the gem - genomics, epidemics & microbes - Feb 2025
the gem
The BRAIN Program
International Start-up innovation comes to SA
UK and South Africa
Global collaboration to fight infectious diseases
Artificial Intelligence (AI)
A rapid & accurate classification system for viruses read it online
BRAIN Bootcamp
The BRAIN Regional Bootcamp brought together 10 high-potential African startups for an intensive five-day programme in Cape Town and Stellenbosch, South Africa.
AI & Infectious Diseases
In just five years, AI could transform how we predict and respond to disease outbreaks. Our team participates in a recent publication in Nature that provides a clear perspective of what to expect from AI in the next decade.
Pedalling for a Purpose
CERI join the #Move4Maties movement at the 2025 Cape Town Cycle Tour to Help Bridge the Financial Gap for Students
the gem: Centre for Epidemic Response and Innovation (CERI) & South African Centre for Epidemiology and Modelling Analysis (SACEMA), Stellenbosch University & KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), UKZN, Durban; director: Tulio de Oliveira; editors: Cheryl Baxter, Maambele Khosa ; art director: Victor Hugo Szortyka; graphic designers: Maam bele Khosa, Ronison Guimaraes, Tulio de Oliveira; websites: https://ceri.org.za/ https://www.krisp.org.za/, https://www.sacema.org/
African STARS Fellowship Scientific Videos
Application open! We invite applications for the African STARS Fellowship Programme, in partnership with the Mastercard Foundation. This prestigious initiative is designed to train the next generation of African leaders.
Here, we present some of our Videos and TV appearances.
U.S. Funding Cuts Threaten African Research: CERI Director Speaks Out. From Bench to Bedside: Pioneering the Genital Inflammation Test for Women’s Health
UK & SA Partnership
A North-South partnership between the Genomic Surveillance Unit (GSU) at the Wellcome Sanger Institute and CERI at Stellenbosch University, has received funding under the UK Foreign, Commonwealth & Development Office’s (FCDO) UK-SA Health System Strengthening Partnership.
editorial
We had another great month focused on creating and developing the innovation ecosystem in South Africa, despite a decrease in funding from the USA. We successfully launched the open call for the African STARS Fellowship, aimed at bridging the gap between research and industry to foster meaningful employment in Africa. This fellowship will support 40 brilliant scientists who will spend either 4 months or 1 year with us to transform how innovation enters the market on the African continent.
To enhance the health innovation ecosystem in South Africa, we hosted the Open International Start-up program called BRAIN (Bridging Research And Innovation). This Pan-African initiative aims to strengthen the DeepTech ecosystem in Africa through a holistic approach, enabling scientist-entrepreneurs addressing critical challenges to access world-class opportunities and resources. The BRAIN bootcamp was an intensive 5-day program (14 hours a day), featuring 10 of Africa’s most exciting start-ups that worked to advance their business plans and pitch to venture capitalists in South Africa.
In addition, we concentrated on high-level science and partnerships. In February 2025, we published two significant papers in artificial intelligence: the first, a collaborative perspective in Nature with Oxford University and the University of Copenhagen, discusses how AI will enhance infectious diseases research and innovation. We also released a new software application employing a machine learning approach for dengue subtyping, named Craft (Chaos Random Forest). This software innovatively uses a feature extraction technique that modifies the Frequency Chaos Game to be bitwise, combined with a Random Forest classification model for rapid and accurate classification of thousands of dengue genomes in seconds. Amid all this hard work, we trained for the 100 Km Cape Town Cycle Tour to help raise funding for students in need at Stellenbosch.
text: Prof Tulio de Oliveira
AFRICAN STARS
BRAIN Bootcamp
text: Maambele Khosa
photo: BRAIN, OST
Africa’s DeepTech and HealthTech sectors are on the rise, but many promising startups struggle to access the right mentorship, investment, and strategic guidance to scale globally. To bridge this gap, the BRAIN Regional Bootcamp brought together 10 highpotential African startups for an intensive five-day programme in Cape Town and Stellenbosch, South Africa.
This bootcamp, part of the BRAIN Accelerator 2025, is a year-long initiative powered by Africa Grow, Digital Africa, and Sanofi’s Global Health Unit for sustainable impact. It is run in partnership with MIT-Africa, MIT Executive MBA, AfricInvest, InstaDeep, and Bpifrance. The regional bootcamp was primarily hosted by Stellenbosch University, LaunchLab, CERI, and Fluorobiotech, with sponsorship from Octoco, Technopark, and Workshack, and local support from Wesgro and Innovation City.
Over the course of five days, the bootcamp provided expert-led training and hands-on mentorship, helping startups navigate challenges unique to the African market.
Sessions covered AI-driven business growth, commercialization strategies, product scaling, pricing, and investor pitching, equipping founders with the tools needed to secure funding and drive impact. Houda Ghozzi, CEO of Open Startup (OST), emphasized the importance of visibility for African startups during the opening event at Innovation City, stating: “Nothing happens if you don’t have exposure. Your efforts can remain in vain—that’s why BRAIN ensures that African startups and entrepreneurs are visible.”
In addition to workshops, side events such as Scaling HealthTech Innovation in Africa convened investors, researchers, and industry leaders to discuss Africa’s growing role in the global biotech and digital health landscape. Reflecting on the initiative, Prof. Tulio de Oliveira, Director of CERI, noted: “Supporting African startups in AI and HealthTech is essential for driving home-
grown solutions to global challenges. This programme is a game-changer in equipping them for success.”
Guided by renowned MIT faculty and leading global experts, the bootcamp covered essential topics including: AI integration in business, commercialization strategies, product scaling, pricing and marketing, and investor pitching. Participants also received one-on-one mentorship from MIT Executive MBA experts and Stellenbosch University MBA experts, along with tailored guidance from global and local industry mentors.
In addition to the core bootcamp activities, two key side events took place:
Deep Dive into South Africa’s Thriving DeepTech Ecosystem:
Date: February 25, 2025 | Location: Cape Town Innovation City. Hosted by Innovation City, this event featured a panel discussion with top industry leaders showcasing South Africa’s rapidly evolving DeepTech landscape
followed by a networking session designed to connect local and international stakeholders. Dr. Richard Gordon from CERI & the South African Medical Research Council was one of the keynote speakers in this event.
Scaling HealthTech Innovation in Africa:
Date: February 27, 2025 | Location: Stellenbosch Technopark.
Hosted by Octoco, Stellenbosch Technopark, & Workshack, this event convened leading HealthTech experts and investors to discuss scalability challenges and opportunities within Africa’s HealthTech sector followed by a networking session to foster valuable connections within the HealthTech ecosystem. Prof Tulio de Oliveira, CERI Director was the keynote speaker and the panel discussion was lead by Dr. Richard Gordon from CERI & SAMRC.
AI & Infectious Diseases Machine Learning
In just five years, AI could transform how we predict and respond to disease outbreaks.
A publication at Nature 2025.
Anew paper in Nature demonstrates how artificial intelligence (AI) can transform infectious disease research and pandemic preparedness by enhancing predictive modeling, outbreak tracking, and healthcare responses.
Co-authored by a global network of scientists, the study emphasizes AI’s potential to save lives by identifying high-risk areas, accelerating vaccine development, and improving pathogen analysis.
Experts from CERI at Stellenbosch University played a key role in this research, contributing advanced AI methodologies to epidemiology and public health. While AI presents remarkable opportunities, the authors stress the need for transparency, collaboration, and safety measures to ensure responsible implementation.
As the world continues to face the threat of emerging infectious diseases, this article emphasises the urgent need to integrate AI into public health systems. The scientists call for a global effort to collaborate across academia, government, and industry to ensure AI is used safely and ethically while addressing challenges such as limited data availability and the complexities of disease prediction.
According to the article, AI has the potential to transform pandemic preparedness in the next five years by improving the accuracy of disease spread models and predicting the trajectory of outbreaks. AI can help identify high-risk areas and allocate healthcare resources more effectively, ensuring timely intervention where it is needed most.
Dr Houriiyah Tegally, head of the Data Science unit at the Centre for Epidemic Response and Innovation (CERI), at Stellenbosch University (SU), said: “We’re thrilled to collaborate with AI scientists globally to shape the future of infectious
disease modelling. At CERI, we believe AI is poised to revolutionise science, particularly in epidemiology, by enhancing data analysis. Our team is already using AI and machine learning to tackle pressing research questions, from disease distribution and virus classification to phylogenetics and predicting climate-driven migrations—addressing pathogens like dengue, SARS-CoV-2, and more.”
The article outlines several key areas where AI can make a significant impact on pandemic preparedness:
• Improving disease spread models: By making predictions more robust, accurate, and realistic.
• Targeting high-transmission areas: Ensuring healthcare resources are allocated efficiently.
• Accelerating vaccine development: By improving genetic data in disease surveillance.
• Monitoring and detecting outbreaks: Integrating AI with population-level data, including wearable technologies, to better track and monitor disease trends.
While AI is poised to drive remarkable advancements, the authors caution that collaboration, transparency, and rigorous safety protocols are essential to address potential risks associated with its deployment. Ensuring that AI models are accessible, accountable, and free from biases will be crucial to maximising their positive impact on global health.
“The AI program in South Africa is well advanced in collaboration with Oxford University, University of Copenhagen, African Institute of Mathematical Sciences (AIMS) and Google DeepMind. We now have a whole team of mathematicians, data scientists and engineers working together to advance the use of AI in infectious diseases,” said Prof. Tulio de Oliveira, Director of CERI.
Through cutting-edge research and collaboration, CERI is at the forefront of advancing global health initiatives, applying AI and other innovative technologies to tackle infectious diseases.
Click here to access the media release from Oxford University (https://www.oxfordmartin.ox.ac.uk/ news/advances-in-ai-can-help-prepare-world-for-next-pandemic)
Click here to read the full article (https://www.nature.com/articles/ s41586-024-08564-w )
AI
is revolutionizing epidemiology, particularly through machine learning techniques applied to disease distribution and virus classification.
Dr.
Houryiiah Tegally, Head of Data Science, CERI
text: Tulio de Oliveira adapted from Van Zyl et al. 2025 image: Daniel Van Zyl
The traditional classification of the dengue virus is structured around four primary serotypes, each subdivided into distinct genotypes. Initially, genotypes were defined by a pairwise genetic distance greater than 6% within a 240 nucleotide sequence of the envelope (E) coding region. With the accumulation of more extensive sequence data, this classification expanded to incorporate entire protein-coding regions. Many of these genotypes were established two to three decades ago. This traditional framework has played a pivotal role in capturing the transmission dynamics of the dengue virus. However, enhanced global sequencing capacity, coupled with its integration into public health systems, has the opportunity to achieve finer granularity in classifying the diversity of dengue.
A refined dengue virus nomenclature system was proposed by Hill and colleagues in 2024. This new system introduces additional classification levels, termed major and minor lineages, within each genotype. This addresses key limitations of the traditional genotype-based classification system, including its inability to fully capture the genetic diversity of the virus and the growing demand for finer spatial resolution
In 2024, van Zyl and colleagues evaluated six alignment-free (AF) methods as feature extraction techniques for rapid and scalable machine learning-based viral sequence classification. They showed that word-based techniques achieve over
97% classification accuracy when distinguishing 3 502 distinct SARS-CoV-2 lineages using a dataset of 297186 sequences. Additionally, they applied AF feature extraction techniques to dengue and HIV datasets and achieve near-perfect classification accuracy for dengue (serotype and genotype) and over 89% accuracy for HIV.
In this study, we introduce Craft (Chaos Random Forest), a machine learning approach for dengue subtyping under the newly proposed dengue nomenclature. Craft uses a novel feature extraction technique which modifies the Frequency Chaos Game to be bitwise in combination with a Random Forest classification model. With Craft, we are able to achieve highly competitive classification performance compared to Genome Detective, NextClade and GLUE, whilst being significantly less computationally expensive.
Craft (Chaos Random Forest), a machine learning framework for dengue subtyping was capable of faster classification speeds while matching or surpassing the accuracy of existing tools. Craft achieves 99.5% accuracy on a hold-out test set and processes over 140 000 sequences per minute.
Notably, Craft maintains remarkably high accuracy even when classifying sequence segments as short as 700 nucleotides.
OPEN Access manuscript: https://www.biorxiv.org/conte nt/10.1101/2025.02.10.637410v1. full.pdf
Move4Maties
Pedalling for a Purpose
CERI is joining the #Move4Maties movement at the 2025 Cape Town Cycle Tour to Help Bridge the Financial Gap for Students
CERI is participating in the 47th Cape Town Cycle Tour as part of the #Move4Maties campaign to support students at Stellenbosch University facing financial hardships. This initiative aims to raise funds and awareness to ensure that no student has to abandon their education due to financial constraints. Join us by donating, spreading the word, or supporting the ride to make education accessible for all.
Education is a powerful force for change, but for many students at Stellenbosch University, financial constraints threaten to derail their academic dreams. These students, known as the “missing middle,” fall into a difficult gap; they do not qualify for state financial aid (NSFAS), yet they struggle to afford their education. As the economic climate worsens, more talented students face the prospect of dropping out.
But together, we can change their story.
This year, the Centre for Epidemic Response and Innovation (CERI) team ( Danilo Silva, Monika Moir , Marije Hofstra and friends) is proud to participate in the 47th edition of the iconic Cape Town Cycle Tour as part of the
#Move4Maties fundraising campaign on 9 March. For the #Maties community, this race is more than just a physical challenge; it’s a movement to create opportunities for students who need them most.
Why We Ride?
At CERI, we are deeply committed to building a better future through science, education, and community engagement. Supporting #Move4Maties aligns with our mission to drive meaningful change. By taking part in this initiative, we aim to raise awareness and critical funds to ensure that no student at Stellenbosch University is forced to abandon their education due to financial hardships.
How You Can Support?
Every contribution—whether through donating or simply spreading the word—brings us closer to a future where education is accessible to all. Here’s how you can get involved:
Donate: Every donation, big or small, directly funds scholarships, essential resources, and support programs for students in need. Click Here to donate from as little as R50
Join the Ride: If you’re in Cape Town, consider cheering on the riders as they take on the challenge.
Spread the Word: Share this initiative with your network to help us reach more people who can make a difference.
Be a Beacon of Support
Education is not just about textbooks and exams; it’s about unlocking potential and shaping a brighter future. Let’s rally together to support students who are #CaughtInTheMiddle and show them that they are not alone.
Join us, join Stellenbosch University , support the ride, and be a part of a movement that changes lives. Together, we can turn every kilometer into hope and every donation into opportunity.
Let’s pedal for a cause—because when we move together, we move forward.
Click here to read more and donate: (https://www. givengain.com/project/ceri-raising-funds-for-stellenboschuniversity-south-africa-94947)
“” Let’s pedal for a causebecause when we move together, we move forward...
The Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University (South Africa) and the Institut Pasteur de Dakar (IPD) (Senegal) invite applications for the African STARS Fellowship Programme, in partnership with the Mastercard Foundation. This prestigious initiative is designed to train the next generation of African leaders in genomics, diagnostics, vaccine development, and biotechnology innovation.
Fellowship Opportunities
1) Advanced and Translational Training (ATT) Fellowship (4 months)
2) Young Professional Programme (YPP) Fellowship (12 months)
How to Apply?
starsfellows.africa/apply
starsfellows.africa/faqs
Why Apply?
Fully funded training (travel, visa, accommodation)
Monthly stipend
Mentorship & career development
Placement in top research institutes, biotech hubs & industry partners
Experience in genomics, diagnostics, biotech, or vaccine development
Leadership potential & commitment to Africa’s scientific growth
Fluent in English or French (both is an advantage)
Women are strongly encouraged to apply
Call for Applications:
A f r i c a n S T A R S
A T T F e l l o w s h i p
Advanced and Translational Training (ATT)
Are you an early-career scientist born in or based in Africa with a passion for genomics, diagnostics, or vaccine development?
The Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University (South Africa) and the Institut Pasteur de Dakar (IPD) (Senegal) invite applications for the Advanced and Translational Training (ATT) Fellowship under the African STARS Fellowship Programme.
This fully funded 4 months fellowship offers hands-on training in:
Advanced genomics for public health
Genomic diagnostic design
Vaccine & biomanufacturing
Eligibility:
Born in and/or residing in Africa
35 years or younger
Background in a relevant field (BSc required, MSc/PhD preferred)
Strong leadership potential & commitment to Africa’s scientific growth
Fluent in English or French (both is an advantage)
Fellowship Benefits:
Fully funded training (travel, visa, & accommodation)
Monthly stipend
Mentorship & leadership development
Access to an exclusive alumni network
Application Deadline
4 Months Fellowship
PREVIOUS FELLOWS:
Elminah Saru Bianca Sansom
Elminah Saru is a Research Associate from Kenya working at the KEMRI Wellcome Trust. She leads laboratory operations for the IHCoR study, focusing on hypertension genetics and its link to organ damage.
This training was hosted in collaboration with Roche Diagnostics
Elizabeth Gyamfi is the National Lab Manager at SYNLAB Ghana Limited, based in Ghana. She holds a PhD and specializes in diagnostic laboratory management. Dr. Gyamfi expressed her intent to attend the training to refresh her knowledge of Next Generation Sequencing (NGS) technologies. This was particularly important as her team at SYNLAB Ghana plans to expand their molecular lab to include NGS-based genetic testing. The training aimed to enhance her ability to set up NGS workflows and train other staff members on these advanced techniques.
This training was hosted in collaboration with Roche Diagnostics.
Bianca Sansom is the CEO of GeneWay Laboratory in South Africa, holding a PhD. With 4–8 years of experience as a Laboratory Director, she is focused on implementing advanced workflows and exploring solutions like the KAPA Roche panel for diagnostic applications.
This training was hosted in collaboration with Roche Diagnostics
Elizabeth Gyamfi
Andrew Ajang Othow
Andrew is a Medical Laboratory Scientist at the National Public Health Laboratory (Department of Molecular Virology) in South Sudan, specializing in Microbiology. He holds a master’s degree in medical laboratory science, with a focus on Medical Diagnostics and Microbiology. With five years of experience in performing molecular diagnostic techniques and providing technical support in outbreak detection and response, his dissertation at Mbarara University of Science and Technology addressed non-mycobacteria among TB-suspected patients and their susceptibility patterns
Sibusiso Mahlangu
Sibusiso Mahlangu holds an MSc in Zoology from the University of Johannesburg, focusing on DNA barcoding and eDNA metabarcoding of estuarine macrobenthos. He joined the WWF Environmental Leaders Graduate Programme and worked at SANBI, enhancing his genomic analysis skills. He also completed an internship in Norway through the BioDATA Advanced Project. Sibusiso aims to apply machine learning to biodiversity genomics and pursue a PhD
Niguse Kelile Lema
Niguse Kelile Lema is a researcher at the Bio and Emerging Technology Institute in Addis Ababa, Ethiopia. His research focuses on shotgun metagenomics, studying antibiotic resistance genes and biosynthetic gene clusters in microbial communities. Niguse aims to pursue a PhD in bacterial or viral metagenomics to deepen his research in these areas.
US aid cuts: ‘A short-sighted move that threatens global health
Cuts to US spending on aid and medical research have caused widespread havoc and anxiety over the past month. Professor Tulio de Oliveira sat down with Spotlight’s Biénne Huisman to talk through what it might mean for health research in South Africa.
Speaking to Spotlight in a boardroom at the Centre for Epidemic Response and Innovation at Stellenbosch University, De Oliveira said: “Spending on biosecurity is an investment in the future — I think the US benefits much more from our research and our work than what we cost them.” Biosecurity refers to measures designed to protect populations against harmful biological or biochemical substances.
Read Full article: https://www.dailymaverick.co.za/article/2025-02-28-usaid-cuts-a-short-sighted-move-thatthreatens-global-health-and-scientific-collaboration/
Dr. Houriiyah Tegally Receives Prestigious Grant to Investigate Climate Change’s Impact
Dr. Houriiyah Tegally from the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, has been awarded a significant grant by the Global Science Summit Programme of the Novo Nordisk Foundation. Valued at 6.5 million Danish Krone, the grant will support her project, “Uncovering Climate Change Impacts on Arbovirus Transmission Dynamics at the Intersection of Phylodynamics, Ecological Modelling, and Machine Learning,” set to commence in February 2025.
This project is a collaboration between CERI, the Laboratory for Arboviruses and Hemorrhagic Viruses at the Oswaldo Cruz Foundation (Fiocruz) in Brazil, and the Pandemic Sciences Institute at the University of Oxford. Alongside Dr. Tegally, Dr. Marta Giovanetti from Fiocruz and Dr. Moritz Kraemer from the University of Oxford will work to investigate the complex relationship between climate change and the transmission of arboviruses, such as dengue, Zika, chikungunya, and yellow fever.
The research will focus on two primary areas: uncovering the transmission dynamics and dispersal patterns of arboviruses in various outbreak settings, and mapping global transmission risks, including viral movement between endemic and non-endemic regions. By exploring these aspects, the project aims to predict future shifts in arboviral diseases across ecologically distinct regions in Latin America, Africa, and Europe—areas that are becoming increasingly connected through global human mobility.
Funder: Novo Nordisk Foundation
Publication: New Sequencing Protocol Enhances Hepatitis B Virus Surveillance
A new study has developed a sequencing protocol using Oxford Nanopore Technology (ONT), addressing critical limitations in current diagnostic methods for Hepatitis B Virus (HBV). Chronic HBV infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is classified into ten phylogenetically distinct genotypes (A–J), and existing diagnostic tests often fall short in providing comprehensive genetic insights. Beyond its clinical and public health applications, the protocol’s affordability and ease of use make it ideal for laboratories with limited resources. Highthroughput sequencing of HBV genomes can become routine, enhancing diagnostic capabilities and improving patient care.
Full publication:https://www.mdpi.com/1422-0067/25/21/1170
Celebrating Academic Excellence: Congratulations to
our Graduates!
We are thrilled to extend our heartfelt congratulations to the remarkable individuals from the CERI team who recently graduated from Stellenbosch University. Their dedication and hard work have led to personal milestones and significant contributions to the academic and scientific community.
Proudly, we celebrate the graduation of more than 12 postgraduate students, including Honours, MSc, and PhD candidates. Their achievements reflect CERI’s commitment to advancing knowledge and fostering the next generation of scientists.
As we look forward to another cohort graduating in March, we commend these scholars for their perseverance and excellence. Congratulations once again—your journey is an inspiration to us all!
Welcoming Dr. Lavanya Singh
We are delighted to welcome Dr. Lavanya Singh as the new Head of the Laboratory and Quality Management at CERI, Stellenbosch University. With a PhD in Virology and over a decade of experience as an HPCSAregistered Medical Scientist, Dr.
Singh brings a wealth of expertise to our team.
Her research has focused on HIV drug resistance, and her PhD work explored the design of gold nanoparticles with HIV-inhibitory properties.
Dakar, Senegal
VEME BACK IN AFRICA: APPLICATIONS OPEN
text: Tulio de Oliveira photo: IPD
Are you a scientist working in virus evolution, bioinformatics, or genomic surveillance? Don’t miss your chance to apply for the Virus Evolution & Molecular Epidemiology (VEME) 2025 workshop, one of the world’s most advanced training programmes in genomics and bioinformatics. Taking place in Dakar, Senegal in August 2025, this 6-day intensive workshop will equip you with cutting-edge skills in virus genome analysis, bioinformatics, and epidemic tracking.
VEME brings together leading global researchers to offer handson training in phylogenetic inference, evolutionary hypothesis testing,
next-generation sequencing (NGS) analysis, and how to apply genomics to public health responses. This program is an excellent opportunity for researchers, epidemiologists, bioinformaticians, virologists, and public health professionals who are eager to enhance their expertise in molecular epidemiology and virus evolution while networking with some of the world’s leading scientists and peers.
The workshop is designed to provide participants with invaluable insights into virus genome analysis and outbreak tracking, all while strengthening global public health systems. You’ll be learning from toptier researchers and gaining practical skills that are essential for tackling global health challenges, including emerging infectious diseases.
The application deadline is 30 April 2025, and candidates will be selected based on the quality of their abstract and motivation statement. The application fee is $700, which covers attendance, coffee, and lunch. Scholarships are available for eligible candidates from resource-limited settings, covering travel, accommodation, and registration fees, thanks to funding from the Ministry of Health.
Apply now for the chance to gain world-class training in bioinformatics and virus evolution! Don’t miss this opportunity to advance your career and make a meaningful impact on global health.
Apply here: https://veme.climade.health/
“”
The VEME Workshop is the top international programme on advanved virus evolutionary and bioinformatics analysis. We are proud that it is back in Africa
Prof Tulio de Oliveira, Director CERI & Prof Amadou Sall, CEO Institut Pasteur de Dakar (IPD)
SCIENTISTS ON VIDEO
Here, we present some of our recent videos and TV appearances
U.S. Funding Cuts Threaten African Research
Newzroom Afrika journalist Latashia Naidoo visited the Centre for Epidemic Response and Innovation (CERI) labs to discuss the impact of U.S. President Donald Trump’s decision to halt foreign aid. In an exclusive interview, CERI Director Tulio de Oliveira shared insights on how the funding cuts could disrupt vital research at local universities. For years, U.S.-funded initiatives have supported African scientists in tackling regional and global health challenges. With this decision, the future of groundbreaking research hangs in the balance.
Access full video: https://youtu.be/DGiUf2njoAU
From Bench to Bedside Pioneering the Genital Inflammation Test
In this seminar, Professor Jo-Ann Passmore, Principal Medical Scientist (NHLS) and Professor of Medical Virology (UCT), introduced the Genital Inflammation Test (GIFT)—a groundbreaking, affordable point-of-care diagnostic tool for sexually transmitted infections and bacterial vaginosis. She also shared key insights from her research on genital tract inflammation and its impact on HIV risk in women. This discussion highlighted the crucial role of innovative diagnostics in advancing women’s health.
Access full video: https://youtu.be/XHyE3m5v63Y
Climate Change & Human Mobility
In this seminar, Prof. Ilse Ruyssen, Associate Research Professor in Migration Economics at Ghent University, presented a set of quantitative case studies examining the impact of temperature and rainfall anomalies, as well as droughts, on human mobility in West Africa. Her research delves into the complex factors driving migration decisions and immobility, with a particular focus on climate change, health, and retention factors. Prof. Ruyssen also highlighted the broader implications of migration on individuals and communities’ livelihoods, drawing on her expertise as a leader in the intersection of climate change, migration, and health.
Access full video: https://youtu.be/c833W1OcI0w
UK-SA Partnership Strengthens Global Disease Surveillance
A new partnership between Stellenbosch University’s Centre for Epidemic Response and Innovation (CERI) and the Wellcome Sanger Institute has been launched to strengthen global disease surveillance. Funded by the UK Foreign, Commonwealth & Development Office, the project focuses on real-time genomic monitoring of respiratory viruses to improve pandemic preparedness in both South Africa and the UK. The collaboration aims to enhance data sharing, track emerging variants, and support public health responses worldwide.
Access full video: https://youtu.be/zWrDj-YspDE
South Africa & U.K.
CERI & SANGER
Top Genomics Labs partner with UK Foreign, Commonwealth & Development Office to strengthen surveillance of respiratory pathogens
text: Maambele Khosa
photo: Tulio de Oliveira
The project was officially launch on February 6, 2025 with a signing event involving the UK High Commissioner of South Africa and the Director of the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University medical campus in Tygerberg, Cape Town.
At the event, representatives from CERI, the Wellcome Sanger Institute, key stakeholders, and UK and SA government leaders outlined their vision for transforming disease surveillance and collaborate on global health, security and science.
This North-South partnership between the Genomic Surveillance Unit (GSU) at the Wellcome Sanger Institute and the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University (SU), has received approximately 8.7 million South African Rands in funding under the UK Foreign, Commonwealth & Development Office’s (FCDO)
UK-SA Health System Strengthening Partnership.
This project will leverage genomic surveillance to monitor respiratory viruses, like Influenza, Metapneumovirus, Respiratory syncytial virus and COVID-19 in real-time to boost pandemic preparedness in both the United Kingdom and South Africa.
This initiative underscores the vital role of data sharing and international collaboration to create a unified, robust surveillance system for faster, more coordinated responses to emerging global health threats. The project will advance seasonal disease preparedness and build local capacity to address global health challenges.
“This partnership is about building bridges between the northern and southern hemispheres to ensure that both regions are better prepared for future health challenges,” said Professor Tulio de Oliveira, Director of CERI and the lead of the
of the team that discovered SARSCoV-2 Beta and Omicron variants. “In the age of nationalism and global division, our collaboration with the Wellcome Sanger Institute and the UK FDCO will not only improve global genomic surveillance capabilities but also create a framework for knowledge exchange, biosecurity and capacity building.”
The project will focus on genomic monitoring of respiratory viruses; key culprits behind seasonal infections and potential pandemics. By harnessing advanced genomic techniques, researchers aim to track emerging variants, identify drug and vaccine resistance strains, and provide actionable insights to public health authorities and the development of medical countermeasures.
John Sillitoe, Director of the Genomic Surveillance Unit at the Wellcome Sanger Institute, emphasised the global impact of this endeavour: “Our joint efforts with CERI will enable the development of a robust, integrated surveillance system that will inform public health responses across continents. By combining expertise and infrastructure, we can accelerate the fight against infectious diseases and build capacity to improve global health.”
The start of the programme was preceded by a visit of Lord Collins of Highbury, Parliamentary Under Secretary of State in the FDCO, and Deputy Leader of the House of Lords in the UK, to CERI on 4 November 2024. During his visit to CERI last year, UK Minister for Africa Lord Collins of Highbury commented: “South Africa is taking a leading role in science and research across the continent, and the UK is proud to be supporting this. Together we are collaborating on global health, security and science for a stronger, more resilient future.”
In addition to the research milestones, this initiative sets a precedent for fostering equitable global partnerships in health innovation. It builds on previous investments by
the South African and UK governments, the Rockefeller Foundation, the World Bank and the Wellcome Trust, and other stakeholders, maximising existing infrastructure and human capital to ensure impactful outcomes.
Antony Phillipson, High Commissioner to South Africa stated “Investing in global health is in all our interests and strengthening our cooperation in disease surveillance is key if we are to be better prepared for pandemics and work together on shared global health challenges. I’m excited to see this boost to our bilateral partnership; it is a key part of our programme to support South Africa in health systems strengthening.”
“This partnership is a testament to the power of global collaboration in advancing public health. By combining world-class expertise from South Africa and the UK, we are not only strengthening genomic surveillance but also fostering innovation that will enhance pandemic preparedness worldwide. Stellenbosch University is proud to be at the forefront of this crucial work, ensuring that science serves society by enabling faster, more effective responses to emerging health threats.” said Prof Wim de Villiers, SU Rector and Vice-Chancellor.
The project also positions South Africa as a leader in genomic surveillance and pandemic preparedness, emphasising the critical role of global data sharing to enhance public health responses. By fostering collaboration between experts in the UK and South Africa, the initiative aims to establish an interconnected system that enables real-time detection, analysis, and action against emerging health threats.
This partnership is about building bridges between the northern and southern hemispheres to better prepar for future health challenges “”
The Genomic Surveillance Unit at the Wellcome Sanger Institute is a leading facility in Cambridgeshire, UK, focused on using genomics to tackle global health challenges, including malaria, COVID-19, and other respiratory viruses.
The GSU/CERI Partnership – was established in early 2024 to bring together the Genomic surveillance laboratories in the UK and South Africa that were both renowned for their work identifying new variants during the COVID-19 pandemic.
