Translation of genomic epidemiology of infectious pathogens: Enhancing African genomics hubs for outbreaks

Oboh, Mary Aigbiremo; Omoleke, Semeeh Akinwale; Ajibola, Olumide; Manneh, Jarra; Kanteh, Abdoulie; Sesay, Abdul-Karim; Amambua-Ngwa, Alfred

BACKGROUND: Deadly emerging infectious pathogens place unprecedented challenge on health systems and economies, especially across Africa where health care infrastructures are weak, and poverty rates remain high. Genomic technologies have been vital in enhancing the understanding and development of intervention approaches against these, such as Ebola, and recently the novel coronavirus disease 2019 (COVID-19). DISCUSSION: Africa has contributed a limited number of SARS-CoV-2 genomes to the global pool in growing open access repositories. To bridge this gap, the Africa Centre for Disease Control and Prevention (ACDC) is coordinating initiatives across the continent to establish genomic hubs in selected well-resourced African centres of excellence. This will allow for standardisation, efficient and rapid data generation and curation. However, the strategy to ensure capacity for high-throughput genomics at selected genomics hubs should not overshadow the deployment of portable, field-friendly and technically less demanding genomics technologies in all affected countries. This will enhance small scale local genomic surveillance in outbreaks, leaving validation and large-scale approaches at central genomic hubs. CONCLUSION: The ACDC needs to scale-up its campaign for government support across African Union countries to ensure sustainable financing of its strategy for increased pathogen genomic intelligence and other interventions in current and inevitable future epidemics in Africa.