the gem genomics epidemics microbes April 2025

volume 8 - issue 4 April 2025

genomics, epidemics & microbes

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Data Science HQ School for Data Science and Computational Thinking has a new home in Stellenbosch

Data Science & AI International collaboration with Oxford & Copenhagen Universities read it online

Capacity Building in Africa Our work on Strengthening Genomic Surveillance is featured by the World Bank

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Cherry Blossom in Copehagem

Genomics Training in Africa

Reflections from Switzerland

CERI’s data science team participated in a joint scientific collaboration meeting with Universitie of Oxford and Copenhagen as part of funded projects by the Wellcome Trust and NovoNordisk Foundation

Strengthening Genomic Surveillance in Africa: Capacity Building Beyond COVID-19 - Our training programme is featured at the World Bank

Presentations and attendance to one of the top emergent pathogens symposium in the world in the time attack to WHO and global health

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/

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Increase in HIV Drug Resistance

Prof Wim de Villiers joins CERI

Grand Openning Data School HQ

New Study published at the Lancet Global Health warns of rising Dolutegravir drug resistance in South Africa’s HIV Epidemic

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

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

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editorial

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hat an intense and rewarding month it has been.

In April 2025, we dedicated significant effort to pushing forward the frontiers of data science and artificial intelligence (AI) research. Building on the momentum of our recent publication in Nature on AI advancements in tackling infectious diseases, we collaborated closely with teams from Oxford and Copenhagen to launch an ambitious program. Altogether, nearly 50 AI researchers convened in Denmark, working under major global health grants supported by the Wellcome Trust and the Novo Nordisk Foundation.

At the same time, we expanded our training initiatives across Africa. In partnership with the World Bank, we hosted hundreds of fellows for advanced training in genomics surveillance and bioinformatics. In April, we also welcomed delegations from Togo and Côte d’Ivoire, working together to sequence hundreds of genomes during one of the largest dengue outbreaks ever recorded in West Africa.

In response to an increasingly polarized global landscape, I traveled to Switzerland and the United States to collaborate with leading scientists on emerging viral threats. In Geneva, we convened to identify critical gaps and chart a path forward for strengthening genomic surveillance and developing medical countermeasures for some of the world’s most dangerous pathogens. I also spent valuable time in Seattle with one of my longtime mentors and role models, Professor Alan Aderem—cofounder of the world’s first Institute for Systems Biology alongside the legendary Leroy Hood.

Back home in South Africa, we continued progressing toward ISO accreditation for KRISP labs at UKZN and made strides in establishing our new Data Science Headquarters in Stellenbosch. To cap off the month, we were thrilled to welcome another visionary leader, Professor Wim de Villiers, who joined us as Chief Strategic Officer of CERI. Together, we aim to further elevate our impactful work in medical research and capacity development.

All in all, April was filled with important milestones and energy—a month we’re excited to share with you in this latest edition of the gem...

text: Tulio de Oliveira

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Artificial Intelligence (AI)

DATA SCIENCE & AI CERI’s data science team participated in a joint scientific collaboration meeting with Universities of Oxford and Copenhagen as part of funded projects by the Wellcome Trust and NovoNordisk Foundation text: D r Ho ur iiya h Tega l l y photo s: D r Ho ur iiya h Tega l l y

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ERI’s data science team participated in a joint collaboration meeting in Copenhagen with various international collaborators, including the Computational and Mathematical Global Health Group at The University of Copenhagen (PIs: Samir Bhatt, David Duchene), University of Oxford (Moritz U G Kraemer and Mahan Ghafari) and the Royal Veterinary College (Oliver Pybus, Jayna Raghwani and Divya Venkatesh). This two-day meeting during beautiful spring days in Copenhagen involved exciting discussions about AI, health, infectious diseases and genetics! One of the aims from this meeting was to identify major themes in these

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intersecting fields moving forward.

The various groups left the meeting collectively looking forward to working on these problems together.

The CERI team was represented by our data scientists: Dr. Houriiyah Tegally (Head of Data Science Unit), Dr. Monika Moir (Researcher), Dr. Gaspary Mwanyika (Postdoc), Jenicca Poongavanan (PhD Student), Graeme Dor (PhD Student), Carlin Foka (PhD student), Haingo Andry (PhD Student), and Daniel Van Zyl (PhD Student). The team presented our breadth of work on arbovirus genomic epidemiology, transmission risk mapping, deep learning for disease distribution mapping and climate migration. We heard from our collaborators about their research involving theoretical

methods development, one health research, mathematical modelling, and more. The whole group then split into 4 breakout sessions to discuss emerging research ideas in climate & health, pathogen genomics, optimal public health decision making, and emergence and expansion of pathogens with pandemic potential. The breakout groups further designed specific projects on these topics to be tackled collaboratively over the rest of the year.

In addition to the meeting, the team enjoyed networking over Copenhagen’s breakfast pastries, cycling through cherry blossoms across the city, and during a boat ride to Reffen street foods.

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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.

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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

We are advancing data science and AI with two of the leading groups in the world...

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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

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revealed the huge, underexplord potential in this area, especially when tackled across disciplines. It’s clear there’s a well of possibilities where fields like biology, mathematics, and climate science can meet to spark new questions. The discussions showed how much we can gain by learning from each other, mixing technical skills with other domains for more complete research”

are working on, and spent time intentionally searching for projects we can collaboratively develop. We anticipate it to have been a productive meeting that will yield grant applications and scientific publications.

The University of Copenhagen hosts gave us a taste of the Danish experience of ‘hygge’ by creating a warm and welcoming atmosphere for our discussions.

Graeme Dor: “The trip was a fantastic opportunity to engage with like-minded researchers from diverse yet complementary backgrounds and to experience the impactful research being conducted across the different groups. The complementarity of approaches across the research groups enabled engaging discussions that lead to the identification of potential areas for collaboration.

Meeting in person with researchers I had only met once before, or solely online, added a personal dimension that strengthened our connections and made future collaboration feel more actionable. Beyond the research side, it was also my first time visiting Copenhagen, and the trip offered a wonderful chance to explore the beautiful city and bond with colleagues.”

Carlin Foka: “The Copenhagen retreat was a truly rewarding experience. It marked the first time I presented my research project, Deep Learning for Disease Distribution Modelling, to an international panel of researchers. I received valuable feedback and insightful suggestions to refine my methodology. One highlight of the retreat was the Hackathon, where I had the opportunity to collaborate with and learn from more experienced participants. I also appreciated the social events, which helped break down barriers and foster potential future collaborations.”

Monika Moir: The meeting held in Copenhagen with Moritz Kramer’s lab from Oxford and Samir Bhatt’s group from the University of Copenhagen was an inspiring showcase of truly highlevel public health science. We learnt about the broad range of theoretical and applied projects the teams

to discuss my future ideas and research aspirations with the Oxford and Copenhagen teams, which has better equipped me to navigate the path ahead. I truly look forward to any future collaborations we may have.”

Daniel van Zyl: “The Copenhagen retreat was a wonderful experience. Copenhagen is a beautiful city, and a wonderful venue for the meeting; and I’m very grateful to the Copenhagen team for having us. It was so fantastic to feel more a part of a bigger picture of epidemic response, and to see what so many amazing minds have been working on. The trip has significantly advanced my work in two key ways: not only did I receive valuable feedback on my presentation, but I also had the opportunity

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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.

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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: D a n ie l Va n Zyl a nd C o l l e a g ue s photo : Figure 1 - BMC Genomics 2025

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n this paper, we comprehensively evaluated the effectiveness of alignment-free (AF) methods for the classification of viral sequences on a large scale, focusing on both classification performance and computational efficiency. We used six established AF techniques to extract feature vectors from viral genomes and trained Random Forest classifiers on these features.

We experimented with various parameters for AF techniques and evaluated the effects of removing versus replacing degenerate nucleotides. The findings from our primary dataset, consisting of 297,186 SARS-CoV- 2 nucleotide sequences categorized into 3,502 distinct lineages, demonstrate that AF methods can achieve high classification accuracy and efficiency even with large-scale datasets. We also evaluated class-wise accuracy based on the number of sublineages, training samples, and the depth of each class to determine the factors that influence classification difficulty.

Despite the high dimensionality, we found that word-based AF methods could effectively represent the SARS-CoV- 2 sequences, achieving classification accuracies close to 98% on the test set. Furthermore, we validated our models using moderately sized HIV (4,177 samples) and Dengue (18,970 samples) datasets to ensure their robustness across different viral types.

Our findings further contribute to the practical advantages of AF sequence classification. AF viral

sequence classification is considerably faster than alignment-based techniques. Moreover, the ability to train models and classify viral sequences using only modest computational resources, without reliance on cloud infrastructure, underscores the accessibility and scalability of these methods for researchers worldwide.

Background The rapid increase in nucleotide sequence data generated by next-generation sequencing (NGS) technologies demands efficient computational tools for sequence comparison. Alignment-free (AF) methods offer a scalable alternative to traditional alignment-based approaches such as BLAST. This study evaluates alignment-free methods as scalable and rapid alternatives for viral sequence classification, focusing on identifying techniques that maintain high accuracy and efficiency when applied to extremely large datasets.

Results We employed six established AF techniques to extract feature vectors from viral genomes, which were subsequently used to train Random Forest classifiers. Our primary dataset comprises 297,186 SARS-CoV- 2 nucleotide sequences, categorized into 3502 distinct lineages. Furthermore, we validated our models using dengue and HIV sequences to demonstrate robustness across different viral datasets. Our AF classifiers achieved 97.8% accuracy on the SARS-CoV- 2 test set, and 99.8% and 89.1% accuracy on dengue and HIV test sets, respectively.

Conclusion Despite the high-class dimensionality, we show that word-based AF methods effectively represent viral sequences. Our study highlights the practical advantages of AF techniques, including significantly faster processing compared to alignmentbased methods and the ability to classify sequences using modest computational resources.

Figure legend: The SARS-CoV2 testing accuracy results of each AF feature extraction method on a class-wise basis. The findings provide insights into the distribution of model performance across classes.

Classes are ordered in descending order of average classification accuracy across all models. The standard deviations of the accuracy for each model are also depicted. For the purposes of visual clarity, the values depicted have been smoothed using a sliding window of 50 classes. On the right-hand side, we provide isolated views of the top performing models.

Link to the Scientific paper: van Zyl, D.J., Dunaiski, M., Tegally, H. et al. Alignment-free viral sequence classification at scale. BMC Genomics 26, 389 (2025). https://doi. org/10.1186/s12864-025-11554-5

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Wo r l d B a n k

Genomics Capacity in Africa Strengthening Genomic Surveillance in Africa: Capacity Building Beyond COVID-19 - Our training programme is featured at the World Bank.

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n 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

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the strengthening of the Network for Genomics Surveillance in South Africa (NGS-SA), a consortium that unites laboratories across the country, including CERI, to sequence and track pathogens in real time. CERI, as a key member of NGS-SA, plays a central role in these efforts. The project supports NGS-SA by providing essential resources such as equipment, reagents, and skilled personnel to enhance genomic surveillance capacity. Through this collaboration, CERI and NGS-SA have become powerful tools in safeguarding public health across Africa, allowing for faster and more effective responses to both emerging and ongoing health threats.

Building a Stronger, Healthier Africa The future of genomic surveillance in Africa is bright. CERI is also a specialized genomics facility of the Africa Centres for Disease Control’s Pathogen Genomics Initiative (PGI).

CERI’s mandate in this role is to support and provide genomics sequencing and training to other National Public Health Institutes (NPHIs), academic, and non-governmental organizations in Africa. The World Bank has played a pivotal role in building this capacity across the continent by supporting genomics training, expanding bioinformatics expertise, and empowering laboratories across the continent. Through this project CERI has trained over 600 scientists, laboratory technicians and public health personnel from across the continent.

By hosting fellows from countries such as Nigeria, Mozambique, Kenya, Ghana, Senegal, Zambia, and Uganda, CERI fosters collaboration across borders, enhancing the collective capacity for genomic surveillance and research. This pan-African approach is key to ensuring a coordinated response to infectious diseases and strengthens the continent’s

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ability to address future health challenges. The skills and knowledge gained from these training sessions empower local laboratories to continue conducting high-level genomic research, ensuring that Africa remains at the forefront of epidemic preparedness and response.

Once fellows return to their home institutions, they are better equipped to respond to ongoing and emerging epidemics. There are already several success stories. For example, Dr. Abdou Padane from the Institut de Recherche en Santé de Surveillance Epidémiologique et de Formation (IRESSEF) in Senegal, has been at the forefront of initiating and establishing viral surveillance in West Africa since his return to Senegal.

Dr. Padane was awarded a longterm fellowship in 2022 and spent several months at CERI in South Africa to gain experience in Whole Genome Sequencing (WGS) and epidemic response. Upon his return to Senegal, he established the WGS technologies at IRESSEF that has enabled him to characterise both past and emerging outbreaks of dengue and chikungunya virus (CHIKV). In July 2023, CERI supported Dr. Padane and his team at IRESSEF to produce, for the first time, CHIKV genomes in Senegal. This support enabled the IRESSEF team to conduct real-time genomic analysis during the 2023 CHIKV outbreak in the country.

The project has also assisted several other countries by providing sequencing services or providing reagents, ensuring that these nations can effectively respond to emerging health threats.

Read the full article at the World Bank website: https://www.worldbank.org/en/ news/feature/2025/04/07/strengthening-genomic-surveillance-in-afe-africa-capacity-building-beyond-covid-19

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“” 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

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TO G O & I VO RY C OAST

STRENGTHENING AFRICA’S DENGUE RESPONSE H A N DS - O N N GS AND B I OI NFORMATI CS TRA IN IN G FOR W EST AF RI CAN SCI ENTI STS text: M a a m be l e K ho sa photo : M a a m be l e K ho sa

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n April we hosted a two-week 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.

Dengue virus is a mosquito-borne infection with symptoms ranging from fever and body aches to potentially fatal complications. In 2023 alone, over 6.5 million cases and 7300 deaths were reported globally, with climate change, population movement, and fragile health systems exacerbating the spread in many endemic regions.

This training equiped 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, and samples from recent outbreaks were sequenced during the training.

This initiative forms part of our broader efforts to strengthen disease surveillance across the continent.

We’ve previously supported partners in Ethiopia, Mauritius, Malawi, Senegal, and many more.

Interested in future training or collaboration? Keep an eye on CERI’s social media for upcoming calls or join our monthly CLIMADE consortium meetings—a platform where researchers and public health professionals can collaborate on climate-amplified diseases. For those currently experiencing outbreaks, we welcome interest in tailored support and training. Reach out to us at ceri@sun.ac.za.

Watch the videos of our fellows and traineers: - Melissa Ahou Koffi (Cote d’Ivore) https://youtu.be/gHhw47QXjME - Issaka Maman (Togo) https://youtu.be/gHhw47QXjME - Eninam Kouma (Togo) https://youtu.be/ATZ6g7GUooE

Participants included Melissa Ahou Koffi from Unité des Virus Respiratoires (UVR), Département des Virus Epidémiques (DVE), Côte d’Ivoire, Issaka Maman from the Institut National d’Hygiène, Togo and Eninam Kouma, also from the Institut National d’Hygiène in Togo.

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Communication

YOUTUBE VIDEOS Our engagement in videos and TV

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

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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

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Emerging Pathogens

Reflections from Switzerland Presentations and attendance at one of the top emergent pathogens symposiums text a nd photo s: Tul io de Ol ive ir a

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recently traveled to Switzerland to attend and present at the Emerging Virus Diseases Symposium in Geneva, held from April 7–10.

Following that, from April 10–12, I visited collaborators and delivered a keynote lecture at the University of Zurich. In the following paragraphs, I share my reflections on this significant scientific journey, which took place at a time when the U.S. administration announced major cuts to USAID and NIH funding, and the World Health Organization (WHO) faces a drastically changing global health funding environment.

The symposium opened with a keynote and public lecture by Dr. Maria Van Kerkhove, a colleague and friend, and a prominent figure in global health. She currently serves as Acting Director of the Department for Epidemic and Pandemic Threat Management at WHO. In her presentation, she emphasized the major advancements in global health surveillance, including the early identification of viral variants such as SARS-CoV-2 Omicron, the Mpox clade Ib, and new Marburg virus genomes. She also outlined strategies to strengthen pandemic preparedness.

However, during her speech, she grew visibly emotional as she spoke about the difficult situation WHO is currently facing—having to downsize between 30% to 60% of its staff if financial support does not improve. After her

presentation, Dr. Van Kerkhove approached me to discuss how research teams in the Global South—such as CERI and KRISP—are increasingly vital in supporting genomic surveillance and the early detection of emerging pathogens.

The second keynote, delivered by Prof. Melanie Saville from PATH (UK), addressed the importance of focusing research on entire viral families to enhance immunogen discovery and vaccine development. She highlighted families such as Arenaviridae (including Lassa fever), Filoviridae (with Zaire and Sudan Ebola viruses, and Marburg virus), Nairoviridae (with Crimean-Congo Hemorrhagic Fever), and Togaviridae (which includes Chikungunya virus). Prof.

Saville emphasized the need to apply diverse computational tools to accurately predict immunogenic targets, adjuvants, and immune modulators. She also discussed progress in mRNA-based vaccine platforms, including SelfAmplifying RNA (saRNA), Trans-Amplifying RNA (taRNA), and Circular RNA for Chikungunya vaccine development.

One of the most promising strategies involves creating vaccine libraries and identifying appropriate receptors in animals and humans. These are then used to guide immunogen design, cloned into cDNA constructs, tested in preclinical platforms, and eventually assessed in clinical trials for safety and efficacy.

Following the keynote addresses, the symposium

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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 24

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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.

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The Lancet Global Health

INCREASE IN HIV DRUG RESISTANCE New study warns of rising dolutegravir resistance in South Africa’s HIV epidemic text: D r R icha r d Le sse l l s photo : Figure 3 - The Lancet Global Health 2025

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new study published in The Lancet Global Health forecasts a significant rise in resistance to dolutegravir, the cornerstone of HIV treatment in South Africa, potentially threatening progress made in controlling the epidemic.

Over 25 million people living with HIV in low- and middle-income countries are receiving dolutegravir (DTG)-based antiretroviral therapy (ART). Most of the 6.2 million people on ART in South Africa now receive DTG-based ART – most commonly in the form of the fixed-dose combination of tenofovir, lamivudine and DTG (known as TLD). This widescale transition to DTG-based ART has been associated with high population levels of viral load suppression. Although DTG resistance is currently rare, it is inevitable that drug resistance will increase over the next few years and this could threaten our efforts to end HIV as a public health threat. What is uncertain is the extent to which DTG resistance will increase, and the speed at which this might occur.

Together with collaborators in Switzerland and other international partners, the researchers used a mathematical modelling framework to predict how DTG resistance might change over time in South Africa, and to identify opportunities for interventions to limit the emergence and spread of drug resistance. Their findings reveal that while dolutegravir-based therapy remains effective for most patients—with viral suppression projected at 93% by

2035—the rate of resistance among those failing treatment could more than double, rising from 18.5% in 2023 to 41.7% by 2035.

The results of the model suggest that, although DTG resistance will increase quite substantially over time in people who do not achieve viral load suppression on ART, levels of transmitted resistance levels will remain at relatively low levels (<5%) up to 2035. Switching people with virological failure to alternative ART regimens (based on protease-inhibitors), with or without genotypic resistance testing to inform the switch, was predicted to significantly limit the increase in drug resistance levels.

“This research provides reassurance that, although dolutegravir resistance will increase, there are things that we can do to limit this and to ensure the long-term sustainability of these highly effective ART regimens. As is often the case with mathematical modelling, there are many uncertainties, as we still have a lot to learn about DTG resistance and about the best approach to managing patients with virological failure on TLD. We hope that our ongoing research with the DTG Resist project and with the RESOLVE trial will help to address some of those knowledge gaps and inform our treatment and monitoring guidelines,” commented Dr Richard Lessells, co-author on the paper.

current guidelines recommend resistance testing only after prolonged viraemia—often too late to prevent mutation development and spread.

However, the research offers hope. Counterfactual modelling scenarios suggest that early intervention—particularly switching patients with failing therapy to protease-inhibitor regimens within six months— could drastically curb resistance.

The study, supported by the US National Institutes of Health and the Swiss National Science Foundation, highlights the critical need for vigilance and adaptability in HIV treatment programs, particularly in resource-limited settings facing high HIV burdens.

Figure Legend: Effects of the counterfactual scenario and modelled resistanceemergence-mitigation strategies on acquired dolutegravir resistance (A) and transmitted dolutegravir resistance (B).

Link to the Scientific paper: Predicted dolutegravir resistance in people living with HIV in South Africa during 2020-35: a modelling study. Loosli T, et al. Lancet Glob Health 2025;13(4):e698-e706. doi: 10.1016/s2214-109x(24)00553-9

The study underscores key factors driving resistance, including delayed switching from failing regimens and limited access to genotypic-resistance testing. South Africa’s

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the gem

Meeting a mentor in Seattle Prof Alan Aderem is an idol and mentor to Prof Tulio de Oliveira. Aderem joined the anti-apartheid movement as a teen in South Africa. He played a role in trade unions and community movements, and edited a township newspaper. Aderem was banned and put under house arrest for 5 years from 1977 to 1982.

In 2012, Aderem became president of Seattle Biomedical Research Institute (Seattle BioMed). Aderem co-founded the Institute for Systems Biology with Leroy Hood and Ruedi Aebersold in 2000 and served as its director until 2011. The ISB, the first institute for systems biology worldwide, focuses on a holistic understanding of biology, health, and disease.

When Prof Tulio de Oliveira founded KRISP at UKZN, Aderem was a mentor, who spent 100s of hours providing mentorship on how to build world leading research institutes.

As Prof de Oliveira visited Seattle in April 2025, he spent many hours with Prof Aderem to discuss ideas about science, leadership and how to make a positive impact in the world.

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KRISP team Complete SANAS Accreditation

Durban, April 2025 — The scientific scientists from the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) have taken a major step forward in strengthening laboratory excellence by completing a rigorous five-day training course on the ISO/IEC 17025 standard — the global benchmark for testing and calibration laboratories.

The training, which took place under the guidance of Mponeng Poo, Managing Director of QualExpect Consulting Services, provided the KRISP team with an in-depth understanding of the legal, structural, and documentation requirements necessary to align with the South African National Accreditation System (SANAS). The course is considered essential preparation for laboratories seeking ISO/IEC 17025 accreditation.

Poo, a seasoned expert in laboratory accreditation, not only coached the team through the fine print of the standard but also demonstrated how the principles of ISO/IEC 17025 would apply specifically to KRISP’s cutting-edge research and diagnostic operations. The training included practical strategies to ensure competence and consistency in providing accurate and reliable results — a critical component in achieving and maintaining accreditation.

KRISP is already ISO 15189 accredited for Sanger sequencing and drug resistance testing and it is now preparing the NGS laboratory to also achieve ISO 17025 accrediation. In addition, KRISP is increasing its not-for-profit service as a platform of the South African Technology Innovation Agency (TIA).

genomics, epidemics & microbes

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the gem

Chief Strategic Officer

Prof Wim de Villiers joins CERI text: F M H S & C ER I M a r ke ting & C o m m unica tio ns photo : Stellenbosch University

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rof 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

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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.”

genomics, epidemics & microbes

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

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the gem

Stellenboch University

DATA S C H O O L Grand Opening of new offices for the School for Data Science & Computational Thinking, Stellenbosch University text : SU C orp orate Co m m u n ica tio n an d M ar ket i ng p h otos : C ERI M ed i a S to c k

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genomics, epidemics & microbes

M

ore than five years since it was launched,

Stellenbosch University’s globally renowned 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”.

Affectionately referred to as the “data science HQ”, it symbolises the ethos of the school, representing “possibility, partnership, and purpose”, explained Prof Kanshukan Rajaratnam, the School’s Director, at the symbolic ribbon-cutting ceremony.

Addressing guests – including Rector and Vice-Chancellor Prof Deresh Ramjungernath and former Rector and now Fundraising and Strategic Projects Lead for the Faculty of Medicine and Health Sciences (FMHS) and Centre for Epidemic Response and Innovation

(CERI), Prof Wim de Villiers, Lawrence Matemba, Chief Policy Analyst with the Presidency, students and stakeholders – Prof Sibusiso Moyo, Deputy Vice Chancellor: Research, Innovation and Postgraduate Studies, said the school had become a “force to be reckoned with”, locally and internationally, establishing itself as a hub for interdisciplinary, collaborative research.

Commenting on the work the School does with the Presidency, Matemba described it as a national asset, saying: “This [opening] is not just good news for Stellenbosch, it is good news for the whole country.”

Ramjungernath commended the School for contributing to the University’s “bold vision” of being one of the top 100 universities globally.

“This school is a manifestation of a vision that places SU at the forefront of transdisciplinary research.” He also acknowledged the exponential growth of the School and its prolific research output.

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the gem

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

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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

“” This opening is not just good news for Stellenbosch, it is good news for the whole country Lawrence Matemba, Chief Policy Analyst, SA Presidency

genomics, epidemics & microbes

Photos Previous page: Prof Deresh Ramjugernath Rector and Vice Chancellor of Stellenbosch University cut the ribbon to open the School for Data Science and Computational Thinking HQ. He is accompany by Prof Wim de Villiers, previous Rector and Vice Chancellor and now Chief Strategic Officer at CERI. This page: From left, Dr Itai Mokone, Researcher, Policy Innovation Lab, Monique Bennett, Research Assistant, Policy Innovation lab, Prof Kanshu Rajaratnam Director of Data School and Maambele Khosa, head of marketing and communication at CERI celebrate the opening of the School for Data Science HQ.

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SACEMA

South African Centre for Epidemiology and Modeling Analysis

Dr. Odianosen Ehiakhamen, Nigeria CDC during his fellowship at CERI, 2024

SACEMA

South African Centre for Epidemiology and Modeling Analysis

SCHOOL

for Data Science and Computational Thinking

krisp