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30 November 2022
African experts discuss how to improve disease surveillance using pathogen genomics and bioinformatics
The University of the Western Cape (UWC), through the South African National Bioinformatics Institute (SANBI), is playing a leading role at the ‘Beyond COVID-19: Pathogen Genomics and Bioinformatics for Health Security in Africa’ symposium being held this week at the African Union (AU) Headquarters in Addis Ababa, Ethiopia.
The three-day event brings representatives from 50 AU Member States together to discuss the continued rollout of pathogen genomics and next-generation sequencing (NGS) capacity and infrastructure across Africa. The goal is to improve the surveillance of disease outbreaks and public health responses to epidemics on the continent. Delegates are taking stock of how ready, in a post-COVID-19 world, African countries are to handle the next outbreak of a known disease such as Ebola, dengue fever or malaria, or even the emergence of an unknown so-called Pathogen X.
UWC’s Prof Alan Christoffels has, as senior advisor
to Africa CDC, helped guide the expansion of
pathogen genomics capacity in Africa.

The event is hosted by the Africa Centres for Disease Control and Prevention (Africa CDC), the autonomous health institution of the African Union (AU). SANBI director, Professor Alan Christoffels, is a Senior Advisor to Africa CDC and its Africa Pathogen Genomics Initiative (Africa PGI) and co-organised the symposium.
During the COVID-19 pandemic, SANBI has been one of the much-valued specialised centres that form part of a broader pathogen genomics network.
About the value of the “Beyond COVID-19” symposium for pathogen genomics in Africa, Prof Christoffels says: “It is important to have such a platform so that people can communicate their views and experience. It creates a sense of ownership and helps us as a continent to be more prepared for the next health emergency.
“Health officials on the continent have learnt a lot during the COVID-19 pandemic. After two years of operational work and responding, at best, to the crisis, the pandemic has now moved into a different phase. In this lies an opportunity to take stock.
“At the symposium, we are therefore getting experts from across Africa together to engage on sensitive issues such as data sharing, the transfer of biospecimens for public health responses and research. These are extremely important factors that need proper planning and national buy-in before it can be implemented,” Prof Christoffels noted.
According to Prof Christoffels, improvements in this regard has also helped African researchers and public health officials to “move from being data consumers to being data producers”.
"Before COVID-19, next generation sequencing technology was only available in public labs of seven AU member states. By 2022, it's now available in 31 African countries, and work is progressing well on helping another six countries,” Dr Sofonias Tessema, programme lead for the Africa PGI, reported at the symposium.
The Africa PGI was set up in 2019. It has since played a leading role in developing genomic capacity, infrastructure and training in AU member states.
“COVID-19 was a powerful case study for how useful next-generation sequencing technology can be used to handle public health issues and informing related decisions,” commented Mr Nqobile Ndlovu, chief executive officer of the African Society for Laboratory Medicine (ASLM), a key partner to Africa CDC.
“The pandemic is not over; it now requires a different context. COVID-19 will not be our last pandemic. We must learn from the previous to be prepared for the next,” said Dr Yenew Kebede, Acting Head: Division of Disease Surveillance and Intelligence at Africa CDC.