community, as they enhance our collective ability to anticipate, detect, and respond to future health threats.
