Revolutionizing Public Health in Africa: Genomic Surveillance and Capacity Building

The project has already made substantial strides in improving genomic surveillance capabilities, particularly in South Africa, which is leading the way.

In an era of growing global health threats, the need for robust and proactive genomic surveillance has never been clearer. This critical tool allows scientists to track pathogens’ genetic evolution in real time, enabling the development of vaccines, treatment plans, and public health interventions. For regions like Africa, where infectious diseases remain a significant burden, strengthening genomic surveillance is essential to safeguard public health and prepare for future outbreaks.

One of the leading initiatives in advancing genomic surveillance across Africa is 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), the project aims to revolutionize pathogen monitoring across the continent. Launched in June 2022, it is playing a key role in tracking a variety of infectious diseases, including COVID-19, malaria, cholera, and influenza.

Transforming Genomic Surveillance Across Africa

The project has already made substantial strides in improving genomic surveillance capabilities, particularly in South Africa, which is leading the way. By enabling the sequencing of over 10,000 SARS-CoV-2 genomes, CERI has significantly enhanced the country’s ability to monitor viral evolution. As of now, 4,277 of these sequences have been uploaded to GISAID, a global platform dedicated to sharing viral genomic data. Despite the global decline in COVID-19 cases and testing, CERI continues to sequence samples, underscoring the importance of maintaining strong surveillance capabilities.

While much of the focus has been on COVID-19, the project’s reach extends far beyond the pandemic. It now targets other pressing health concerns like malaria, cholera, and influenza, with the Network for Genomics Surveillance in South Africa (NGS-SA) playing a pivotal role in this expanded effort. NGS-SA brings together laboratories from across South Africa, including CERI, to monitor pathogens in real time, allowing for faster, more efficient responses to emerging health threats. Through its partnership with NGS-SA, the project has helped provide essential resources like sequencing equipment, reagents, and skilled personnel, strengthening the entire surveillance network.

Building a Stronger, Healthier Africa

The long-term vision of this project goes beyond monitoring current outbreaks; it is about preparing Africa for future health challenges. A key component of the project’s success is the capacity-building efforts that empower local scientists and health professionals to independently manage genomic surveillance in their own countries. CERI’s role as a specialized genomics facility of the Africa Centres for Disease Control (Africa CDC) under the Pathogen Genomics Initiative (PGI) highlights this commitment. Through this initiative, CERI provides training and support to National Public Health Institutes (NPHIs) and other stakeholders across the continent.

The World Bank’s involvement in the project has been instrumental in fostering collaboration and building the infrastructure necessary to scale up genomic research in Africa. Over 600 scientists, laboratory technicians, and public health personnel have received training, equipping them with the skills needed to contribute to cutting-edge research in genomics and bioinformatics. In addition to fostering skills in genomic sequencing, the project has played a key role in expanding Africa’s bioinformatics expertise, which is crucial for analyzing large genomic datasets.

Pan-African Collaboration: A Model for Global Health Security

The training sessions organized by CERI have brought together professionals from across the continent, fostering a pan-African approach to genomic surveillance. The project’s fellows come from a wide range of African countries, including Nigeria, Kenya, Ghana, Zambia, and Uganda, with each bringing a unique perspective to the shared goal of improving public health. These collaborations are vital to ensuring a coordinated response to emerging infectious diseases and building a network of expertise that spans the entire continent.

One standout example is Dr. Abdou Padane, who participated in a long-term fellowship at CERI in 2022. After returning to Senegal, Dr. Padane spearheaded the establishment of Whole Genome Sequencing (WGS) capabilities at the Institut de Recherche en Santé de Surveillance Epidémiologique et de Formation (IRESSEF). In July 2023, with the support of CERI, Dr. Padane and his team conducted real-time genomic analysis during a Chikungunya virus (CHIKV) outbreak in Senegal, marking a significant milestone for genomic surveillance in West Africa.

This type of cross-border collaboration and knowledge-sharing is key to ensuring that the continent can respond effectively to future health emergencies. Countries benefiting from CERI’s support have received sequencing services, reagents, and essential resources, which have helped them address current and emerging public health threats.

Advancing Laboratory Capabilities: NovaSeq X Plus

One of the most exciting developments in this project is the acquisition of the NovaSeq X Plus sequencing platform, which has greatly expanded South Africa's genomic sequencing capabilities. This cutting-edge technology allows for more cost-effective sequencing and has the potential to address a wide array of health challenges, including whole-human genome sequencing. By enabling high-throughput sequencing locally, the NovaSeq X Plus eliminates the need for sending samples abroad, reducing turnaround times and fostering scientific independence in the region.

This platform supports not only pathogen detection but also provides crucial insights into Africa's unique health challenges, enabling the continent to become a leader in global genomics. With its speed, accuracy, and efficiency, the NovaSeq X strengthens Africa’s scientific capabilities, bolstering public health genomics and enhancing the region’s ability to tackle emerging diseases.

Voices from the Field: Real Impact

The success of this initiative is most evident through the voices of the fellows and participants who have benefited from CERI’s training programs. These professionals, coming from diverse backgrounds, have not only gained valuable skills but have also seen firsthand the transformative impact of the project on public health efforts across the continent.

Andrew Musyoki, a Senior Lecturer and Scientist from Sefako Makgatho Health Sciences University, South Africa, shared his gratitude: “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, an One Health specialist from the National Institute of Health, Democratic Republic of Congo, expressed his appreciation for the interdisciplinary nature of the training: “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.”

Plácida Iliany Maholela, a researcher at the National Health Institute (INS) of Mozambique, reflected on how the hands-on training has improved their sequencing efforts: “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 highlight the importance of such training programs in advancing public health and medical research across the continent. They also reflect the deep sense of gratitude and recognition for the support provided by CERI and its partners.

Ensuring Long-Term Health Resilience

As the global focus shifts from the immediate threat of COVID-19 to broader health challenges, the continued investment in genomic surveillance will remain a cornerstone of Africa's public health strategy. The infrastructure, knowledge, and partnerships established through the Accelerating Genomics-based Surveillance for Disease-Causing Pathogens in South Africa Project are helping to strengthen the region's ability to respond to both current and future health emergencies.

This project is more than just a response to a pandemic; it is a long-term investment in Africa’s health system resilience. By fostering international collaboration, advancing research, and strengthening local capacities, CERI and its partners are ensuring that Africa is prepared to face the health challenges of tomorrow.

CERI, with continued support from the World Bank, remains committed to advancing genomic surveillance and capacity building not only within Africa but globally. Those interested in collaborating with CERI or participating in its training programs can sign up for notifications through The Gem, ensuring that opportunities for collaboration and capacity building continue to grow.