New Study published at the Lancet Global Health warns of rising Dolutegravir drug resistance in South Africa’s HIV Epidemic
Prof Wim de Villiers
joins CERI
Professor Wim de Villiers, who recently stepped down as Rector and Vice Chancellor, will be continuing his journey at Stellenbosch University in a new capacity as Fundraising and Strategic Projects Lead
Grand Openning Data School HQ
The School for Data Science and Computational Thinking has a new home at the JC Smuts building, occupying a space designed for connection, collaboration, and exploration
The CERI team reflected on their expereince:
Jenicca Poongavanan:
“It was inspiring to see what everyone is working on, smart people tackling big problems. The energy in the room made me proud to be part of this team. Copenhagen’s cherry blossoms and biking culture were stunning, but everytime I meet with our data science team I leave more inspired and this time it was no different. Sharing ideas, facing common PhD struggles, and exchanging feedback in such a collaborative space reminded me how lucky I am to be part of this group.
Gaspary Mwanyika:
“During my recent trip to Copenhagen, I had the opportunity to share preliminary findings from my research on dengue virus genomic surveillance and transmission dynamics in Africa. The discussions were highly productive, with valuable input from international experts on improving molecular clock approaches using single and multigene models for analyzing the rapidly evolving viral strains such as dengue, Influenza and SARS-CoV-2 . It was a great platform to refine novel ideas and foster collaboration. Outside the academic sessions, our data science team from CERI enjoyed exploring the city—highlights included a stroll through the beautiful King’s Garden, listening to the Royal Guards that
further enriched our experience, underscoring the importance of interdisciplinary collaboration in global health research”
Haingo Andry:
“My time at the Copenhagen retreat was a rewarding experience. I presented my initial research on human climate migration to a varied group. The feedback was useful and offered fresh viewpoints on how to tackle the problem. Connecting with people from different fields was just as important. These exchanges showed how interesting it is to combine diverse expertise to address complex global issues like public health. A standout moment was a breakout session on using machine learning for climate challenges. It
We are advancing data science and AI with two of the leading groups in the world...
Photos
Previous page: Copenhagen’s cherry blossoms and team walking in a park
This page: From left, Dr Houriiyah Tegally, Head of Data Sciences CERI, Dr. Monika Moir, Senior Researcher, Haingo Andry and Carlin Foka AI mathematicians at CERI, Graeme Dor, Spatial Epidemiologist, Jenicca Poongavanan and Daniel van Zyl, PhD students at CERI.
ARTIFICIAL INTELLIGENCE
ALIGNMENT-FREE VIRAL SEQUENCE
CLASSIFICATION AT SCALE
Development and application of AI methods to rapidly and accurately classify 1000s of genome sequences in seconds
text: Daniel Van Zyl and Colleagues
photo:
Figure 1 - BMC Genomics 2025
Genomics Capacity in Africa World Bank
Strengthening Genomic Surveillance in Africa: Capacity Building Beyond COVID-19 - Our training programme is featured
at the World Bank.
In the face of global health threats, robust genomic surveillance is more critical than ever. This innovative approach to monitoring pathogens allows scientists to track the genetic evolution of viruses and bacteria, providing real-time data that informs vaccine development, treatment plans, and public health interventions. For regions like Africa, where the burden of infectious diseases remains high, strengthening genomic surveillance is a priority and a necessity for safeguarding public health and preparing for future outbreaks.
The Accelerating Genomicsbased Surveillance for DiseaseCausing 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), is revolutionizing genomic surveillance capabilities across Africa. This project, launched in June 2022, is transforming genomic sequencing capacity on the
continent, enabling a more proactive approach to tracking and managing not just COVID-19 but a range of infectious diseases that pose ongoing threats to the continent.
Genomic Surveillance Capacity Building
The project has supported the sequencing of over 10,000 SARS-CoV-2 genomes, with 4,277 sequences uploaded to GISAID, a global platform for sharing viral data. CERI and its partners have continued to sequence samples, even though there has been a decrease in COVID-19 cases and testing across the world. Despite the dominance of the Omicron variant since 2021, hospitalization rates stayed manageable, demonstrating the ongoing value of genomic surveillance in monitoring the virus.
The project’s scope expanded beyond COVID-19 to include genomic surveillance efforts targeting other pressing health concerns, such as malaria, cholera, and influenza. This is made possible through the
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!
Plácida Iliany Maholela, Researcher at the National Health Institute (INS) of Mozambique
YOUTUBE VIDEOS
Our engagement in videos and TV Communication
Trailblazers
In the first episode of “Trailblazers with Gary,” Global Health Matters WHO podcast host Dr Garry Aslanyan sat down in South Africa with Professor Tulio de Oliveira — one of TIME Magazine’s 100 most influential people in global health. Aslanyan and Oliveira met in Oliveira’s lab to talk about the real story behind the Omicron discovery, how Africa came together to fight the pandemic, and why pandemic preparedness must remain a top priority, even as the world moves on.
Watch full video: https://youtu.be/IO3QJmuRKBw
Eninam Kouma
Eninam Kouma, Institut National d’Hygiène, Togo has come to South Africa for three weeks to participate in hands-on next-generation sequencing (NGS) and bioinformatics training at CERI Stellenbosch University , supported by The World Bank and coordinated through the #CLIMADE consortium. This training aims to improve our collective ability to monitor, report, and respond to dengue outbreaks, a critical public health need for Africa and beyond.
Watch full video: https://youtu.be/ATZ6g7GUooE
Issaka Maman
Issaka Maman, Institut National d’Hygiène, Togo Fellowship to strengthen Africa’s Dengue Response This training equips participants from Togo and Côte d’Ivoire with technical lab skills and bioinformatics workflows to build local capacity for outbreak response. As part of our collaboration, material transfer agreements were set up prior to the training and samples from recent outbreaks were sequenced ad analysed during the training.
Watch full video: https://youtu.be/gHhw47QXjME
Melissa Koffi
Strengthening Africa’s Dengue Response: Hands-On NGS and Bioinformatics Training for West African Scientists. Melissa Ahou Koffi, Département des Virus Epidémiques, Côte d’Ivoire has came to South Africa to receive hands-on nextgeneration sequencing (NGS) and bioinformatics training at CERI Stellenbosch University , supported by The World Bank.
Watch full video: https://youtu.be/5QSHH3ir0cg
Wim de Villiers
Stellenbosch, 21 April 2025, Professor Wim de Villiers, who recently stepped down as Rector and Vice Chancellor, will be continuing his journey with the institution in a new capacity. The role will involve managing targeted fundraising initiatives and developing strategic partnerships with both local and international stakeholders to ensure sustainability and global growth.
Watch full video: https://youtu.be/ZXWapImXxDg
Following the keynote addresses, the symposium continued with a session on Switzerland’s pandemic preparedness program. Six speakers contributed to this segment, and what stood out was how efficiently Swiss scientists collaborate. They demonstrated that a successful pandemic response plan isn’t only about drafting comprehensive documents, but also involves clear communication, securing a reliable supply of reagents and biologicals, and ensuring the availability of trained personnel.
The afternoon sessions focused on arboviruses— viruses transmitted by mosquitoes. The session began with a perplexing clinical case: a patient in Switzerland, immunocompromised and hospitalized with meningitis, was eventually diagnosed with West Nile virus after PCR testing of plasma and cerebrospinal fluid. Following treatment with Remdesivir, the patient cleared the infection, later developing a rash and hepatitis but ultimately recovered. This case illustrated how challenging it can be to diagnose rare viral diseases outside their typical endemic regions.
Another presentation discussed the rapid spread of Aedes albopictus mosquitoes in France, with over 10,000 cases of Chikungunya reported weekly in Réunion Island during April. The outbreak subsequently spread to Mayotte, Mauritius, and Seychelles, with more than 100 imported cases per week detected in mainland France. The rise in Chikungunya and West Nile virus infections across Europe is increasingly linked to climate change, which is enabling arboviruses to expand into new territories.
The first day of the symposium concluded around 9 p.m., featuring over 12 hours of intense presentations and discussion—an effort to make the most of the gathering of around 100 of the world’s leading virologists. That evening, sessions also addressed the rise in Enteroviruses since the COVID-19 pandemic. The session was led by Prof. Heli
Harvala, who recently returned to Finland after two decades in Oxford. Enteroviruses, a broad family with over 100 lineages (grouped into types A–D), were discussed in depth. One of the key viruses was Coxsackievirus A6 (CVA6), which emerged in Finland in 2009 and has since spread across Europe. Infections rose rapidly after 2010, affecting nearly the entire population.
Another important virus discussed was Enterovirus D68, which emerged in 2014 and has been associated with a polio-like illness called acute flaccid myelitis. That year, the U.S. and Canada reported over 1,100 cases and 58 deaths. Since then, D68 has spread widely, becoming more pathogenic. The family also includes polioviruses, and although polio has been nearly eradicated thanks to vaccines introduced in the 1950s, declining vaccination rates led to a case of circulating vaccine-derived poliovirus type 2 (cVDPV2) in the U.S. in 2022. Prof. Harvala warned that if immunization efforts continue to weaken, new enteroviruses—such as a hypothetical “Enterovirus X”—could emerge and trigger future global outbreaks.
Day Two: Respiratory and Poxviruses
The second morning session focused on respiratory viruses, which pose a significant pandemic threat. One of the highlights was a compelling presentation by Prof. Marion Koopmans from Erasmus University in the Netherlands. She presented data on a zoonotic H5N8 vaccine developed and tested at Erasmus MC, showing strong cross-reactivity with H5N1 strains. The vaccine is based on an H5N8 strain with hemagglutinin (HA) closely resembling that found in recent H5N1 infections in Texan cattle, and showed promising reactivity against clade 2.3.4.4b H5N1 viruses.
The next segment addressed poxviruses, particularly the re-emergence of Mpox. Since the end of smallpox
“” The rise of nationalism, and shrinking international funding are all converging to increase the risk of emerging viruses and epidemics
Prof Tulio de Oliveira
vaccination in Africa, Mpox cases have risen, especially in Central African forest regions. The clinical presentation closely resembles other poxviruses, often resulting in bacterial superinfections and complications such as blindness. Initial Mpox outbreaks mostly affected children, but between 2017 and 2019, it reappeared in Nigeria. While the first cases involved children, the virus eventually entered sexual transmission networks, particularly among MSM, leading to a global spread of clade IIb.
Although Mpox is a DNA virus, it is evolving at an unusually fast rate—about 28 times faster—more similar to RNA viruses. A surge of cases occurred between 2023 and 2025. Surprisingly, some of the recent outbreaks were linked not to clade IIb, but to clade I. In Eastern DRC, a novel variant—clade Ib—was identified, showing a high number of APOBEC-mediated mutations and adaptations to human-to-human transmission.
Day Three: Hemorrhagic viruses
The sessions started with strategies for identifying viral spillovers with the case of Nipah virus in Bangladesh was presented by Prof. Emily Gurley from the Johns Hopkins Bloomberg School of Public Health. Human infections with Nipah virus are rare and typically originate from contact with infected bats, pigs, or horses. Although person-to-person transmission can occur, it is relatively limited (with an R0 of less than 1), which makes widespread outbreaks unlikely. Nevertheless, due to Nipah’s high mortality rate and the close contact between humans
and a range of domestic animals, the potential for spillover events remains significant. The hemorrhagic fever sessions also highlighted the recent Marburg virus outbreak in Rwanda. In 2024, the country experienced its first known outbreak of Marburg virus disease, which led to 66 reported cases and 15 deaths. The majority of infections occurred among healthcare workers in Kigali. The outbreak was initially challenging to contain and began spreading within a hospital ward. However, through active case detection, isolation efforts, and the use of a new vaccine supported by CEPI, the spread was eventually brought under control. The outbreak was officially declared over on December 20, 2024, following a 42-day period with no new confirmed cases.
Reflections:
Reflecting on this important scientific symposium and my interactions with nearly one hundred of the world’s top virologists, I am deeply aware of the turbulent state of the world. Climate change, environmental degradation, rapid urbanization, the rise of nationalism, and shrinking international funding are all converging to increase the risk of emerging viruses and epidemics. As countries become more isolated and less cooperative, the emergence of new pathogens becomes more likely. In many cases, even when surveillance systems exist, emerging threats may be ignored or hidden—either due to misinformation, disbelief, or a reluctance to take responsibility for the consequences of disclosing new scientific discoveries.
The Lancet Global Health
INCREASE IN HIV DRUG RESISTANCE
New study warns of rising dolutegravir resistance in South Africa’s HIV epidemic
text: Dr Richard Lessells
photo:
Figure 3 - The Lancet Global Health 2025
Prof Wim de Villiers joins CERI Chief Strategic Officer
text:
FMHS & CERI Marketing & Communications photo: Stellenbosch University
Prof de Villers will work with leading academics and executives at the Centre for Epidemic Response and Innovation (CERI) and the Faculty of Medicine and Health Sciences (FMHS) to turbocharge the development of medical science and innovation in Africa
Professor Wim de Villiers, who recently stepped down as Rector and Vice Chancellor, will be continuing his journey with the institution in a new capacity as Fundraising and Strategic Projects Lead on Medical Science at Stellenbosch University (SU).
The role will involve managing targeted fundraising initiatives and developing strategic partnerships with both local and international stakeholders to ensure sustainability and global growth.
It was under Prof de Villers that Stellenbosch constructed the multi-billion Biomedical Research Institute. He will now join the teams of Prof Tulio de Oliveira and
Prof Elmi Muller, Dean of FMHS, to fundraise and provide strategic guidance to the development of research and training programs on medical sciences that impact lives.
“I’m excited to join the dynamic teams at FMHS and CERI to support fundraising and other strategic initiatives that will advance and ensure sustainability of their educational and scientific activities. Throughout my career, I have gained valuable experience and established important connections that I can leverage in this new position,” says De Villiers, whose focus on fundraising helped SU raise over R3 billion during his tenure as Rector and Vice Chancellor.
Prof Tulio de Oliveira comment: “We have managed to create one of the most impactful programs on epidemic response in the world at Stellenbosch University. So, as we expand our program in the time of reduced global health funding, we decided to hire Prof de Villers, which to the best of my knowledge, is one of the best ever fundraiser, academic leader and medical professionals that South Africa has produced.”
FMHS Dean, Prof Elmi Muller, expressed enthusiasm about De Villiers’ new role at the faculty. “His vast experience and knowledge will be invaluable to us, and I look forward to collaborating with Prof De Villiers on many projects within our faculty,” says Muller.
The role will involve managing targeted fundraising initiatives and developing strategic partnerships with both local and international stakeholders to ensure sustainability and global growth of FMHS and CERI projects.
SU’s Senior Director: Development and Alumni Relations, Ms Karen Bruns, says De Villiers’ appointment to this role comes at precisely the right time. “His contribution as a globally respected clinician and seasoned academic leader arrives at a pivotal moment for advancing health sciences and innovation in South Africa. He brings invaluable experience in strategic partnership-building and fundraising, which will significantly strengthen the ambitions of both FMHS and CERI. I look forward to working with him.”
Prof de Villers further comment “I am delighted to continuing in a leadership position in my alma mater in this new role that will help advance the FHMS and CERI in their mission to improve healthcare across Africa and beyond,” says De Villiers, who obtained his medical degree from the FMHS in Stellenbosch in 1983. He subsequently specialised in gastroenterology and built an illustrious career in medicine and healthcare leadership in the United States and South Africa before becoming Rector and Vice Chancellor at SU in 2015.
View Short video of the vision of Prof de Villiers at CERI: https://youtu.be/ZXWapImXxDg
It has, he added, helped to drive the academic excellence of the University. Through its work, the School has shown how to translate outcomes into impacts that are easily seen by the man on the street, added Ramjungernath. “Computational science can have significant societal impact.”
Reflecting on the School’s first five years, Rajaratnam said, “We’ve built global collaborations, and we’ve built local relevance.” He proudly celebrated the world-class researchers associated with the School, including Prof Tulio de Oliveira who discovered the Omicron variant and was recognised twice by Time magazine for his work;
Prof Francesco Petruccione, recipient of the Italian Order of the Star and Director of the National Institute for Theoretical and Computational Sciences; and Prof Thulani Makhalanyane, recipient of the Silver Medal of the South African Society of Biochemistry and Molecular Biology.
Rajaratnam said the School was intentional about unlocking data science for students, professionals and policymakers. It has provided online short courses and free bootcamps to more than 10 000 students. A recent cybersecurity summer school attracted more than 3 000 students, while an introduction to coding course had more than 3 500 registrants.
Milestone achievements include the launch of CERI and later the Policy Innovation Lab and the introduction of several research chairs – many in collaboration with the School’s partners.
Looking ahead, Rajaratnam said: “We aim to grow, build bridges and more collaborations deep into faculties, schools and external entities.” Key focus areas will include bringing more researchers from non-traditional areas into data science, securing more student funding and bringing faculties closer to the
school. “Our unofficial vison statement should be: the School for Data Science and Computational Thinking will work with faculties and schools to lead the University into the Top 100.
Watch the video of the grand opening of the School for Data Sciences and Computational Thinking Head Quarters (HQ) in Stellenbosch:
https://www.youtube.com/ watch?v=moPNTKHX7Mo
Read the news piece at Stellenbosch University Website: https://www.sun.ac.za/english/ Lists/news/DispForm.aspx?ID=11261
Lawrence Matemba, Chief Policy Analyst, SA Presidency “”
This opening is not just good news for Stellenbosch, it is good news for the whole country
