Mapping Disease Emergence in Africa
Prof Houriiyah Tegally’s Wellcome-funded research programme brings genomics, data science, and environmental insight together to better understand how infectious diseases emerge and spread across Africa.
Understanding why some pathogens spill over into human populations – and why some go on to spread while others do not – is one of the most complex and urgent challenges in global health. For Prof Houriiyah Tegally, Head of Data Science at the Centre for Epidemic Response and Innovation (CERI), this question sits at the centre of a new research programme supported by a prestigious Wellcome Career Development Award.
Her project focuses on pathogen emergence and expansion in Africa, a region where ecological diversity, rapid urbanisation and shifting environmental conditions are reshaping how diseases move between animals and people. By developing new analytical approaches, the work aims to better understand the conditions that allow pathogens to spill over, establish, and expand.
“This project will bring together genomics, epidemiology, and advanced data science through an integrated, multi-layered analytical framework designed to capture the full complexity of pathogen transmission in changing environments,” Prof Tegally explains.
At its core, the research integrates multiple data streams to build a more complete picture of disease dynamics. Genomic data is used to reconstruct how pathogens evolve and spread, while epidemiological data provides insight into population-level processes. Environmental and climate data, in turn, help define the ecological conditions in which transmission occurs. These datasets are brought together using phylodynamic approaches, ecological modelling, and machine learning to generate both retrospective understanding and forward-looking predictions.
“These diverse data streams will be integrated into unified models that can both explain past dynamics and generate forward-looking risk predictions,” says Prof Tegally.
The scale of this ambition is matched by the long-term support of the Wellcome award, which provides eight years of funding – a rarity in research environments often constrained by shorter funding cycles. For Prof Tegally, this creates space not only to explore complex questions in depth, but also to build sustainable research capacity.
“This award allows us to drive longer-term and more robust exploration around this topic,” she explains. “It also allows us to grow our team, support postdocs in developing their own careers, and integrate novel technologies – such as artificial intelligence – into pathogen transmission research.”
Within CERI, Prof Tegally leads a multidisciplinary team working at the intersection of data science and infectious disease research. The group brings together modellers, genomic epidemiologists, computational biologists, ecologists, and geospatial specialists. “We focus on building analytical solutions to solve research challenges related to pathogen genomics and infectious disease risk distribution,” she explains, describing a collaborative environment where research direction is shaped collectively and training and mentorship are central.
Working with large, complex datasets presents its own set of challenges. Data must often be harmonised across formats and sources, while some inputs – such as satellite imagery used to infer environmental context – can be costly and technically demanding to process. In response, the team is exploring new approaches, including the use of artificial intelligence and strengthened data engineering capacity, to streamline workflows and unlock new insights.
A key outcome of this work is a deeper understanding not only of how outbreaks grow, but also of why they sometimes do not. “By understanding exactly the factors that help or hinder pathogens to spread in human populations, we can better detect, monitor, and respond to emerging infectious disease threats,” she explains.
Leading a project of this scale from Africa carries particular significance for Prof Tegally. “The quality of science coming out of Africa is often overlooked,” she notes. “This is a chance for us to lead high-quality, highly novel research on the continent.”
Her own journey reflects that commitment. After studying in the United States and the United Kingdom, she returned to South Africa for her PhD and has since built her career within leading African research institutions. “I have always been passionate about returning to Africa to do high-quality science here,” she says, adding that recognition at this level also holds broader meaning. “It means a lot to be a young African woman in science and to be recognised in this way.”
Alongside her research career, Prof Tegally is also navigating a new personal chapter. Becoming a mother, she says, has reshaped how she approaches both time and ambition. “It has reminded me that I can do hard things and that I am strong even on the most overwhelming days,” she reflects. “I’m thinking more long-term, being more time-efficient, and learning to balance both.”
Outside of research, she finds balance in simple, grounding activities – swimming, spending time at the beach, and being in nature.
Together, her Prof Tegally’s work and trajectory point to a broader shift in global health science: one where data, context and leadership from within Africa are central to understanding and responding to the diseases of the future.
Elucidating Pathways of Pathogen Emergence and Expansion within Shifting Landscapes in Africa
Project summary, research questions, and conceptual figure.
Shifting global trends such as urbanisation, land-use change, wildlife trade, and increased connectivity are amplifying pathogen spillover and expansion. Africa is central to this dynamic. The continent faces converging factors which make it both highly vulnerable to emerging pathogens, but also ideally positioned for better preparedness.
While Africa’s primary forests, savannas and wetlands, and wildlife diversity already positions the continent as an ecological hotspot for zoonotic emergence, rapid urbanisation, growing population numbers, agricultural demands, changing land-use, and climate change increase human-animal-pathogen interactions.
The goal of this project is to develop and execute integrated data analytical methods and propose a new framework to improve understanding of pathogen emergence and expansion in Africa. The main hypothesis is that the latter is determined by the dynamic interplay between reservoir ecology, pathogen evolution, human-mediated introduction pathways, and local transmission conditions.
This fellowship will focus on three categories of pathogens, spanning distinct transmission modes, disease ecology and geographical distributions:
i) Arboviruses, ii) Mpox virus, and iii) Respiratory viruses.
It will tackle disease spillover dynamics in the context of reservoir distributions, genetic evolution, contact at human-animal interface, and imported introductions, and forecast epidemic expansion potential after emergence across shifting landscapes in Africa, towards better pandemic preparedness.
RQ 1: What ecological, evolutionary, and behavioral conditions determine whether a pathogen successfully spills over from wildlife reservoirs into human populations?
RQ 2: What factors influence the risks of pathogen introduction and subsequent establishment in secondary populations?
RQ 3: Can we accurately predict pathogen epidemic expansion by integrating genomic, ecological, and mobility data using phylodynamic, epidemic forecasting and machine learning models?
Stellenbosch University Research and Innovation Excellence Award
Last year, Prof Houriiyah Tegally received the Stellenbosch University Research and Innovation Excellence Award for Most Cited Open-Access Output, recognising her contributions to publications characterising SARS-CoV-2 variants as they emerged and spread globally during the pandemic.
The award reflects the far-reaching impact of this work, demonstrating how research originating in South Africa informed global understanding of the virus. “It is clear the impact of this work emanating from South Africa was global,” says Prof Tegally. “It’s an honour to be recognised at the institutional level, which reminds me of the value that our work brings locally as well as internationally.”
Text: Katrine Anker-Nilssen
Photos: CERI Media
News date: 2026-04-07
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