Capacity building for genomic surveillance of mpox and other emerging diseases in resource-limited settings within the African Great Lakes region

Genomic surveillance has become an indispensable tool for the identification of pathogens and tracking of transmission chains. Building upon the global sequencing and surveillance infrastructure developed and expanded during the COVID-19 pandemic, these capacities are now being adapted to track other pathogens in low- and middle-income countries which remain disproportionately affected by infectious diseases. This is evident in the recent and unprecedented spread of mpox virus in regions experiencing multiple concurrent infectious disease outbreaks, highlighting the need for broad, adaptable diagnostic detection and sequencing capacity. In this Perspective, we describe the applications, insights, and challenges encountered during ongoing capacity building efforts for the characterization of the mpox outbreak and other emerging pathogens in the African Great Lakes Region. Schuele et al. share practical insights from collaborative initiatives across the African Great Lakes region aimed at expanding access to pathogen genomic surveillance. They highlight applications, key challenges and context specific solutions for establishing and sustaining local sequencing capacity.