African Scientists Set Genomics ‘World Speed Record’ in Confirming Ebola Case

In a milestone for Africa’s genomic surveillance capabilities, scientists in Uganda and South Africa confirmed within 24 hours that Ebola was the cause of death of a 32-year-old nurse at Mulago Supra-National Hospital in January 2025. This swift diagnosis was made possible by a collaborative genomic response team that had, just a few years ago, been shaped by the exigencies of the COVID-19 pandemic.

The confirmation of Sudan Virus Disease (SVD), one of the six strains of Ebola virus, was not only crucial for public health officials in determining the origin of the infection, but also in ruling out a resurgence of the more recent and widely feared 2022 outbreak. Uganda has endured five Ebola outbreaks since 2000, making it the second most affected African country after the Democratic Republic of Congo.

A Race Against Time

Led by Dr Isaac Ssewanyana, Director of Laboratory Services at the Central Public Health Laboratories (CPHL) in Uganda, a dedicated team of scientists worked overnight in January, camping out in their offices to sequence and analyse the viral genome. They confirmed the results from the initial PCR tests, then began whole genome sequencing (WGS)—a powerful method that allows for deep insight into viral mutations and origin.

“We had one night, one chance, to give the country clarity,” said Dr Ssewanyana.

The results were crucial. They showed that the virus shared more genetic similarity with the 2012 Luwero outbreak than the 2022 strain, refuting concerns that a chain of undetected infections from the 2022 outbreak had persisted undetected.

Scientific Solidarity Across Borders

This scientific achievement was underpinned by collaborative networks built during COVID-19, particularly between Uganda’s CPHL and the South African National Bioinformatics Institute (SANBI) at the University of the Western Cape.

“What we achieved might be something close to a world speed record for genomic surveillance,” said Peter van Heusden, a SANBI researcher who previously contributed to South Africa’s first sequencing of SARS-CoV-2 in 2020.

Using genomic data, SANBI bioinformaticians helped Ugandan scientists construct a phylogenetic tree tracing the current Ebola strain’s lineage. According to Prof Alan Christoffels, SANBI Director, their analysis ruled out ongoing transmission from undetected cases linked to the 2022 outbreak.

“This confirmation was essential in guiding Uganda’s Ministry of Health to make informed decisions on response and containment,” Christoffels explained.

An African Model for Genomic Health Preparedness

The speed and success of the operation reflect Africa’s growing self-reliance in genomics, a field that was once heavily dependent on foreign labs. The CPHL–SANBI partnership demonstrates how regional collaboration and the legacy of COVID-19 investments can catalyse Africa’s ability to respond to future outbreaks.

“We were ready. We had the equipment, the expertise, and we had each other’s phone numbers,” said Van Heusden.

Their findings have since been shared globally via platforms like virological.org and Pathoplexus, to encourage international cooperation in managing epidemics.

Looking Ahead

This joint initiative sets a new benchmark for rapid response and information sharing in Africa’s fight against infectious disease. With persistent threats such as Ebola, Lassa fever, and Marburg virus, experts say intra-African collaboration, not only in genomics but across the health spectrum, is essential for effective continental response.

“This case shows what Africa can do when we work together and invest in our own capacities,” said Dr Ssewanyana. “We are not just responding — we are leading.”

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Source: Nature