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Genomics Capacity in Africa
In the face of global health threats, robust genomic surveillance is more critical than ever. This innovative approach to monitoring pathogens allows scientists to track the genetic evolution of viruses and bacteria, providing real-time data that informs vaccine development, treatment plans, and public health interventions. For regions like Africa, where the burden of infectious diseases remains high, strengthening genomic surveillance is a priority and a necessity for safeguarding public health and preparing for future outbreaks.
The Accelerating Genomics-based Surveillance for Disease-Causing Pathogens in South Africa Project , supported by the World Bank through the Health Emergency Preparedness and Response Trust Fund (HEPR TF) and led by the Centre for Epidemic Response and Innovation (CERI), is revolutionizing genomic surveillance capabilities across Africa. This project, launched in June 2022, is transforming genomic sequencing capacity on the continent, enabling a more proactive approach to tracking and managing not just COVID-19 but a range of infectious diseases that pose ongoing threats to the continent.
Genomic Surveillance Capacity Building
The project has supported the sequencing of over 10,000 SARS-CoV-2 genomes, with 4,277 sequences uploaded to GISAID, a global platform for sharing viral data. CERI and its partners have continued to sequence samples, even though there has been a decrease in COVID-19 cases and testing across the world. Despite the dominance of the Omicron variant since 2021, hospitalization rates stayed manageable, demonstrating the ongoing value of genomic surveillance in monitoring the virus.
The project’s scope expanded beyond COVID-19 to include genomic surveillance efforts targeting other pressing health concerns, such as malaria, cholera, and influenza. This is made possible through the strengthening of the Network for Genomics Surveillance in South Africa (NGS-SA), a consortium that unites laboratories across the country, including CERI, to sequence and track pathogens in real time. CERI, as a key member of NGS-SA, plays a central role in these efforts. The project supports NGS-SA by providing essential resources such as equipment, reagents, and skilled personnel to enhance genomic surveillance capacity. Through this collaboration, CERI and NGS-SA have become powerful tools in safeguarding public health across Africa, allowing for faster and more effective responses to both emerging and ongoing health threats.
Building a Stronger, Healthier Africa
The future of genomic surveillance in Africa is bright. CERI is also a specialized genomics facility of the Africa Centres for Disease Control’s Pathogen Genomics Initiative (PGI). CERI’s mandate in this role is to support and provide genomics sequencing and training to other National Public Health Institutes (NPHIs), academic, and non-governmental organizations in Africa. The World Bank has played a pivotal role in building this capacity across the continent by supporting genomics training, expanding bioinformatics expertise, and empowering laboratories across the continent. Through this project CERI has trained over 600 scientists, laboratory technicians and public health personnel from across the continent.
By hosting fellows from countries such as Nigeria, Mozambique, Kenya, Ghana, Senegal, Zambia, and Uganda, CERI fosters collaboration across borders, enhancing the collective capacity for genomic surveillance and research. This pan-African approach is key to ensuring a coordinated response to infectious diseases and strengthens the continent’s ability to address future health challenges. The skills and knowledge gained from these training sessions empower local laboratories to continue conducting high-level genomic research, ensuring that Africa remains at the forefront of epidemic preparedness and response.
Once fellows return to their home institutions, they are better equipped to respond to ongoing and emerging epidemics. There are already several success stories. For example, Dr. Abdou Padane from the Institut de Recherche en Santé de Surveillance Epidémiologique et de Formation (IRESSEF) in Senegal, has been at the forefront of initiating and establishing viral surveillance in West Africa since his return to Senegal.
Dr. Padane was awarded a long-term fellowship in 2022 and spent several months at CERI in South Africa to gain experience in Whole Genome Sequencing (WGS) and epidemic response. Upon his return to Senegal, he established the WGS technologies at IRESSEF that has enabled him to characterise both past and emerging outbreaks of dengue and chikungunya virus (CHIKV). In July 2023, CERI supported Dr. Padane and his team at IRESSEF to produce, for the first time, CHIKV genomes in Senegal. This support enabled the IRESSEF team to conduct real-time genomic analysis during the 2023 CHIKV outbreak in the country.
The project has also assisted several other countries by providing sequencing services or providing reagents, ensuring that these nations can effectively respond to emerging health threats.
Read the full article at the World Bank website:
