Abstract
Sub-Saharan Africa has made remarkable progress in genomic surveillance, with over 50% of
countries now possessing in-country sequencing capacity and 98% contributing data to global
repositories. Catalyzed by the COVID-19 pandemic, these efforts are extending beyond SARSCoV-2 to encompass antimicrobial resistance (AMR), zoonotic spillovers, and endemic diseases
such as malaria, HIV, and tuberculosis. Genomic surveillance provides real-time, high-resolution
data essential for outbreak detection, pathogen evolution tracking, and informing targeted
responses. Historically reliant on slower, less precise methods like microbiology and serology,
Africa’s public health systems are transitioning toward next-generation sequencing (NGS) and
integrated data platforms. Supported by initiatives such as the Africa Pathogen Genomics Initiative
(Africa PGI), H3AbioNet, and global partnerships, countries are investing in bioinformatics,
infrastructure, and legal frameworks for data protection. However, challenges remain in workforce
development, data analysis capacity, and ensuring timely and actionable outputs. Lessons from
high-income countries underscore the benefits of embedding genomics into public health, where
timely variant detection, rapid data sharing, and cross-sectoral partnerships have proven critical.
Africa’s genetic and epidemiological diversity provides a unique advantage for leading innovation
in pathogen surveillance. Strategic priorities now include strengthening regional networks,
harmonizing data systems, and securing sustainable funding.
This paper explores Africa’s evolving genomic surveillance landscape, highlighting transformative
progress and key opportunities to embed genomics into resilient, equitable health systems. With
sustained investment and collaboration, Africa is positioned not only to address current health
threats but also to shape the future of global health security