the_gem_July_2025

issue 7 - volume 8 July 2025

genomics, epidemics & microbes

the gem

Climate Change Hurts Minds Too The WEMA Project Brings Climate and Mental Health Science to Communities

Tuberculosis Genomics Hands-On Bioinformatics Training at Stellenbosch University read it online

Women’s Health HPV Therapeutic Vaccines and Live Biotherapeutics for Genital Health

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Climate Change Hurts Minds Too

Celebrating Women at CERI

Genomic Surveillance

Mental health is increasingly recognised as one of the most urgent yet overlooked consequences of the climate crisis. The Weather Events and Mental Health Analysis (WEMA) Project Brings Climate and Mental Health Science to Communities.

At CERI many of the projects and breakthroughs taking place are being led and supported by dedicated female scientists and researchers. Let’s learn more about their roles, what brought them into science, and how they see their work making a difference.

West Nile virus (WNV), a highpriority pathogen endemic to Africa, has limited genomic data available despite widespread detection. This review reveals major gaps in molecular surveillance and the urgent need for a One Health approach in disease surveillance.

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 & Katrine Anker-Nilssen art director: Victor Hugo Szortyka graphic designers: Maambele 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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Tubercolosis Genomics

Predicting Dengue in Africa

A Visit of Vision

Even though Tuberculosis (TB) has been around for a long time, it remains a major public health problem. Dr Emilyn Costa Conceição recently facilitated hands-on theoretical and practical training in tuberculosis genomics bioinformatics at Stellenbosch University.

Dengue is a mosquito-borne viral disease with expanding global impact. Accurately mapping dengue risk is essential for identifying areas of high transmission and targeting interventions effectively.

KRISP had the distinct honour of hosting Dr Mlungisi Cele, the newly appointed DirectorGeneral of South Africa’s Department of Science, Technology and Innovation (DSTI), for a guided walkthrough of our genomics laboratories at the University of KwaZulu-Natal.

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editorial

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ear gem readers, allow me to introduce myself. I am Katrine Anker-Nilssen, and I have just joined the CERI team as a consultant. Already, I feel that this role is more than temporary – in time, I am certain I will become a firm member of this wonderful team.

I am truly honoured to be part of such a dynamic organisation, one that is not only shaping the future of science in Africa but also changing the global health landscape every single day.

My professional background lies in print magazines and storytelling, and I am excited to bring those skills to the gem. Over the next few months I look forward to uplifiting an already established publication, co-editing it alongside Prof Tulio de Oliveira – whose vision and leadership continue to inspire both within CERI and across the world.

Equally exciting is my involvement with the African STARS Fellowship Programme. This initiative – which brings together the Young Professional Programme (YPP) and Advanced Talented Trainers (ATT) – is a powerful investment in the next generation of African scientists. The new fellows have just arrived at Stellenbosch University, and in the next issue of the gem, and across our online platforms, you will have the chance to meet these remarkable minds, hear about their aspirations, and see how they are contributing to Africa’s scientific future.

This edition is a special one. It shines a spotlight on some of the incredible women at CERI – changemakers who are pushing boundaries in genomics and public health. Their dedication, innovation, and leadership remind us how vital it is to create space for diverse voices in science. We also highlight Prof Lenine Liebenberg’s cutting-edge research in women’s health – from the HPV therapeutic vaccine, to promising developments in live biotherapeutics for genital health.

At CERI, science is never just about the data – it is about people, communities, and impact. It is a platform for science communication, a space where we can celebrate science, share stories, and showcase the people behind the research. From expanding genomic surveillance across the continent to pioneering AIdriven epidemic modelling, CERI continues to prove that African-led research can make a difference both locally and globally.

Thank you for welcoming me into this community.

I look forward to contributing to the growth of the gem, and to sharing the many stories, discoveries, and achievements that make CERI such a unique and important organisation.

Warm regards, Katrine Anker-Nilssen

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Community voices at the centre of climate and health research

Climate Change Hurts Minds Too text: Maambele Khosa and Dr. Astrid Treffry-Goatley photo :

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s Climate change is intensifying extreme weather events across Africa, from floods to heatwaves and droughts. These events disproportionately affect resource-poor communities already carrying the weight of multiple health challenges, often leading to higher rates of injury, illness, and death. While much attention has been paid to the physical impacts of climate change, the mental health consequences, particularly in sub-Saharan Africa (SSA), are largely overlooked. In low- and middle-income countries, nearly three-quarters of people with mental health conditions still receive no treatment, an alarming gap made worse by climate-related stressors and resource constraints.

The Impact of Extreme Weather Events on the Mental Health of Vulnerable Populations in Africa (WEMA) Project emerges as a timely and urgent response to these realities, seeking to answer a research question long ignored in Africa: How do floods, heatwaves, and other extreme weather events affect mental health?

Funded through the Wellcome Trust’s Climate Impacts Award, WEMA is a bold, transdisciplinary initiative involving institutions in Burkina Faso, Kenya, Mozambique, and South Africa. A diverse team of climate scientists, psychiatrists, epidemiologists, statisticians, social scientists, civil society representatives, policymakers, and community members have come together to generate robust evidence and develop community-informed adaptation strategies.

The consortium is led by Prof. Collins Iwuji of the Africa Health Research Institute (AHRI) and involves co-

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investigators from the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, the African Population and Health Research Center (APHRC), the Centre de Recherche en Santé de Nouna (CRSN), Comité para a Saúde de Moçambique (CSM), Bhekisisa Centre for Health Journalism, and the Heidelberg Institute of Global Health.

Generating Evidence WEMA is active in six Health and Demographic Surveillance System (HDSS) sites across the continent.

The project uses a mixed-methods approach, combining: - A rapid literature review of climate-related mental health research in Africa (under review), - Secondary data analysis of health records and extreme weather patterns, - Surveys and structured interviews measuring depression, anxiety, and PTSD, - Digital storytelling workshops led by local facilitators, - Community-led intervention development and advocacy campaigns.

Despite staggered progress across sites due to local ethics approvals and linguistic barriers (with teams working in English, isiZulu, Swahili, Portuguese, Dioula and French), the WEMA consortium is steadily building a model of equitable, decolonial science.

Science that Listens and Learns What makes WEMA powerful is its communityinvolved approach. The community engagement and involvement (CEI) strategy is co-led by Dr Astrid Treffry-Goatley (CERI) and Dr Gill Black (independent researcher). At each site, Community Engagement

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Teams (CETs) and Community-Based Co-Researchers (CBCRs) have been recruited and trained in participatory research methodologies, including digital storytelling.

Digital stories enable people to narrate personal experiences using their own voices, images, and artwork. These short first-person films provide insights into how communities experience extreme weather and potential solutions to mitigate the impact on their mental health. To date, two five-day workshops have been conducted—one in May at APHRC (Kenya) and another in June at AHRI (South Africa). In September, workshops will run in Burkina Faso and Mozambique.

From Stories to Systems Change In WEMA, digital stories are both creative outputs and data. They are analysed in participatory thematic analysis workshops, where community members and researchers identify themes linking extreme weather and mental health. This process will be followed by knowledge exchange events between CBCRs and climate scientists in late 2025. In 2026, community-authored results will be combined with other project evidence at brainstorming sessions with health professionals and policymakers. These events will spark dialogue, enable cross-sectoral exchange, and connect lived experiences to climate and health research. The stories will also catalyse

policy engagement, allowing decision-makers to see and hear realities behind the data. As Dr. Chanelle Mulopo, a WEMA postdoctoral researcher at CERI, leads the qualitative research component. “The digital stories we’re co-creating with communities are crucial,” she explains. “They ensure that evidence doesn’t just sit in journals, it reaches the right people, in the right form, to inspire meaningful action.”

Science for All As National Science Week calls us to celebrate science for society, WEMA stands as an example of inclusive, responsive science. It’s not just about measuring weather patterns or tracking diagnoses. It’s about connecting scientific inquiry with lived experiences and ensuring that voices from affected communities shape the policies that influence their futures.

Building Science That Heals Ultimately, WEMA aims to influence how African nations respond to both the visible and invisible impacts of climate change. By embedding mental health into climate adaptation strategies, WEMA is not only making science more human, it’s making policy more compassionate.

As South Africa celebrates National Science Week, the WEMA project offers a reminder: science isn’t just what we know—it is how we care, and who we include.

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text : Katrine Anker-Nilssen ph otos : Supplied

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Wo m e n i n S c i e n c e

BREAKING BARRIERS, BUILDING KNOWLEDGE Celebrating some of CERI’s Inspiring Women

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t the Centre for Epidemic Response and Innovation, many of the projects and breakthroughs taking place are being led and supported by dedicated female scientists and researchers.

Aligning with Women’s Day and Women’s Month 2025, we

are celebrating a few of these inspiring women to learn more about their roles, what brought them into science, and how they see their work making a difference – both within CERI and beyond.

Let’s find out a bit more about Dr Nonsikelelo Precious Hlongwa, Dr Cari van Schalkwyk, Dr Yuri Munsamy, Dr Chanelle Mulopo, Mrs Gugulethu Mkhize, and Dr Emilyn Costa Conceição.

Dr Nonsikelelo Precious Hlongwa Dr Nonsikelelo Precious Hlongwa grew up in a semi-rural community in Mpumalanga, where she witnessed how health challenges, especially preventable diseases, affected many of her family members – including her parents. She explains that this sparked a deep curiosity about microbes, water, and health. “Even though I had limited access to labs, libraries, or even computers in school, I worked twice as hard to catch up,” says Nonsie. “My passion grew through each academic step, and led to a PhD focused on molecular detection of pathogens in wastewater.”

CLICK HERE TO READ THE FULL STORY

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Dr Cari van Schalkwyk Dr Cari van Schalkwyk’s fascination with mathematics and health began during her studies in Actuarial Science and Mathematical Statistics at Stellenbosch University (BComm 2006, MComm 2009). “My introduction to epidemiological modelling started during my Master’s project, estimating incidence of recent HIV infection among pregnant women in Zimbabwe, when I joined SACEMA (South African Centre for Epidemiological Modelling & Analysis) initially as a statistician in 2010,” explains Cari. Driven by this interdisciplinary path, she went on to earn a PhD in Epidemiology and Biostatistics from the University of Cape Town, specialising in transmission dynamics of HIV and HPV. CLICK HERE TO READ THE FULL STORY

Dr Yuri Munsamy Dr Yuri Munsamy’s journey into science began at the age of 10, when she became fascinated by iron shavings being drawn to a magnet. “Years later, in my first microbiology lecture, I was captivated by bacteriophages (viruses that infect bacteria) and blown away by the engineering precision of a non-living organism that packs lightly in terms of genetic material,” she says with a smile.

CLICK HERE TO READ THE FULL STORY

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Dr Chanelle Mulopo Dr Chanelle Mulopo’s journey into science, particularly health sciences, has been deeply personal and shaped by lived experiences. “Growing up in various low- and middleincome countries, I witnessed stark disparities in access to healthcare. While my family had access to private care, I saw many around me – often my playmates – suffer due to lack of access, especially during a dysentery outbreak that claimed the lives of several children,” she explains. “My brother and I also fell ill, but thanks to private healthcare, we recovered. That moment left a lasting impression on me and sparked my interest in health equity.”

CLICK HERE TO READ THE FULL STORY

Gugulethu Mkhize Gugulethu Mkhize thoroughly enjoyed biological sciences as a learner during her basic education years, and always achieved good grades in this subject. “Enrolling for a qualification in science had a lot to do with the influence of my family and the environment I grew up in; there was a strong focus on the fact that STEM subjects are important and will lead to good careers,” says Gugu.

After working for few years in the laboratory, an opportunity to join the clinical trials group in a support role of Grant Manager arose. “I was attracted to this opportunity, mainly due to the impact of their research in the community,” she explains.

CLICK HERE TO READ THE FULL STORY

Dr Emilyn Costa Conceição Dr Emilyn Costa Conceição’s journey into science started in the Brazilian Amazon, where she was born and raised.

“Growing up in a region deeply affected by infectious diseases, I became curious about the biology behind illness and health disparities,” she explains. “This led me to study biology at the Federal University of Pará, and later pursue a master’s in infectious diseases and a PhD in microbiology.”

CLICK HERE TO READ THE FULL STORY

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CLIMADE

GENOMIC SURVEILLANCE GAPS IN AFRICA FOR WEST NILE VIRUS Publication at the Lancet Microbe Moir et al. 2025

Ope n Acce ss: Scan the QRCode to access the publication f ig ur e : Monika Moir

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est Nile virus (WNV), a high-priority pathogen endemic to Africa, has limited genomic data available despite widespread detection. This review reveals major gaps in molecular surveillance and the urgent need for a One Health approach in disease surveillance.

Summary West Nile virus (WNV) is a priority pathogen that poses a high risk for public health emergencies of global concern. Although WNV is endemic to Africa, only few (n=63) whole genomic sequences are available from the continent. In this review, we examined the status of the molecular testing and genomic sequencing of WNV across Africa and mapped its global spatiotemporal spread. WNV has been detected in 39 African countries, the Canary Islands, and Réunion Island. Although publications, including those with molecular data, originated from 24 of these countries, genomic sequences were available from only 16 countries. Our analysis identified regions with detected viral circulation but without molecular surveillance.

The current literature has substantial knowledge gaps in terms of the disease burden, molecular epidemiology, and distribution of WNV in Africa.

Addressing these gaps requires an integrated One Health surveillance approach, which is challenging to establish. We propose three key surveillance

needs that could improve the current understanding of the WNV disease burden in Africa, to strengthen the global public health response to this vector-borne disease.

Discussion of the Findings Although WNV is a priority pathogen of international concern, our analysis identified key knowledge gaps in the true burden of disease, molecular epidemiology, and distribution of WNV in Africa. We found evidence of viral circulation in 39 of the 55 African countries. Molecular data for WNV are available from 24 of these countries, but most of them have insufficient data for all hosts and vectors. Only 63 genomic sequences from 16 African countries are available publicly.

For some countries, evidence of WNV circulation is solely based on studies that used serological methods, as there are no existing molecular data.

Serological cross-reactivity among flaviviruses and cocirculation of multiple antigenically related flaviviruses in Africa might have resulted in an overestimation of the true extent of WNV circulation in these countries. The use of virus neutralisation tests to confirm IgM and IgG serology is important to accurately assess the incidence of cases and seroprevalence.

back as 1939), research efforts have largely focused on the virus’s spread in North America and Europe, with comparatively little work conducted in Africa. Here, we discuss three key challenges, which are aligned with WHO’s technical brief on research prioritisation for pandemic and epidemic intelligence.

Conclusion The burden of WNV (in addition to that of other arboviruses) remains under-recognised in Africa, with fragmented data and weak surveillance. Clinical and genomic surveillance for WNV are inadequate, hindering public health responses and obscuring the true disease burden.

Open Access Publication Identifying genomic surveillance gaps in Africa for the global public health response to West Nile virus: a systematic review.

Monika Moir and Colleagues.

The Lancet Microbe, 2025. https://www.thelancet.com/ journals/lanmic/article/ PIIS2666-5247(25)00104-1/fulltext

Our findings show that Africa is the origin of internationally important WNV lineages. However, despite early epidemics in Uganda, Sudan, the Democratic Republic of the Congo, and Kenya (as far

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ADVANCING TUBERCULOSIS GENOMICS IN AFRICA Hands-On Theoretical and Practical Training at Stellenbosch University

text: Dr Emilyn Costa Conceição photo : Supplied

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rom 7 to 10 July 2025, I had the privilege of facilitating the Theoretical and Practical Training in Tuberculosis Genomics Bioinformatics, hosted at the Biomedical Research Institute (BMRI), Stellenbosch University, Cape Town, South Africa. This intensive, in-person training brought together 30 trainees and eight facilitators as part of a collaborative effort spanning several work packages (WPs) under the GenPath Africa initiative’s working packages (WP): WP-1 (Genomic Surveillance), WP-2 (Precision Action for RifampicinResistant TB - PARR-TB), WP4 (Bioinformatics), and WP-5 (Capacity Building).

Why is this Initiative necessary in Africa?

Even though Tuberculosis (TB) has been around for a long time, it remains a major public health problem. Each year, around 10 million people get sick with TB, and more than 1 million lose their lives to the disease. Africa bears a disproportionate burden of TB, particularly in regions with high HIV prevalence, limited access to healthcare, and constrained public health infrastructure. On top of that, TB is becoming harder to treat because some strains of the bacteria no longer respond to the usual medicines. These drugresistant forms of TB are more complicated and expensive to treat and can spread quickly if not caught in time.

This is where new technologies play a key role, helping to make

TB diagnosis faster and more accurate. One example is wholegenome sequencing (WGS), which allows us to gain detailed insights into the TB bacteria. This initiative is especially important because it supports countries across Africa in using advanced tools like WGS to better understand how TB spreads, detect drug resistance sooner, and guide more effective treatment. By strengthening local expertise and infrastructure, we can help build more resilient public health systems, protect vulnerable populations, and take meaningful steps toward ending TB.

de Oliveira, Dr Eduan Wilkinson, and Dr Thomas Sanko), and the Bioinformatics team (Prof Gian van der Spuy, Dr Elizna Maasdorp, and MSc Abhinav Sharma).

Where were the Trainees from?

Trainees represented a diverse range of institutions such as Stellenbosch University, the National Health Laboratory Service (NHLS), Namibia University of Science and Technology (NUST), Instituto Nacional de Saúde (Mozambique), the University of Cape Town, and Groote Schuur Hospital.

How did the Training Course go?

Who supported us?

Over four days, the program offered both foundational and advanced modules covering key topics in TB genomics and bioinformatics. These included an introduction to sequencing technologies, use of package managers and containers, version control with Git and GitHub, downloading and submitting genome data to repositories such as NCBI and ENA, secure data handling, and hands-on analysis using the MAGMA pipeline. We also introduced participants to the Nextstrain platform for genomic epidemiology and visualisation.

Which research groups were involved in the process?

The initiative was co-funded by the Global Health EDCTP3, the European Union, and the World Bank.

What is next?

The training fostered an enriching environment of scientific exchange, skill development, and cross-border collaboration, contributing meaningfully to strengthening TB genomics capacity across Africa. We plan to carry out more initiatives like this, guided by participants’ feedback, and to further strengthen our strategies for building capacity in the highly limited field of Bioinformatics.

The course was led by research teams from Stellenbosch University, including the TB Genomics group (Prof Rob Warren, Dr Emilyn Costa Conceição, and Dr Nabila Ismail), the Centre for Epidemic Response and Innovation (CERI; Prof Tulio

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Inspiring The Next Generation Learners Explore Genomics at KRISP

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text: Paul Harris photo : Shirelle Naidoo

n July, KRISP had the privilege of hosting a group of bright young learners from CAPRISA’s Young Adults Workplace Experience Programme, as part of a broader effort to inspire and equip South Africa’s next generation of healthcare professionals.

These students, with aspirations in medicine, nursing, and pharmacy, were given a rare behind-the-scenes look at one of Africa’s leading genomics facilities. From touring the state-of-the-art laboratories to participating in a fun, hands-on DNA extraction experiment using frozen strawberries, the visit offered a unique blend of scientific discovery and career exploration.

For many of the participants, it was their first time inside a research lab. Yet, their curiosity, enthusiasm, and sharp questions spoke volumes. “These moments of engagement are powerful,” noted Dr Richard Lessells, Infectious Disease specialist at KRISP.

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“They reveal the potential of the next generation in South Africa when exposed to the right environments and opportunities.”

This initiative is part of CAPRISA and UKZN’s broader mission to bridge the gap between education and meaningful career pathways. KRISP’s involvement reflects its own commitment to nurturing local talent, reversing the brain drain and promoting science in Africa, for Africa.

Congratulations to CAPRISA for leading such an impactful programme. At KRISP, we’re proud to support initiatives that open doors, spark curiosity, and build a generation of scientists who will carry African science forward.

Caption: Dr Jennifer Giandhari and Dr Sureshnee Pillay of KRISP supervise learners as they work through a simple DNA extraction experiment.

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Postgraduate Open Day The Faculty of Medicine and Health Sciences (FMHS) text: Yusasha Pillay photo : Supplied

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he Faculty of Medicine and Health Science (FHMS) hosted its Postgraduate Open Day 2025 on 11 and 12 July at Stellenbosch University’s Biomedical Research Institute (BMRI), Tygerberg Campus.

Over the two-day event, prospective students explored the diverse range of postgraduate programmes, cutting-edge research opportunities, and worldclass facilities offered at FMHS. Faculty departments showcased their work at dedicated exhibition stands, while visitors gathered valuable information about scholarships, funding, and career development in science, medicine, and health sciences.

Among the standout participants was the Centre for Epidemic Response and Innovation (CERI), which drew strong interest with an interactive stall showcasing flow cells, sequencing cartridges, and a variety of other materials central to our groundbreaking work in pathogen genomic surveillance.

funding, and mentorship was a compelling highlight for many aspiring scientists.

Attendees also took part in BMRI and campus tours exposing them to CERI’s state of the art facilities, received guidance from the Postgraduate Office, and enjoyed a fun incentive - a lucky draw for Matie shop vouchers for those who visited 10 or more stands.

The event successfully inspired the next generation of researchers and health professionals, showcasing FMHS’s ongoing commitment to academic excellence, scientific innovation, and the future of healthcare in Africa.

A heartfelt thank you to all attendees, exhibitors, and organisers for making this event such a success.

CERI’s vision - to respond effectively to epidemics, enhance biomedical discovery, and improve disease prevention and treatment in Africa - was brought to life through engaging conversations with staff, postdocs, and students. As part of both the School for Data Science and Computational Thinking and the FMHS, CERI is a leading hub for innovation and epidemic response in Africa.

Visitors to the CERI stall learned about the centre’s advanced sequencing technologies, including the Illumina NovaSeq X Plus, NovaSeq 6000, NextSeq 2000, MiSeq, and Oxford Nanopore’s GridION, as well as our local capacity for producing human, animal, plant, and microbial genomic data. CERI’s dedication to building Africa’s genomic self-reliance through training,

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Predicting Dengue Risk in Africa text: Tulio de Oliveira f ig ur e : Jenicca Poongavanan

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engue is a mosquito-borne viral disease with expanding global impact. Accurately mapping dengue risk is essential for identifying areas of high transmission and targeting interventions effectively.

Most current approaches to mapping dengue risk focus on environmental suitability for the virus or its mosquito vector, rather than estimating actual disease burden. In this study, we used an incidence-based approach; disaggregation regression, to estimate dengue cases at high spatial resolution using national and regional case data from Latin America. We then applied the model to Africa, where surveillance data are limited, and compared its predictions to three other common types of dengue risk maps.

Our results showed that while all approaches provided some insight into geographic risk patterns, they often highlighted different areas as priorities. Our incidencebased model captured both where dengue might occur and how intense transmission may be, helping bridge the gap between environmental and ecological suitability of transmission and real-world disease burden. This approach can support more informed decision-making in areas with limited surveillance and guide targeted control efforts.

Results from the prediction models To estimate fine-scale dengue burden from aggregated case data, we applied a disaggregation regression model trained on subnational case reports from 14 countries in Central and South America, using data from 2018 and 2019 to maximise spatial coverage and resolution. The model uses environmental and

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demographic covariates to downscale aggregated case counts to ∼10 km2 resolution. Model performance was evaluated using 5-fold spatial block cross-validation, wherein the study area was divided into five spatial blocks of approximately equal size. We selected five spatial blocks to balance spatial representativeness with computational feasibility, as increasing the number of folds would have substantially raised the computational burden given the scale and resolution of the dataset.

The model was iteratively trained on four blocks and tested on the fifth to assess predictive accuracy within the training region. The reported correlation reflects the agreement between observed and modelpredicted dengue incidence at the administrative level, calculated by aggregating pixel-level model predictions and comparing them to reported surveillance data. We used Spearman’s correlation.

Overlap Between Model-Predicted Incidence and Other Dengue Risk Indicators in Africa To assess how our model qualitatively compares with existing risk frameworks, we compared the spatial estimate output from our disaggregation model: predicted incidence (Figure 3A) and three widely used dengue risk indicators: (i) the dengue Suitability Index (Figure 3C), (ii) the transmission potential (Index P) (Figure 3D), and (iii) the vector suitability index for Aedes aegypti (Figure 3B). Assessing agreement and divergence among them provides insight into where models converge to flag consistently high-risk areas, and where uncertainties remain.

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To enable direct spatial comparison and identify areas of high-risk concordance, we applied model-specific thresholds to each risk surface: >0.5 for both the Aedes vector suitability and dengue environmental suitability indices, >0.5 for the transmission potential (Index P), and >1 predicted case (per 100k inhabitants per pixel) for the disaggregation-derived incidence map (Figure 4-Inset). We then created binary high-risk maps and overlaid them to count how many models flagged each pixel as high-risk (Figure 4 - above).

Figure 4 Legend (Above) Agreement among dengue risk models across Africa.

Map showing the number of dengue risk indicators: predicted incidence, transmission potential, dengue suitability index and vector suitability index, that classify each pixel as high risk. High-risk classification was determined using model-specific thresholds: >0.5 for suitability indices and transmission potential; >1 of predicted incidence per 100k people (per pixel). Darker red areas indicate strong agreement among all models in predicting high dengue suitability, whereas lighter green areas reflect lower concordance. Grey regions represent areas where all four models predicted low risk based on the respective threshold.

reveal high concordance across much of the coastline of West Africa, in countries such as Nigeria, Benin, Togo, Ghana and Ivory Coast. We also observe notable overlap across parts of the southern Sahel (including Burkina Faso, southern Mali, and southwestern Niger, northern part of Nigeria). In these regions, the predicted incidence from the disaggregation model aligns spatially (Figure 4-Inset) with both high transmission potential and vector suitability, suggesting that environmental and epidemiological conditions are simultaneously favorable for dengue transmission.

Mauritius also seems to be at the intersection of high risk across at least three indicators.

Open Access Publication Disaggregation Regression and Multi-Model Evaluation for Predicting Dengue Risk in Africa.

Jenicca Poongavanan and Colleagues.bioRXiv, 2025. https://www.biorxiv.org/content/10.1101/2025.06.17.66 0069v1.full

The comparison between all four dengue risk maps

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A VISIT OF VISION D R M LUN GI S I CEL E TOUR S K RI S P’S GE N O MI CS FACI L I T I ES text: Pa ul H a r r is photo : Pa ul H a r r is

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his month, KRISP had the distinct honour of hosting Dr Mlungisi Cele, the newly appointed Director-General of South Africa’s Department of Science, Technology and Innovation (DSTI), for a guided walkthrough of our genomics laboratories at the University of KwaZulu-Natal. This was part of his first visit to UKZN as DG to familiarize himself with the work and projects that the DSTI supports.

Dr Cele’s visit comes at a pivotal moment for South African science, as momentum builds to strengthen local research ecosystems and scale innovation-led public health solutions, in light of the recent international funding cuts. During the visit, the KRISP team had the opportunity to showcase how cutting-edge genomic science is being applied to real-world challenges in South Africa and beyond, but also the people—scientists, students, and collaborators—who bring this science to life. From high-throughput sequencing platforms to our training and capacity-building programmes, the KRISP and CERI teams highlight the essential role that local research infrastructure plays in advancing public health, precision medicine, and outbreak response.

The DSTI has long been a steadfast ally of the genomics community, playing an important role in shaping the national research agenda and fostering the conditions for

excellence. Through their ongoing support, initiatives like ours have been able to build and maintain world-class capacity, respond to public health challenges, such as the COVID-19 pandemic, and contribute meaningfully towards the global knowledge base.

“We are so proud to host the new Director-General of DSTI! It is so important to work with our government to advance science, technology and innovation,” said Prof Tulio de Oliveira, Director of KRISP. “Visits like these underscore the importance of sustained collaboration between government, academia, and research institutions,” said Dr Jennifer Giandhari, Laboratory Head at KRISP. “They help to align our shared vision for a more resilient, innovative, and healthsecure South Africa.”

Dr Cele’s visit served as both an endorsement of the work being done and a renewed call to action to strengthen science policy and infrastructure across the continent.

KRISP looks forward to deepening its collaboration with Dr Cele and the DSTI as we continue to build a future where African science leads, informs, and delivers for all.

CAPTION: Dr Mlungisi Cele engages with KRISP staff during his tour of our state-of-the-art genomics facilities at UKZN.

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Reflections from Global Convenings on HPV T h e r a p e u t i c s a n d Va g i n a l Biotherapeutics

Investing In Women’s Health text: Prof Lenine Liebenberg photo : Supplied

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omen’s health remains a critical yet underfunded frontier in global health research, particularly in sub-Saharan Africa, where rates of cervical cancer and reproductive tract infections continue to drive morbidity and mortality. As a scientist dedicated to addressing these inequities, I recently represented CERI by showcasing my research on this front at two pivotal Gates Foundation meetings in Durban, South Africa: the HPV Therapeutic Vaccine Convening and the VIBRANT Consortium Meeting on Live Biotherapeutics for Genital Health.

In KwaZulu-Natal, South Africa, our research shows HPV prevalence reaching 74% among young women, with oncogenic types not targeted by current vaccines contributing significantly to disease burden. Through longitudinal sampling and advanced immunological assays, our team investigates immune cell responses strongly associated with natural HPV clearance, offering promising insights for therapeutic vaccine design.

These meetings provided a forum to share our research and a lens into the remarkable collaborative efforts worldwide to improve women’s health outcomes.

Although the Gates Foundation’s goals are changing, it was heartening to learn at the conference that there is still a strong commitment to exploring new collaborations and ways to carry out this vital work.

The meeting demonstrated remarkable advancements in our understanding of the immunological correlates of HPV control and emphasised the significance of filling in knowledge gaps necessary to develop successful treatments.

Spotlight on HPV Therapeutic Vaccines: A Call for Continued Commitment

VIBRANT: Innovating Live Biotherapeutics for Genital Health

The HPV Therapeutic Vaccine (TxV) Convening brought together leading clinical scientists, laboratory scientists, social scientists and other public health experts to tackle one of the most pressing challenges in women’s health: how to treat persistent human papillomavirus (HPV) infections that can progress to cervical cancer.

The VIBRANT Consortium Meeting focused on live biotherapeutic products (LBPs) containing Lactobacillus crispatus, a beneficial bacterium known to support vaginal health and reduce the risk of bacterial vaginosis (BV). Our contribution centred on defining host immune responses associated with durable colonisation by LBPs, a key determinant of success for these novel interventions.

While prophylactic vaccines effectively prevent infection with HPV types responsible for most cervical cancers, they neither clear existing infections nor address the high prevalence of oncogenic non-vaccine HPV types in many countries.

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By integrating flow cytometry, cytokine profiling, and advanced multi-omics, we investigated early immune signatures predictive of long-term engraftment of beneficial bacteria, laying the foundation for optimising

genomics, epidemics & microbes

future LBP formulations. Discussions about embargoed preliminary data also emphasised actionable research priorities, such as the importance of vaginal mucosal immunity, epithelial barrier integrity, and behavioral factors influencing colonisation.

— to move promising discoveries from bench to bedside, train a new generation of African women’s health research leaders, and develop contextappropriate interventions to save lives.

A Vision for the Future

The vibrancy of the meeting — no pun intended — was a testament to the incredible progress and collaboration across scientific disciplines, with meaningful contributions from microbiologists, immunologists, clinical trialists, and social scientists.

The Imperative for Investment Both meetings underscored an undeniable truth: women’s health research needs to be sustained, and targeted investment must be made to realise its transformative potential. As highlighted by the Gates Foundation, maternal mortality, reproductive cancers, and infectious diseases disproportionately affect women in sub-Saharan Africa, yet locally driven research efforts remain chronically underfunded.

CERI is proud to partner with other worldrenowned institutions and invest our intellectual and infrastructural resources into research on HPV, STIs, and live biotherapeutic strategies, leveraging state-ofthe-art laboratories and a track record of impactful, community-embedded studies. However, financial investment is vital to sustain and expand this work

I returned from these gatherings feeling motivated and uplifted by so many bright minds coming together to address the urgent problem of STIs and BV. The research community is steadfast in its commitment to guaranteeing that women everywhere receive the health interventions they are entitled to. However, these initiatives risk stalling in the absence of strong finance.

We invite collaborators, donors, and legislators to work with us toward a future where women’s health research is given the urgent attention it needs. We can transform innovation into equity by working together to empower women, build stronger communities, and improve health outcomes in Africa and beyond.

CAPTION: The HPV convening group, including Gates Foundation representatives and leading clinician and bench scientists driving the HPV therapeutic vaccine agenda.

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the gem

ADVANCING HIV SCIENCE KRISP Contributes to IAS 2025 with Drug Resistance Research text: Paul Harris photo : Tulio de Oliveira

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his July, members of the KRISP team participated virtually in the 13th International AIDS Society (IAS) Conference on HIV Science, hosted in Kigali, Rwanda. The hybrid conference convened leading researchers, clinicians, and advocates from around the world to share cutting-edge developments in HIV prevention, treatment, and care.

With over 1400 scientific posters and 142 oral abstract presentations, IAS 2025 reaffirmed its place as one of the most influential platforms for shaping the global HIV research agenda. For KRISP, it was an opportunity to both contribute to and learn from this vibrant international scientific community.

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The team presented two eposters from the DTG RESIST study, our international collaborative study focused on resistance to dolutegravir-based antiretroviral therapy (ART). One of the research posters led by Dr Jennifer Giandhari and Shirelle Janine Naidoo focused on lowfrequency dolutegravir resistance mutations (sometimes referred to as minority variants) - an area where evidence is needed to guide treatment monitoring policies and practices.

The research showed that, whilst low-frequency drug resistance mutations were observed, their detection generally did not change the predicted level of DTG resistance. This gives reassurance that drug resistance testing using either Sanger sequencing or nextgeneration sequencing platforms

remains appropriate.

“This work highlights how international collaborations can lead to actionable insights that can improve the way we care for and monitor people living with HIV,” said Shirelle Naidoo, a Medical Scientist at KRISP. “It also demonstrates our ongoing commitment to applying advanced genomics to address major public health challenges.”

KRISP extends its thanks to the many collaborators and partner institutions that made this work possible, and the funders, including the Technology Innovation Agency and U.S. National Institutes of Health.

genomics, epidemics & microbes

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the gem

Communication

MEDIA COVERAGE Our work showcased in videos and featured on TV

New PI? Feeling overwhelmed?

In this short clip, Prof Tulio de Oliveira shares three survival tips for early-career research leaders navigating the challenging (and often chaotic) start of a PI journey. This is the start of a new hashtag#RealTalkResearch series—bite-sized advice from seasoned scientists to support and uplift the next generation of researchers.

Watch the full video here: https://www.youtube.com/watch?v=C_pKWszgGkk

Can I Start a Family and Build a Research Career?

Starting a research career is tough. Starting a family? Also tough. Doing both at the same time? That’s the big question many early-career scientists are quietly asking. In this video, Prof Tulio de Oliveira shares his thoughts on one of the most personal yet unspoken challenges in academia: balancing/ starting a family life with the demands of building a lab and a scientific career. His advice might surprise you — but it’s grounded in empathy, experience, and a long view of what truly matters.

Watch the full video here: https://www.youtube.com/watch?v=6ECy2wDjOzg

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genomics, epidemics & microbes

Developing the Tools for a Clinical Metagenomics Platform in SA This seminar brought together leading researchers, clinicians, and faculties to explore the tools, data systems, and collaborations needed to make clinical metagenomics a reality in the region. Presentation cover key topics including pathogen surveillance, bioinformatics infrastructure, and real-world clinical applications.

Watch the full video here: https://www.youtube.com/watch?v=umOsVghQZuk

China Records 1000s of Chikungunya cases The NICD has confirmed 10 travel-related cases of Chikungunya Virus in the country so far this year. It’s caused a public health crisis in China with over 7-thousand infected. The mosquitoborne virus is spreading rapidly through Guangdong province.

Watch the full video here: https://www.enca.com/news/ nicd-reports-10-travel-related-cases-chikungunya-virus

Chikungunya: What you need to know Chikungunya, a Category III notifiable medical condition. China has reported 7 000 cases of a mosquito-borne virus since July, prompting measures similar to those taken during the Covid-19 pandemic. Peter Ndoro speaks to Prof Tulio de Oliveira, from the Centre for Epidemic Response and Innovation at Stellenbosch University, about this story.

Watch the full video here: https://www.youtube.com/watch?v=XaSwb9bxx1Q

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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