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 (Figure 2).
By hosting fellows from countries such as Nigeria, Kenya, Ghana, 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. In addition to contributing to the growing number of whole CHIKV genomes sequenced from Senegal, the analysis revealed a novel strain of the West African genotype, distinct from previous outbreaks. The identification of a novel strain underscores the importance of continuous surveillance and the need for targeted interventions.
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.
Continuous Advancements in Genomic Capabilities: Pioneering Innovation with the NovaSeq X Plus
The project has also enabled the expansion of the laboratory capabilities in South Africa. CERI recently acquired a NovaSeq X sequencing platform. This advanced equipment brings cutting-edge capabilities to the continent, making sequencing more cost-effective and significantly expanding its potential beyond pathogen detection to include whole-human genome sequencing, which is a crucial step in addressing Africa's unique health challenges.
High-capacity, local sequencing in South Africa is now a reality, eliminating the need for samples to be shipped internationally. This development not only accelerates the pace of discoveries in healthcare, agriculture, and biodiversity but also fosters scientific independence within the continent. With its unmatched speed, accuracy, and efficiency, the NovaSeq X offers cost-competitive sequencing aligned with global standards. By enabling affordable and accessible sequencing of African samples on African soil, this innovation strengthens regional scientific capabilities, supports critical public health genomics, and positions Africa as a leader in the global genomics landscape.
Voices from the Field: Participant Reflections
The success of CERI's training programs is best reflected in the voices of the scientists and researchers who have taken part. These participants, from diverse African nations, have not only gained invaluable skills but have also highlighted the importance of such opportunities in advancing medical research and public health efforts across the continent. Their testimonials showcase the real impact of CERI's initiatives, while extending gratitude to the funders who make these opportunities possible.
Andrew Musyoki, Senior Lecturer and Scientist at Sefako Makgatho Health Sciences University, South Africa:
“Amazing ideas shared during the CERI Training. So much to learn and absorb! Grateful for this opportunity. Thank you to CERI and the World Bank for making this possible.”
Eric Tshitona, One Health specialist from National institute of Health in the Democratic Republic of Congo:
“Investing in skills that transcend multiple disciplines and have cross-cutting applications in various fields of medical research is the way to go! A huge thank you to CERI, KRISP, and the funder World Bank for making this training possible. Your support is invaluable.”
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Plácida Iliany Maholela, Researcher at the National Health Institute (INS) of Mozambique:
“The hands-on training we received at CERI has been instrumental in improving our pathogen sequencing and bioinformatics efforts in Mozambique. This would not have been possible without the generous support of CERI and the World Bank—thank you!”
These testimonials reflect the diverse backgrounds and goals of the fellows, united by a shared commitment to improving public health through cutting-edge genomics. To hear directly from more participants, check out this YouTube playlist, where fellows share their experiences and insights from the training sessions.
As the world shifts its focus from the immediate threat of COVID-19 to broader health challenges, genomic surveillance will remain a cornerstone of Africa’s public health strategy. The infrastructure, knowledge, and collaborations established through this project will protect the region from current infectious diseases and help prepare it for future outbreaks.
The project is more than just a response to a pandemic but a long-term investment in Africa’s health system resilience. By fostering international cooperation, advancing cutting-edge research, and strengthening local capacities, CERI and its partners are ensuring that Africa is equipped to face whatever health challenges lie ahead.
CERI, supported by the World Bank, continues to seek collaborations in and beyond Africa to advance genomic surveillance for better preparedness and capacity building. Those interested in partnering with CERI, receiving training from CERI and other opportunities can sign up to receive notifications via The Gem.
This article was written by Professor Tulio de Oliveira and Daniel Dulitzky
