the gem genomics epidemics microbes June 2025

volume 8 - issue 6 June 2025

genomics, epidemics & microbes

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AI & Spillover Detection insights from pathogen spillover dynamics to AI for infectious disease in Oxford

Epidemic Preparedness Award for pandemic preparedness from the German GIZ funding agency to CERI read it online

African Leadership EDCTP Scientific Leadership Prize & Forbes Africa 30 Under 30 Award

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AI & Pathogen Spillover

Epidemic Preparedness

Embracing Participation

CERI Data Science on diverse international panel discussions in Oxford and Berlin providing insights from pathogen spillover dynamics to AI for infectious disease modelling.

Award for pandemic preparedness from the German GIZ funding agency to CERI This funding is important to continue genomics surveillance for the most important pathogens in Africa.

At a recent Public Squares lecture, Professor Lynn Hendricks of Stellenbosch University’s Department of Global Health unpacked participation in research and its crucial role in shaping effective transdisciplinary research practices.

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; printers: Gwynneth Louw websites: https://ceri.org.za/ https://www.krisp.org.za/, https://www.sacema.org/

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Drug Resistance on ARVs in Africa

Maambele Khosa: Forbes Top 30

GenPath Africa in Antwerp

In this open access report published in Clinical Infectious Diseases, we present some initial results from the DTG RESIST study, our NIH-funded international collaborative study nested within the IeDEA network (a global network of HIV clinical cohorts).

We’re excited to share that Maambele Khosa (Ambie), Head of Communication at the Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, has been named one of the Forbes Africa 30 Under 30.

The GenPath Africa consortium reunited for its second annual meeting on June 4-5, 2025, this time at the historic Hof van Liere at the University of Antwerp, Belgium. The event brought together partners from across Africa and Europe to reflect on the consortium’s progression and plan the next phase.

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genomics, epidemics & microbes

editorial

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his has been a busy month. In addition to launching three new programs, I also navigated school holidays as a single parent, as my wife was in Portugal to strengthen her Portuguese—essential for her upcoming projects in Lusophone countries. As a result, the release of this edition of the gem came a bit later than usual. That said, it’s a great new issue, packed with timely developments and new grant awards, which are much needed in this era of shrinking global health funding.

The editorial image I chose is a sunrise over the African savannah that my son Rafael took while on holidays. For me, it symbolizes the rebirth of African global health. African scientists, healthcare professionals, and communities are incredibly resilient. We will not only adapt to the shifting landscape but will continue to lead with unwavering commitment to saving lives and improving health outcomes. In my acceptance speech for the African Scientific Leadership Prize of the EDCTP in Kigali, I quoted a powerful African proverb: “A stick on its own is fragile, but sticks in a bundle are unbreakable.” This speaks to the spirit of unity and collaboration that drives our scientific progress across the continent.

In this issue, you’ll find highlights of a new collaborative program with Germany’s GIZ to enhance genomic surveillance, updates on the use of AI to predict epidemics, and significant scientific publications on HIV drug resistance and HBV evolution. We also mark Youth Month in South Africa, celebrating reflections from our young scientists and the inspiring recognition of Maambele Khosa as one of Forbes’ Top 30 Under 30 Africans. She joins a distinguished list of artists, athletes, and entrepreneurs, and we cannot hide how proud we felt to see a scientist among them!

text: Tulio de Oliveira

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Artificial Intelligence

AI & Pathogen Spillover Prediction CERI Data Science on diverse international panel discussions in Oxford and Berlin providing insights from pathogen spillover dynamics to AI for infectious disease modelling

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n the last month, our work within the CERI Data Science Unit was showcased across two international discussion panels contributing to insightful public discourse on pathogen spillover dynamics and AI for infectious disease modelling.

First, the head of CERI’s Data Science Unit, Dr. Houriiyah Tegally, was present at the Oxford Martin School of Oxford University, presenting on an expert panel entitled “What turns spillovers into epidemics?”. Chaired by Professor Jessica Metcalf from Princeton University, this hybrid discussion involved global experts to explore how AI, genomics, climate and ecological data are transforming our ability to predict emerging infectious diseases, featuring leading voices in pathogen genomics, ecology, virology, and data science from Oxford, Glasgow, Edinburgh, Pirbright, and Stellenbosch University.

The panel delved into various critical aspects of understanding why zoonotic disease spillover events sometimes lead to large sustained human-to-human transmission and epidemics, and sometimes not. For instance, the panel discussed the traits of successful pandemic pathogens, emphasizing real-world examples such as the Oropouche virus, which recently escalated from localized spillovers

to a widespread epidemic due to a combination of genetic adaptation, increased ecological suitability in urban-sylvatic interfaces, and high human mobility. Experts highlighted that while spillovers are common, the transition to pandemics depends on key factors like viral evolution, host availability, and environmental conditions. Surveillance systems, though imperfect, must be more dynamic and strategically resourced, including global data-sharing and prioritizing localized outbreak monitoring.

The panel stressed the need for better understanding of pathogen adaptation, especially transmission modes, as these changes can undermine existing interventions.

Promising future strategies that were discussed include proactive surveillance using multi-model risk estimates and AI-driven genomic analysis to predict and respond to emerging threats.

Our Data Science work was then presented at the most recent WHO Hub Pandemic and Epidemic Intelligence Innovation Forum. This online panel session, attended by over 300 participants, was centred around leveraging AI for infectious disease modelling and public health decision making.

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The panel of experts, including Dr. Houriiyah Tegally from CERI, highlighted that the convergence of artificial intelligence (AI) and public health is opening new frontiers in our ability to understand, predict, and respond to infectious disease threats. Speakers explored how AI is transforming infectious disease modelling, enabling more accurate predictions, real-time risk assessments, and adaptive policy responses.

This panel discussion followed the recent AI in Infectious Diseases paper at Nature 2025.

Access full paper in Nature: Kraemer, M.U.G., Tsui, J.LH., Chang, S.Y. et al. Artificial intelligence for modelling infectious disease epidemics. Nature 638, 623–635 (2025). https://doi.org/10.1038/s41586-024-08564-w

Houriiyah presented an integrated AI-driven modelling framework for genomic epidemiology and pandemic risk mapping. This work combines diverse data sources, genomes, epidemiological, environmental, and demographic data, with advanced phylodynamic, ecological, and epidemiological models. AI methods, including anomaly detection, deep learning, and large language models (LLMs), are enhancing both insight generation and model efficiency.

Applications range from rapid variant detection and disease distribution prediction to estimating human migration via satellite imagery. These innovations are directly supporting outbreak response by enabling faster, more localized disease risk mapping and streamlining genomic surveillance outputs for public health decision-makers.

These initiatives are part of CERI’s commitment towards broad scientific communication, ensuring that our research work not only reaches far and wide, but is also directly put into context of immediate public health applications.

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CERI team is recognized as one of the top global experts in the use of Artificial Intelligence (AI) for infectious diseases

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Poster adertising the panel discussion at Oxford with Dr. Houriyah Tegally, Head of Data Science at CERI.

Watch the Panel Discussion: ‘What turns spillovers into epidemics?’ - https:// www.youtube.com/watch?v=V5EX3DRzyvs

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Publication

Conserved recombination patterns across hepatitis B genotypes Tshiabuila, D., San, J.E., Wilkinson, E. et al. Conserved recombination patterns across hepatitis B genotypes: a retrospective study. Virol J 22, 220 (2025). https://doi.org/10.1186/ s12985-025-02829-0

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epatitis B virus (HBV) infection is a major public health concern, as chronic HBV infection can lead to liver cirrhosis and increase a person’s risk of developing hepatocellular carcinoma (HCC). HBV has been classified into ten genotypes (A to J). Here, we analysed the genotypic diversity and recombination patterns of HBV using 14486 publicly available HBV genome sequences.

Partial sequences and sequences with no metadata were filtered out, resulting in a final dataset of 8823 HBV genomes. These sequences were then combined with 41 HBV reference genomes from NCBI GenBank, and a maximum-likelihood phylogenetic tree was constructed to generate ten HBV genotype datasets. Multiple sequence alignment was performed for each HBV dataset, and using RDP5.64, we identified 288 unique recombination events.

Inter-genotype B/C recombination events were most common (found in 626/1194 identified recombinants), including 22/66 recombination events detected in viruses that are phylogenetically genotype B and 22/78 that are phylogenetically genotype C. The HBx (X) and pre-Core (preC) regions of the HBV genome were identified as recombination breakpoint hotspots, with the pre-C region also being the most frequently transferred genome region during recombination. As with many other viruses, the observed recombination breakpoint patterns in HBV genomes are significantly attributable

to factors such as local sequence similarity, GC content, or selection against recombination-induced protein misfolding.

It also remains plausible that many of the detected recombination events in the pre-C/X region and in other genome regions have been impacted by selective processes that are more difficult to test for directly.

Specifically, some recombination events might be favoured by natural selection if they transfer persistence and/or transmissibility-enhancing mutations between genomes. For example, we observed that pre-S/Sencoding genome segments tend to be transferred as an entire unit during recombination and that some pre-S/S mutations are related to vaccine failure, immune escape, and occult HBV infection.

pathogenicity-enhancing defective replicative intermediates This study highlights the complexity of the genetic diversity and recombination of HBV, with important implications for understanding its evolution and informing tailored public health interventions.

Access full publication: Tshiabuila, D., San, J.E., Wilkinson, E. et al. Conserved recombination patterns across hepatitis B genotypes: a retrospective study. Virol J 22, 220 (2025). https:// doi.org/10.1186/s12985-025-02829-0 h t t ps : // v i r o l o gy j . b i o m e d central.com/articles/10.1186/ s12985-025-02829-0

Similarly, mutations within the part of Pol that also tends to be recombinationally transferred as a complete unit are associated with resistance to nucleos(t)ide analoguebased antivirals; however, while drug resistance and HBsAg vaccine escape are theoretically subject to the influence of recombination, based on this dataset, recombination is unlikely to have a significant influence at the public health/population level because Pol is a recombination cold spot.

Furthermore, it is also difficult to test for direct evidence of selective processes that impact virus pathogenicity. For example, there are a multitude of mutations within the C and pre-C regions that, by disrupting viral replication, result in

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CERI-GIZ

EPID E M I C P R E PA RE DN E S S Award for pandemic preparedness from the German GIZ funding agency to CERI

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stablishing robust systems to monitor and analyze genetic information from pathogens helps South Africa to quickly detect and track changes in viruses proactively. This allows for faster responses to outbreaks and enhances pandemic preparedness in the country and the entire region. On 24th of June, the new phase of the Genomic Surveillance Project - a major public health collaboration to scale up monitoring and analyzing genetic information from pathogens – was officially launched in Cape Town.

It is a collaboration between the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University and the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) as part of the GIZ SAVax Programme. SAVax is cofunded by the German Government, the Federal Ministry for Economic Cooperation and Development (BMZ), and the European Union (EU) and implemented in partnership with the

South African Department of Health and the Department of Science, Technology and Innovation. The funding is part of the Team Europe Initiative on manufacturing and access to vaccines, medicines and health technologies in Africa (MAV+), which aims to bolster local vaccine and pharmaceutical manufacturing capacity and access to health technologies on the continent.

The new phase of the Genomic Surveillance Project will build on existing progress with additional funding of ZAR 9 million, bringing total investment in the partnership to ZAR 12 million. This funding is important to continue genomics surveillance for the most important pathogens, including respiratory pathogens of pandemic potential like Avian Influenza H5N1 and potential new coronaviruses. This collaboration shows the strong partnership between South Africa, Germany and European Union in cooperation on science for global health security and pandemic preparedness.

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Through capacity building measures and increased data sharing, national and regional data repositories and networks can be built and fostered. The partnership therefore reinforces a shared commitment to scientific excellence, equity, and proactive epidemic response across Africa.

The launch event at CERI Headquarters on Stellenbosch University’s Tygerberg Campus included a tour of laboratories, a panel discussion and a grant award ceremony attended by senior officials and dignitaries.

Mr. Fulgencio Garrido Ruiz, EU Deputy Ambassador to South Africa, emphasized the importance of South Africa as a strategic partner: “We are delighted to expand the collaboration with South Africa”. To support pandemic preparedness and equity across the African continent, the Team Europe Initiative MAV+ mobilizes resources among EU member states.

In South Africa the European Union through MAV+ has mobilized already over 700 Mio EUR of which 10 Mio EUR so far support research infrastructure. Mr. Garrido stated: “There is one aspect at the core of the approach which is research and development.

A robust local research framework that enhances self-sufficiency and empowers nations to respond independently to health crisis.”

Emphasizing on the importance of the Team Europe Initiative MAV+ Sven Hartwig, Deputy Consul General to the German Consulate General in Cape Town stated: “It is an honor for the German cooperation to contribute to the Team Europe Initiative MAV+ and to work alongside dedicated partners like CERI.” He also empathized the importance of collaboration for global health: “This launch highlights that surveillance for pandemic preparedness relies on partnership and collaboration between the public and private sectors, academia, and civil society. Germany is therefore particularly proud to continue supporting genomic surveillance and remains steadfast in its commitment to share global health goals.”

Dr. Anban Pillay, Deputy Director General from the National

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Department of Health underlined the importance of this partnership and the new programme by stating: “The work of CERI and the University of Stellenbosch foster a culture of collaboration.”

Claudia Aguirre, head of the GIZ SAVax programme underlined the strong partnership with CERI, which has started in 2023. Looking ahead she stated: “In this new collaboration these capacity building efforts will be expanded. We look forward to supporting CERI in its journey to develop science on the African continent and contribute to the development of solutions by African scientists for Africa”.

“This partnership exemplifies how science, government, and international cooperation can come together to strengthen public health systems and respond more effectively to epidemic threats,” said Professor Tulio de Oliveira, Director of CERI. “This is especially important for respiratory pathogens and new pathogens like Mpox, which have pandemic potential. The economic cost of a pandemic is so large that preventing it is a very wise and cost-effective investment”.

During the first phase of the CERI project (2023-2024) the initiative sequenced over 1,000 pathogen genomes, trained over 50 African scientists, and enhanced data-sharing protocols to improve outbreak response capabilities.

In the second CERI project phase (2025-2026) efforts are underway to expand genomic surveillance for respiratory pathogens like influenza, RSV, H5N1 avian flu, and emerging COVID-19 strains, while promoting the integration of genomic data into public health policy. South Africa is a key player in global biosecurity, with becoming the second Southern Hemisphere country after Australia to provide real-time genomic tracking of winter disease pathogens.

Furthermore, efforts are focused on strengthening laboratory infrastructure and testing in under-resourced provinces while supporting the training and career development of scientists at Historically Disadvantaged Universities in South Africa.

“” This partnership exemplifies how science, government, and international cooperation can come together to strengthen public health systems and respond more effectively to epidemic threats

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genomics, epidemics & microbes

Community

Embracing participation: Bringing communities into the heart of research

Text: Ameera Crew, Public Squares

hen addressing social issues such as inequality, the climate crisis, or systemic injustices, conventional research methods can fall short of delivering real-world impact. This is where participation and transdisciplinary research step in, not only as buzzwords, but as necessary shifts in how we understand and produce knowledge.

brings them into the heart of inquiry as co-designers, co-producers and co-translators of knowledge. This approach is especially important in health research, where lived experience offers insights that academic theory cannot.

At a recent Public Squares lecture, Professor Lynn Hendricks of Stellenbosch University’s Department of Global Health unpacked participation in research and its crucial role in shaping effective transdisciplinary research practices.

What makes research transdisciplinary?

Transdisciplinary research does more than bring different academic fields together. It actively integrates non-academic voices such as those of community members, artists and policymakers to generate knowledge that is inclusive, relevant, actionable, and transformative. It is: 1. Problem-driven: Tackling multifaceted issues like inequality and poverty.

2. Co-produced: Built on genuine collaboration with stakeholders throughout all stages of research,

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From research on communities to research with communities Participation in research flips the traditional research process on its head. Instead of viewing community members as passive subjects, it

“Participation should not be an add-on in research,” Hendricks emphasised, “rather, it is foundational for ethical and impactful work, especially when addressing the complex ‘wicked problems’ of our time.”

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3. Inclusive: Recognising and integrating different ways of knowing, beyond traditional scientific norms.

structures that determine whose knowledge counts.”

This method calls for humility, reflection, and adaptability from researchers; qualities often overlooked in traditional academic training.

Lessons for the future of participation in research

Key methods for meaningful participation Through her work at Stellenbosch University and with the Public Squares Initiative, Prof.

Hendricks and her colleagues have identified several techniques that bring non-academic individuals into the heart of research and knowledge production. These include: ● Creative methods such as digital storytelling and participatory theatre performances to amplify community narratives. ● Qualitative research methods that are culturally and contextsensitive, including focus groups, ethnographic observation, and narrative analysis. ● Technological tools that allow broader, more accessible participation, such as mobile surveys and virtual collaboration platforms.

Such tools not only make the research process inclusive but also ensure that findings are grounded in the realities of those most affected.

The benefits and challenges While the benefits of participatory and transdisciplinary research are many such as inclusivity, capacity building, and more sustainable and relevant solutions, challenges still loom. Power imbalances within academia, lack of institutional support, funding constraints and communication barriers can hinder the process of authentic participation.

“It’s not enough to invite communities into research,” Prof. Hendricks noted. “We have to change the

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Drawing from various collaborative projects, Prof. Hendricks offered four key lessons for researchers to ensure that community participation in the research is authentic and ethical: 1. Partnerships between researchers and communities are essential not just at the start, but throughout the research process.

2. Participatory methods should improve the relevance of findings, especially for communities involved 3. Technology and the arts can bridge the gap between academia and community.

4. Institutional change is necessary to scale inclusive research models and ensure that the voices of the vulnerable and marginalised are prioritised.

As Prof. Hendricks succinctly said: “Unconventional problems require unconventional approaches.”

Watch Professor Hendricks’ full lecture here : https://youtu.be/ Z0RcWzprRlA?si=q-xa4Oh3rjCfECIB

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“Participation should not be an add-on in research, rather, it is foundational for ethical and impactful work, especially when addressing the complex ‘wicked problems’ of our time.”

Professor Lynn Hendricks of Stellenbosch University’s Department of Global Health

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Publication

DRUG RESISTANCE IN PEOPLE WITH VIREMIA ON DOLUTEGRAVIR-BASED Loosli et al. 2025 .

Clinical Infectious Diseases, https://doi.org/10.1093/cid/ciaf204

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his month we published a report that helps to build our understanding of HIV resistance to dolutegravir, the antiretroviral drug that is the cornerstone of HIV treatment across the world.

Over 25 million people living with HIV in low- and middle-income countries currently receive treatment with a dolutegravir-containing antiretroviral therapy regimen.

Dolutegravir is in the class of drugs known as integrase-strand transfer inhibitors, and it is highly effective when used in combination with other antiretrovirals. Although HIV resistance to dolutegravir does occur, it is rare - this means we currently have quite a limited understanding of the situations in which resistance emerges, which people are at highest risk of resistance, and how the resistance will affect future treatment options. Our research is designed to plug some of these knowledge gaps.

In this open access report published in Clinical Infectious Diseases, we present some initial results from the DTG RESIST study, our NIHfunded international collaborative study nested within the IeDEA network (a global network of HIV clinical cohorts). In this study, we enroll adults and adolescents (10 years and older) living with HIV who have at least one elevated viral load (≥1000 copies/mL) whilst receiving dolutegravir-based ART. If the elevated viral load is confirmed on the study sample, we perform HIV drug resistance testing - most of that laboratory work for the study happens at our

sequencing laboratories at KRISP at the University of KwaZulu-Natal.

For this report, we included data from 16 clinical sites in seven African countries (Cameroon, Côte d’Ivoire, Malawi, Republic of Congo, Uganda, Zambia, and Zimbabwe). Most participants were receiving TLD (the combination of dolutegravir with two other antiretrovirals, tenofovir and lamivudine); although importantly most had received at least one other antiretroviral regimen prior to this.

We detected dolutegravir resistance in approximately one in four of the participants with confirmed elevated viral load and with successful sequencing (59/227). Most of those with resistance had multiple drug resistance mutations giving rise to high-level dolutegravir resistance (which in simple terms means that dolutegravir will no longer be effective for treatment of that individual)[see figure]. As we enrolled participants from southern, western and central Africa the virus sequences represented a range of HIV subtypes, and we observed a wide range of different mutation patterns.

One of the most important findings, which is consistent with other studies, was that all the observed cases of dolutegravir resistance were participants who had received at least one other antiretroviral regimen prior to starting dolutegravir.

If the risk of resistance is truly concentrated in this group, it will make it easier for HIV programmes to develop clinical algorithms for people with virological failure.

continually feedback results to the clinical sites and to policy makers and programme managers in participating countries, as well as to the HIV drug resistance team at the World Health Organization. The study recently surpassed the mark of 1000 participants enrolled across all the international study sites, and the KRISP laboratory is busy completing the sequencing work on this project. All the sequence data are publicly accessible at the NCBI BioProject database (accession number PRJNA1197182). We are now busy preparing presentations for upcoming conferences (IAS 2025 and HIV drug resistance workshop) and further manuscripts that will provide additional insights into dolutegravir resistance.

Access full publication: Loosli et al. Drug Resistance in People With Viremia on Dolutegravirbased Antiretroviral Therapy in SubSaharan Africa: The DTG RESIST Study. Clinical Infectious Diseases, ciaf204, https://doi.org/10.1093/cid/ ciaf204 https://academic.oup.com/cid/ advance-article/doi/10.1093/cid/ ciaf204/8131783

As part of the project, we

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E D C T P, K i g a l i , R w a n d a

African Scientific Leadership Prize text: Ste l l enbo sch Unive r sity photo : Stefan Els

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enowned bioinformatician and infectious disease expert Professor Tulio de Oliveira has been awarded the 2025 EDCTP Scientific Leadership Prize for African men, honouring his outstanding contributions to genomic surveillance, pandemic preparedness, and capacity building in Africa.

The prize, awarded by the European & Developing Countries Clinical Trials Partnership (EDCTP), recognises researchers from sub-Saharan Africa and Europe whose work on poverty-related diseases has significantly strengthened scientific capacity and public health outcomes. This year, four recipients were honoured, two women and two men, from both continents.

Professor de Oliveira, based at Stellenbosch University, has been instrumental in South Africa’s COVID-19 response, leading the team that identified both the Beta and Omicron variants. His work, powered by world-class facilities like the Biomedical Research Institute (BMRI), has set the standard for real-time outbreak detection

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and response, not only in South Africa but across the continent.

He also leads the GenPath Africa project, an EDCTP3funded initiative that builds genomic surveillance capacity in South Africa, Kenya, and Mozambique, and recently launched CLIMADE, a pioneering, African-led effort to tackle climate-driven infectious diseases.

“This recognition is not just for me, it is for the many African scientists, students, and communities working together to solve problems with science and innovation.

We are showing the world what is possible when Africa leads.”

Prof. de Oliveira’s work extends beyond genomics: by integrating technologies like mRNA vaccines, AI, and data science, his team is at the forefront of shaping Africa’s health response in an era of climate change. His approach emphasises collaboration, skills transfer, and empowering scientists in partner countries through inperson training and shared leadership.

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The award was presented during the 12th EDCTP Forum by Prof. Catherine Hankins and Prof. Souleymane Mboup, both global leaders in health research.

Professor de Oliveira summed up his philosophy with a powerful African proverb: “A stick on its own is fragile, but sticks in a bundle are unbreakable.”

This award is a testament to the strength of African science, when united, it is unstoppable.

Watch the acceptance speech of Prof de Oliveira: https://youtu.be/VBPt1HqCFww

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A stick on its own is fragile, but sticks in a bundle are unbreakable.

An African Proverb mentioned

by Prof de Oliveira in his speech at Kigali, Rwanda

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A F R I C A N S TA R S F E L L O W S H I P

MBA IN HEALTH CARE LEADERSHIP Call for Applications: African STARS MBA Fellowship

text: Maambele Khosa photo : Maambele Khosa

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he Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University (South Africa) and the Institut Pasteur de Dakar (IPD) (Senegal), in partnership with the Mastercard Foundation, invite applications for the African STARS MBA Fellowship; a fully funded opportunity to pursue a Master of Business Administration (MBA) in Health Care Leadership at Stellenbosch Business School, South Africa.

Programme Overview This specialised MBA equips professionals with the skills to lead and transform health systems in Africa.

It integrates strategic, financial, and

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operational training with a focus on navigating complex health care environments.

Duration: 2 years, Jan 2026 – Dec 2027 Format: Blended learning (online and three in-person blocks in Cape Town, South Africa) Eligibility Criteria: Born in and / or living in Africa Age 35 years or younger Minimum of 3 years’ full-time work experience (health sector.

Preferred qualifications: MBChB / MD, BSN (Bachelor of Science in Nursing), MMed (Master of Medicine) or equivalent, MPH (Master of Public Health), PhD (Medical field), CA (Chartered Accountant)

How to Apply Step 1: Apply for the African STARS MBA Fellowship Website: https://starsfellows. africa Deadline: 31 July 2025 Step 2: Submit an application for admission for the MBA Programme in Health Care Leadership to Stellenbosch University Business school Submit a formal application to Stellenbosch Business School for admission.

Deadline: 31 October 2025 Contact: For questions or further information, please visit the FAQ (https://www.starsfellows.africa/ faqs-mba/) or Email: starsfellows@ sun.ac.za

genomics, epidemics & microbes

Call for Applications:

African

STARS

Fellowship

Master of Business Administration (MBA) in Health Care Leadership

https//:www.starsfellows.africa

The Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University (South Africa) and the Institut Pasteur de Dakar (IPD) (Senegal), in partnership with the Mastercard Foundation, invite applications for the African STARS MBA Fellowship; a fully funded opportunity to pursue a Master of Business Administration (MBA) in Health Care Leadership at Stellenbosch Business School, South Africa.

Programme Overview

Fellowship Funding Overview

This specialised MBA equips professionals with the skills to lead and transform health systems in Africa. It integrates strategic, financial, and operational training with a focus on navigating complex health care environments.

The African STARS Fellowship covers the full cost of the MBA, including: Full tuition fees Application fees (for shortlisted candidates) Accommodation during contact blocks Air Travel expense Health insurance

Duration: 2 years, Jan 2026 – Dec 2027 Format: Blended learning (online and three in-person blocks in Cape Town, South Africa)

Specialisation: Health Care Leadership, with modules in Health Care Finance, Health Systems & Policy, and Value-Based Health Care Application Deadline

31 July 2025 starsfellows.africa/

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Industry Partnership

CERI-QIAGEN DIGITAL PCR

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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aving lives often begins with saving time. In diagnostics and research, the ability to detect pathogens or genetic markers quickly and accurately can change the course of public health outcomes. That’s why technologies like the QIAcuity digital PCR system are becoming increasingly valuable, especially across the African continent, where the demand for reliable, high-sensitivity molecular tools continues to grow.

On 11-12 June 2025, the Centre for Epidemic Response and Innovation (CERI), in partnership with QIAGEN, hosted a practical training on digital PCR at Stellenbosch University’s Biomedical Research Institute. The focus was on the QIAcuity system, a platform that integrates partitioning, thermocycling, and imaging in a single instrument, reducing hands-on time while improving accuracy and throughput.

For researchers and diagnostic professionals, this translates into faster workflows, higher sensitivity, and the ability to detect low-abundance targets with precision.

The training brought together a cross-section of scientists from research institutions, clinical laboratories, and industry. For many, it marked a turning point in their ability to apply advanced molecular techniques in their daily work.

“This training means everything to me,” said Siyanda Mazibuko, Associate Lecturer in Biochemistry at Nelson

Mandela University. “I can now accurately and precisely quantify all my antimicrobial resistance genes in a very quick and simple manner.”

Others saw the potential of digital PCR beyond traditional research environments. Rirapee Tjimune, a Laboratory Technician at ABInBev Namibia, reflected: “This training equips me with the knowledge to implement digital PCR in our quality assurance processes. It will improve the detection of microbial contaminants and enhance product safety in the brewing industry.”

Keikeditse Mohomane, a Staff Scientist at Lancet Laboratories, highlighted how the training would benefit both her current role and future academic goals. “With over a decade in molecular diagnostics, I found this training timely. Digital PCR will strengthen our diagnostic capabilities and support my upcoming PhD in Public Health.”

The initiative also underscored the role of partnerships in building lasting scientific infrastructure. “This is about sustainable skill development,” said Dr Yeshnee Naidoo, Training Lead at CERI. “We’re not just transferring knowledge; we’re building a foundation for longterm capacity in molecular diagnostics across Africa.”

Reeva Daniels, QIAGEN, added: “One of the most exciting outcomes is seeing how participants are already thinking about applying these tools in their unique contexts, whether in public health surveillance, quality control, or postgraduate research.”

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Exploring the Ethics of AI Carlin Foka Joins Global Voices at Mila Summer School Artificial Intelligence is reshaping the world, but alongside its promise comes a growing list of ethical challenges. Carlin Foka, a PhD student researcher at CERI, Stellenbosch University, was selected to attend the Mila Summer School on Responsible AI and Human Rights, held from 26 to 30 May in Montreal, Canada.

Hosted by Mila- Quebec AI Institute and the University of Montreal, the programme brought together 40 participants from 33 countries to explore how AI can be developed ethically, with human rights at its core.

Carlin joined interdisciplinary discussions on AI ethics, governance, and policy, and took part in case studies examining real-world applications of responsible AI. “This experience expanded my thinking beyond technical metrics. It reminded me that the tools we build carry real-world impact,” he said. The programme also offered opportunities to connect with peers from around the world, sharing diverse perspectives on the future of AI.

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Forbes Africa 30 under 30 We’re excited to share that Maambele Khosa (Ambie), Head of Communication at the Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, has been named to the Forbes Africa 30 Under 30 list!

This annual list highlights young leaders across the continent who are making a real difference. At CERI, Maambele plays a key role in helping us communicate complex science in clear, meaningful ways, making sure the public understand the importance of our work.

She also brings an entrepreneurial mindset to everything she does. Maambele is the founder of SheCab, a transport service designed to make travel safer and easier for women in South Africa. On top of that, she’s currently doing her PhD in science communication, focusing on how people engage with information about infectious diseases.

Prof Tulio de Oliveira, Director of CERI, adds: “Ambie is fun, super competent, and her energy is electrifying. She’s an inspiration and always willing to learn.

We’re really proud of her.”

We’re happy to celebrate this achievement with Maambele and look forward to what she does next!

genomics, epidemics & microbes

Harriet Ng’ombe Showcases Cholera Genomics Research at 12th EDCTP Forum in Kigali Harriet Ng’ombe, a PhD student at Stellenbosch University and researcher at the Centre for Infectious Disease Research in Zambia (CIDRZ), presented work on genomic research at the 12th EDCTP Forum in Kigali, Rwanda. Representing both CIDRZ and the Centre for Epidemic Response and Innovation (CERI), Ng’ombe shared findings from a study titled “Genomic Analysis and Antimicrobial Resistance of Vibrio cholerae Isolated During Zambia’s 2023 Cholera Epidemic.”

The study applied whole-genome sequencing to understand the diversity, resistance profiles, and transmission dynamics of Vibrio cholerae strains identified during Zambia’s 2023 outbreak. Results revealed two genetically distinct clades linked to broader transmission across Southern Africa, pointing to the urgent need for regional cooperation in disease monitoring and response.

“The poster sessions were a highlight,” said Ng’ombe. “Presenting my work to an audience of global experts and fellow young scientists was both affirming and inspiring. The feedback I received will guide future directions of the project.”

Beyond presenting her research, Ng’ombe engaged in key sessions on antimicrobial resistance, climate and health, and digital innovation in public health.

She also attended high-level discussions on scientific publishing and leadership in African research.

CERI Strategic trip to the UK In June, Prof Wim de Villers and Dr Richard Gordon visited the UK to explore a number of collaboration opportunities. These included the Pharmaceutical sector, funding agencies as well as several UK funding agencies such as UKRI and FCDO. The highlights of the trip included a lunch with a Wellcome Senior executive team as well as a trip to Westminster where the team presented data on the FCDO

Collaboration program to a number of representatives of the Commonwealth sub committee of the UK Government. The meeting was also attended by several members of the Wellcome Sanger Genomic Surveillance senior management team and a number discussions were had on how the CERI-GSU program could be scaled.

Brian Mathew MP, Prof Wim de Villiers and Janet Horton at the UK Houses of Parliament/Westminster, London.

Photo: From left: Prof Saheer Gharbia, Dr. Richard Gordon, HE

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YO U N G P R O F E S S I O N A L S

YOUTH MONTH REFLECTIONS Honouring The Youth, Inspiring the Future: Reflections from KRISP’s Young Professionals

text: Paul Harris photo : Paul Harris

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his June, as South Africa commemorated Youth Day, we at KRISP took a moment to reflect on the importance of this day—not just in remembrance of the past, but in celebration of the present and the promise of the future.

Youth Day marks a powerful moment in our nation’s history, honouring the courage of the 1976 student uprisings and reminding us of the role young people continue to play in driving change.

To mark the occasion, we sat down with eight of our talented young colleagues at KRISP and asked them three questions: 1. What does Youth Day mean to you, and how does its legacy

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influence young professionals today?

2. As a young professional, how do you see your role in shaping a better future for the next generation of South Africans?

3. What advice would you give to a youngster who wants to follow in your professional footsteps?

Their responses were thoughtful, inspiring, and deeply personal— offering a glimpse into how the legacy of Youth Day continues to empower a new generation of scientists, researchers, and changemakers.

Dr. Amsha Viraragavan Postdoctoral Fellow at KRISP 1. For me, Youth Day in South Africa is a symbol of courage and

sacrifice. We pay tribute to the courageous and resilient individuals who fought for equal educational opportunities during the 1976 Soweto Uprising. Youth Day is a significant reminder to us that courage, togetherness and boldness can challenge the status quo, by asking those difficult questions and drive change.”

2. “As a young professional, I envision myself as an element of courage and a voice for progress in spaces where change is needed.

I believe that my role as a young scientist goes beyond research – the knowledge and experience gained helps me inspire others and advocate for solutions that benefit future generations. By leading with integrity, sharing opportunities, and breaking down barriers in science and innovation, I hope to empower the next

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generation of South African youth to dream bigger, think critically, and step confidently into their purpose.”

3. “Own your greatness and use your talents to make a lasting difference in the world. Be bold, be courageous. If you have a burning desire to pursue something you’re passionate about - go for it. Don’t wait for permission or the perfect moment. Start where you are, with what you have, and trust that your efforts will lead you forward. The world needs your voice, your vision, and your energy.”

Anele Zungu - MSc Student at KRISP 1. “Youth Day is a powerful reminder of the courage and resilience.

Hundreds of my brothers and sisters

“”

had to lose their lives just to have a fair education system which is a basic human right across all South Africans. Personally, it reminds me that as a young Black South African I am standing on the shoulders of heroes who fought for the opportunities I now have opportunities to study, to question, and to contribute meaningfully to society. It challenges me to not only honour their legacy but to build on it by grabbing every opportunity I have to learn.”

2. “As a medical science researcher, I see my role as one of representation, innovation and I aspire to become an individual that can contribute to make HIV a problem of the past for the next generation to only read about in History books. I want young South Africans, especially Black girls from underrepresented communities to see someone

Youth Day is a significant reminder to us that courage, togetherness and boldness can challenge the status quo, by asking those difficult questions and drive change 32

who looks like them in science and believe they belong too.”

3. “I would tell them that just having the choice of what they want to do is privilege enough and in everything they do they should put their best foot forward because the sooner you work hard the easier your life becomes later.”

Nqobile Mthembu - MSc Student at KRISP 1. “Youth Day is a powerful reminder of the courage and resilience of young people who stood up against injustice during the 1976 Soweto Uprising. Personally, it symbolizes the strength of youth-led change.

For young professionals today, it serves as a legacy of working towards challenging the norm and current injustice.”

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2. “Being the change you want to see in society. Being visible , working hard and sharing knowledge and guidance.”

3. “My advice would be to work hard, be truthful to yourself, and to always ask for help when in need.”

Thembelihle Tombo - MSc Student at KRISP 1. “Youth Day reminds me of the courage of past generations and inspires young people to lead with purpose and accountability.”

2. “I aim to create opportunities, share knowledge, and mentor others to drive progress and empowerment.”

3. “Stay curious, work hard, and never underestimate the power of discipline and consistency.”

Hlengiwe Shange - MSc Student at KRISP 1. “Youth Day reminds me that we’ve always had power, even when we were toldx we didn’t. The students of 1976 weren’t politicians; they were young, Black learners who chose to speak up. Their stories still echo in today’s township schools, where the struggle continues. And for me, it’s not just a history lesson, it’s a daily call to consider how we’re using the voice they fought to protect. As young professionals, we honour that legacy not just by being visible, but by being intentional, using our skills, platforms, and presence to stand in the gap, open doors, and quietly shift things forward for those who come after us. It may not always be loud, but it’s still resistance. It’s still

change.”

2. “I see my role as a connector, someone who understands where the youth are coming from because I’ve been there. I believe growth means little if it doesn’t create space for others to rise too.

Whether it’s through mentoring or simply checking in on someone who’s overwhelmed, I try to make others feel seen and supported. My grandmother used to say, “Akukho kufika endaweni engenamnyango,” meaning you’ll never arrive at a place with no door. That’s stayed with me, because the true impact lies in leaving the door open for those who come after you.”

3. “I didn’t get here by having it all figured out. I just kept choosing to show up. I followed what felt meaningful: helping classmates, volunteering, saying yes to research opportunities even when I felt unsure. If you want to work in science or health, start by being present where you are. Join things. Ask questions. Find people who care about the same things you do and learn beside them. The real growth happens in moments when you feel a little out of your depth but decide to stay anyway. That’s how I found my footing, not through perfection, but through purpose and showing up with heart.”

Mulalo Raphalalani - KRISP Intern 1. “Youth today to me is a powerful reminder of the courage and resilience of the young people that stood up to fight for the injustice in the education system. It reminds me that it is because of them that a young girl from Gondeni has walked

the path from primary school to postgraduate studies. I think this influences the youth to keep fighting for equal access to educational opportunities as we have seen with fees must fall movements.”

2. “By teaching them the importance of education and continuing being a better version of myself so that they can be inspired. Through education, young people gain essential skills like problem-solving, communication, and critical thinking—that prepare them for the workforce and daily life challenges. Thereby making them independent. If I can set a positive example by showing how education helped me gain independence, I believe it will inspire others to follow the same path.”

3. “I would tell them that education is the key to success, however it requires more than just reading books, they must learn to be brave, accept the failures and try again, have good manners and be persistent. But most importantly they must believe in themselves and be able to voice out their perspectives.”

Kisharia Dharamdev - KRISP Intern 1. “To me, this day is a reminder of the brave youth who stood up for their rights as well as the sacrifices they made during the apartheid regime. Their legacy empowers young South Africans to rise up against an ongoing struggle of inequality and social injustice, to pursue their passions and make a difference towards a better future.”

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Communication

MEDIA COVERAGE Media coverage of our work in videos and in the TV.

CERI-QIAGEN Training CERI, in collaboration with QIAGEN, hosted a fully funded, hands-on Digital PCR (dPCR) training at Stellenbosch University in Cape Town, South Africa, from 11–12 June 2025. This twoday training brought together participants from South Africa, Kenya, Namibia, Botswana, and Zambia, offering practical experience with the QIAcuity Digital PCR system.

Watch full video: https://youtu.be/tVExpR44eUY

Scientific Leadership EDCTP Scientific Leadership Prize winner: Professor Tulio de Oliveira. His work has generated new insights into the transmission of viral infections, including HIV, informing the global policy response. He is a strong advocate for open science and capacity building, and leads the EDCTP3-funded GenPath Africa project, which is strengthening genomics surveillance capabilities in South Africa, Kenya and Mozambique.

Watch full video: https://www.youtube.com/watch?v=4OjNfD_iqh

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genomics, epidemics & microbes

LAUNCHLAB CERI BIO From eNCA “A local biotechnology laboratory is focused on bridging the gap between biotechnology research and its commercial application.At LaunchLab CERIBIO, entrepreneurs are given access to affordable world-class laboratory space where they can test their biotechnology inventions.The laboratory will be operated in collaboration with Stellenbosch University’s Division for Innovation and Commercialization.

Watch full video: https://youtu.be/v2fkH2-ABRM

Genomic Surveillance New funding The funding is part of the Team Europe Initiative on manufacturing and access to vaccines, medicines and health technologies in Africa (MAV+), which aims to bolster local vaccine and pharmaceutical manufacturing capacity and access to health technologies on the continent.

Watch full video: https://youtu.be/gBljBwu6pN8

Dr. Musyoki on genomics expansion Dr Andrew Musyoki, a Seniour Lecturer at Sefako Makgatho Health Sciences University, one of the Genomics Africa fellows at the CERI-GIZ project launch. He talk abou thte importance of expanding genomics to historically disadivantaged insitutiona (HDIs) in South Africa.

Watch full video: https://youtu.be/5P4HSdglcAI

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EDCTP

GENPATH AFRICA HOLDS SECOND ANNUAL MEETING IN ANTWERP text: Dr Claudia Schacht photo s: Dr Cheryl Baxter and Hannah Faber

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wo years into the project, the GenPath Africa consortium reunited for its second annual meeting on June 4-5, 2025, this time at the historic Hof van Liere at the University of Antwerp, Belgium. The hybrid event brought together partners from across Africa and Europe to reflect on the consortium’s progress, strengthen collaboration, and plan the next phase of the project.

Day 1: Scientific Progress and One Health Insights Following a warm welcome by Cheryl Baxter (Stellenbosch University) and Claudia Schacht (LINQ), the meeting opened with in-depth presentations highlighting progress across the consortium. Project coordinator Tulio de Oliveira (Stellenbosch University) began the session with an overview of GenPath Africa’s progress in genomic surveillance, including tracking both existing and emerging pathogens. Annelies Van Rie (University of Antwerp) then shared updates on the PARR-TB study, which recently reached a major milestone with the enrolment of its first patient.

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The study aims to use next-generation sequencing to improve diagnosis and clinical management of drug-resistant tuberculosis.

The afternoon focused on GenPath Africa’s One Health activities. Sam Oyola (International Livestock Research Institute) and Michele Miller (Stellenbosch University) shared progress in wastewater-based and genomic surveillance targeting zoonotic threats, including Rift Valley Fever virus and Mycobacterium tuberculosis, in rural South Africa and Kenya. This was followed by Gian van der Spuy (Stellenbosch University) who presented progress in the development of bioinformatics platforms and digital tools designed to streamline data management and analysis.

Capacity building was also a key focus. Cheryl Baxter and Suné Dyers (Stellenbosch University) highlighted hands-on training initiatives in genomic sequencing and analysis and announced the launch of a structured Master’s programme in Bioinformatics at Stellenbosch University, scheduled to begin in 2026. The day concluded with a dynamic brainstorming session led by

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led by Claudia Schacht (LINQ), exploring key exploitable results (KERs) across GenPath Africa’s work packages. Ranging from methodological innovations and strategic guidance to new insights and capacity-building, these KERs will remain central to all upcoming project activities and will serve as a guiding framework to ensure real-world impact across scientific, policy, and public health domains.

D ay 2: Coordination, Communication, and Community Day two opened with an overview of project management by Christoph Cyranski (LINQ), followed by a presentation on dissemination and communication achievements by Hannah Faber (LINQ). The morning continued with updates from representatives of several GenEpi Network working groups, who shared insights into ongoing collaborative initiatives and GenPath Africa’s contributions to strengthening genomic epidemiology across Sub-Saharan Africa as part of this network. After an interactive group work session and closing remarks by Cheryl Baxter, the meeting wrapped up on a high note with a light-hearted treasure hunt and a group outing through Antwerp’s historic city centre - celebrating both scientific advancement and community spirit.

precision medicine and by using genomic epidemiology to guide the public health response. Recent developments in wastewater and One Health surveillance will be applied to detect emerging pathogens. In addition, capacity development activities will include degree training in South Africa, the transfer of technology to the National Public Health Institute of Mozambique and the South African National Health Laboratory Service, and the collaboration with other key players and existing networks across the continent to harmonise training materials.

Through these activities we aim to make precision medicine and precision public health a reality in southern and eastern Africa.

In its mission to advance the impact of genomic surveillance, GenPath Africa has strong partners by its side. It is one of six projects that were created to form a Genomic Epidemiology Network in Sub-Saharan Africa. Together, this powerful new partnership aims to: 1) Increase the use of genomic epidemiology across Africa to answer critical public health questions.

2) Create data platforms through which integrated epidemiologic, clinical, and genomic data can be collected and combined.

Looking ahead We extend our heartfelt thanks to all attendees – both on-site and online – for making GenPath Africa’s second annual meeting such a success. The consortium’s continued commitment and collaboration are instrumental in advancing the project and its goal to expand genomic surveillance in Africa.

GenPath Africa will expand genomics capacity to combat drug resistant HIV-1 and TB through

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3) Implement selected pilot projects that apply genomic epidemiology to specific disease areas and use the results to inform public health decision-making and product development.

4) Establish a community of practice, training programmes, and fellowship opportunities in genomic epidemiology on the continent.

More info: https://www.genpath-africa.org

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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