the gem genomics, epidemics & microbes Mar 2025

volume 8 - issue 3 March 2025

genomics, epidemics & microbes

the gem

International Women’s Day Celebrating our remarkable women in science who are leading the world

40 Publications in a PhD A Conversation with Dr. Houriiyah Tegally,head of Data Sciences at CERI

Africa’s genomic revolution COVID-19 was the catalyst for Africa’s genomic revolution

read it online

the gem

summary

04

06

10

editorial

40 Publications During a PhD

Oppenheimer Scholarship

In this issue we celebrate international womens’ month and reflect on how science can illuminate during challenging times.

A conversation with Dr. Houriiyah Tegally, head of Data Sciences at CERI, on breaking barriers and leading epidemic response.

At just 25 years old, Nikita is making remarkable strides in the field of viral genomics. As a PhD candidate at Stellenbosch University, she received a Oppenheimer Memorial Trust Scholarship.

the gem: Centre for Epidemic Response and Innovation (CERI) & South African Centre for Epidemiology and Modelling Analysis (SACEMA), Stellenbosch University & KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), UKZN, Durban; director: Tulio de Oliveira; editors: Cheryl Baxter, Maambele Khosa ; art director: Victor Hugo Szortyka; graphic designers: Maam bele Khosa, Ronison Guimaraes, Tulio de Oliveira; websites: https://ceri.org.za/ https://www.krisp.org.za/, https://www.sacema.org/

2

genomics, epidemics & microbes

12

16

22

From Ice to Insights

Africa’s genomic revolution

It is a time for solutions

Nosipho and Mayibongwe, two PhD students in the African Microbiome Group, recently embarked on separate research voyages to Antarctica.

Feature piece in Nature Africa on our work at CERI and KRISP. Five years on: how COVID was the catalyst for Africa’s genomic revolution.

In light of the USA decision to freeze foreign aid, Professor Tulio de Oliveira emphasizes that the U.S. may face greater losses than its 1% investment in foreign assistance.

3

the gem

4

genomics, epidemics & microbes

editorial he month of March passed swiftly, marked by the International Women’s Day. Those familiar with CERI, KRISP, and SACEMA are aware that over 70% of our staff, postdoctoral researchers, and postgraduate students are women.

This is a vital moment to acknowledge and celebrate the remarkable achievements of our female scientists.

T

In this edition of the gem, we feature an insightful conversation with Dr. Houriiyah Tegally, our Head of Data Sciences. Dr. Tegally discusses her impressive accomplishment of publishing 40 manuscripts during her PhD and her success in establishing a large data science team less than two years post-graduation. Additionally, we spotlight the scientific endeavors of two PhD students from the Africa Microbiome Group as they participate in a scientific exhibition in Antarctica. We also commend Dr. Jennifer Giandhari for her recognition for contributions to science, technology, and innovation at TIA’s inaugural Women Technology Innovation Programme, as well as Nikita Sitharam for receiving the Oppenheimer Memorial Trust Scholarship.

This issue of the gem also addresses pressing challenges, including the reduction of U.S. funding to South Africa. Two pieces delve into this topic: an in-depth article featured in Spotlight and an interview that I gave that was aired on national television. Moreover, we are working to advance complex tuberculosis (TB) treatment program with the HARVEST trial, a randomized controlled trial aimed at evaluating the efficacy of high-dose oral rifampicin in improving survival rates among adults living with TB meningitis, both HIV-positive and HIV-negative.

Furthermore, we present novel genomic analyses highlighting the international spread of the Oropouche Virus, and we celebrate another award received by SACEMA. To conclude this editorial, I wish to reflect on an inspiring week spent at the Africa Leadership Initiative of the Aspen Institute in Spier, as exemplified in the accompanying image, which illustrates how science can illuminate during challenging times. text: Tulio de Oliveira

5

the gem

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

40 PUBLICATIONS DURING A PHD AND NOW OVER 70 ONE YEAR AFTER PHD A Conversation with Dr. Houriiyah Tegally on Breaking Barriers and Leading Epidemic Response Picture: Mauritius, Dr. Tegally’s hometown text: Maambele Khosa

6

genomics, epidemics & microbes

F

or International Women’s Day, we spotlight Dr. Houriiyah Tegally, a powerhouse in data science and epidemic response. As the Head of the Data Science Unit at CERI, she has made numerous contributions to infectious disease research, with over 100 publications including 40 during her PhD. From tracking SARS-CoV-2 variants in real time to integrating AI and climate data into epidemic modeling, Dr. Tegally is redefining how we predict and respond to global health threats. In this exclusive conversation, she shares her journey, challenges, and vision for the future of data-driven public health, accelerating action for a healthier future.

1. Your career in data science has grown rapidly.

How did you get started, and what led you to specialize in epidemic response?

Dr. Houriiyah Tegally: I come from a background in computational biology and bioinformatics, and my journey into data science began during the pandemic. I started by analyzing large volumes of pathogen genomic data, which was both challenging and fascinating. Beyond just working

with numbers, I quickly realized that the most powerful part of the process was transforming complex data into compelling, visually clear stories. Science communication became just as important as the research itself.

This field required a lot of self-learning, but I loved the creative side of visualizing epidemiological data. The more I worked with large datasets—integrating phylogenetics, demographics, and mobility data—the more I saw the potential of data science in epidemic response. Today, my work involves using diverse datasets to understand how environmental factors influence disease transmission, helping predict and mitigate future outbreaks.

2. How do you approach cross-disciplinary collaborations, and what role have they played in your research success?

Cross-disciplinary collaborations are vital in epidemic response. Data science does not exist in isolation—it relies on laboratory scientists, virologists, and clinicians who generate the raw disease data. The most impactful research happens when different stakeholders, including public health scientists and policymakers, collaborate to co-create and interpret data.

7

the gem

3. What drives you to keep publishing, and what do you find most rewarding about your research?

In the field of emerging infectious diseases, the most fulfilling aspect is being able to respond to outbreaks in near real-time. Research isn’t just about publishing—it’s about providing critical insights fast enough to make a difference in public health. A publication is just a bonus.

During the SARS-CoV-2 pandemic, our team prioritised rapid data sharing, and our work on the Beta and Omicron variants directly influenced policies on vaccine rollouts and lockdowns in South Africa. More recently, we studied the re-emerging Oropouche virus in South America—an understudied disease system—while the epidemic was still ongoing, ensuring our findings could drive further research and response efforts.

Balancing multiple projects comes down to collaboration. At CERI, we have an incredible team of data scientists, modelers, and students who work together to tackle urgent outbreaks. It’s that spirit of teamwork and shared purpose that makes this work so rewarding.

4. Securing grants and funding is critical to advancing research but can be challenging. What strategies have worked for you in obtaining funding for your projects, and what advice would you give to early-career scientists looking to secure grants?

The key is persistence. Seek as many opportunities as possible and don’t view rejections as failures. Instead, treat them as valuable feedback to improve your next grant proposal. Over time, small grants start coming through, and with experience, larger ones follow.

“”

one person alone cannot go far, so we rely on one another’s strengths 8

Collaboration and mentorship are also essential. In science, it’s rare to succeed alone. Working with established scientists and leveraging their strengths can open doors to funding opportunities and provide invaluable insights into grant-writing strategies.

5. Looking ahead, what are your aspirations for the future, and how do you see data science shaping global health challenges?

The world is changing rapidly due to climate change, population growth, and evolving public health policies.

These changes make epidemics harder to predict. My goal is to develop advanced data analytics frameworks in epidemiology, disease ecology, and phylodynamics to improve our ability to anticipate infectious disease threats.

One promising avenue is the integration of AI into infectious disease modeling, which can help overcome existing methodological barriers and enhance prediction accuracy.

genomics, epidemics & microbes

About Dr. Houriiyah Tegally: Dr. Houriiyah Tegally, 31, is the Head of Data Science at the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, South Africa. She holds a PhD in Virology & Bioinformatics and has become a leading figure in the genomic epidemiology and evolution of viral pathogens in South Africa and across Africa. Her work focuses on the genomic surveillance of infectious diseases, utilizing genomics and phylogenetics within epidemiological and population-scale data to track the transmission dynamics and impact of pathogens.

Her work is a testament to her belief that “in science, one person alone cannot go far, so we rely on one another’s strengths.”

Click here to see most of Tegally’s publications

Dr. Tegally’s pioneering contributions to the COVID-19 pandemic response included the assembly and phylodynamic analysis of SARS-CoV-2 genomes, leading to the identification of the Beta and Omicron variants of concern. She now co-leads the Climate Amplified Diseases and Epidemics in Africa (CLIMADE-Africa) consortium, working to forecast the transmission risks, patterns, and outbreak potential of vector- and waterborne pathogens in the context of climate change, demographic shifts, and increasing human mobility.

9

the gem

10

genomics, epidemics & microbes

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

NIKITA SITHARAM Awarded Prestigious Oppenheimer Memorial Trust Scholarship

I

n honour of International Women’s Month, we celebrate the outstanding achievements of Nikita Sitharam! At just 25 years old, Nikita is making remarkable strides in the field of viral genomics. As a PhD candidate at Stellenbosch University with the Centre for Epidemic Response and Innovation (CERI), her research focuses on understanding the evolutionary dynamics of endemic and reemerging viral pathogens in Africa.

Before embarking on her PhD, Nikita completed her Master’s degree in bioinformatics with CERI, where she worked on developing an Africa-focused arboviral genomic dashboard to support public health decision-making.

Nikita’s dedication and academic excellence have earned her a prestigious recognition; she was recently awarded the Oppenheimer Memorial Trust Postgraduate Scholarship, securing funding for the full three-year duration of her PhD. This highly competitive scholarship had 998 applicants from across South Africa, with only 43 ultimately selected. Nikita’s outstanding academic record, having achieved cum laude in her undergraduate, honours, and master’s degrees, played a significant role in her selection.

Reflecting on her journey, Nikita shares valuable advice for young researchers seeking funding:

“Start preparing well in advance. There are many small pieces of writing—research proposal, motivation, and scientific relevance—that make up these applications, and they require a fair amount of reflection and development of a research narrative. My biggest piece of advice would be to engage with senior researchers who have been through the process of grant writing and been successful.”

She credits much of her success to the support and mentorship she received throughout the application process: “I am very grateful to Dr. Houriiyah Tegally, my supervisor, and Dr. Cheryl Baxter, the head of Scientific Support at CERI, who gave constructive feedback on my application and ensured it was submissionready.” Fellow women who are the pillars of CERI’s success and beacons of hope for the scientific field With this scholarship, Nikita is well-positioned to advance her research and contribute to a deeper understanding of viral pathogens, further strengthening Africa’s scientific landscape. Congratulations, Nikita!

11

the gem

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

FROM ICE TO INSIGHTS: TWO PHD STUDENTS’ ANTARCTIC RESEARCH JOURNEYS text: M ay ibo ngwe a nd N o sipho photo s: M ay ibo n gwe B uthe l ezi o n the A n tar ctic I ce She l f

12

genomics, epidemics & microbes

N

osipho Hlalukana and Mayibongwe Buthelezi, two PhD students in the African Microbiome Group, recently embarked on separate research voyages to Antarctica. Nosipho traveled aboard the South African Agulhas II, while Mayibongwe joined the German Polarstern. Their missions, part of research programs on climate change and marine microbiomes, focused on understanding microbial communities in the Southern Ocean.

Oceans play a key role in absorbing CO2, with microbial communities driving vital biogeochemical cycles.

However, climate change is altering ocean chemistry, with potential consequences for food webs and planetary health. The Southern Ocean, a crucial link between global ocean systems, is essential for studying these changes.

Nosipho and Mayibongwe collected seawater and sea ice samples to address critical scientific questions.

Mayibongwe’s research examines volatile gases released by microbes in sea ice, exploring how melting ice may contribute to climate feedback loops.

Nosipho studies microbial diversity in productive ocean zones, seeking bioactive compounds with potential biotechnological applications.

Despite bouts of seasickness, both completed successful expeditions, collecting valuable samples not only for their own studies but also for several other master’s and PhD projects.

Their research adds to the growing understanding of microbial life in the Southern Ocean and its role in global climate systems.

13

the gem

Nosipho Hlalukana at the South African National Antarctic Expedition (SANAE) base 14

genomics, epidemics & microbes

15

the gem

Nature Africa

FIVE YEARS ON: HOW COVID WAS THE CATALYST FOR AFRICA’S GENOMIC REVOLUTION text: Summary of Nature Africa photo s: CERI

hen the COVID-19 pandemic struck in early 2020, the world braced for an unknown threat, with widespread fears that Africa would struggle to cope with the crisis. Instead, the continent mounted a robust scientific response, leveraging existing expertise in infectious disease research.

W

Among those at the forefront was Tulio de Oliveira, a genomicist in South Africa whose work played a key role in tracking the evolution of the virus. Five years on, reflecting on the lessons and progress made, he says it is evident that Africa’s contributions to global public health have been substantial and far-reaching.

In late 2020, amidst a deadly second wave in South Africa, De Oliveira and his team at the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) identified the variant later designated as Beta, which carried mutations that increased transmissibility and potentially reduced vaccine efficacy.

16

The discovery was made possible by an already-robust genomic surveillance infrastructure, built over years to combat HIV and tuberculosis. De Oliveira recalls receiving a tip-off from doctors in the Eastern Cape province, where an unusual surge in cases was observed.

Within days, his team sequenced the virus and confirmed the presence of significant mutations. Recognising the global implications, he immediately sought an emergency meeting with the World Health Organization (WHO), leading to international recognition of the Beta variant.

Despite the scientific importance of the discovery, South Africa faced an international backlash.

“Instead of sending vaccines and diagnostics, countries imposed restrictions,” De Oliveira recalls.

Disproportionate travel bans or restrictions were imposed by Australia, Brazil, Canada, the European Union, India, Japan, New Zealand, Saudia Arabia, UAE, UK, and US. The same scenario played out a year

genomics, epidemics & microbes

later when his team, now based at both KRISP and the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, identified Omicron. This time, however, detection was even faster – his team sequenced the variant and informed the world within 72 hours.

The backlash was expected, but De Oliveira remains steadfast in his belief that transparency is crucial. “We knew the repercussions, but we also knew that rapid data-sharing was necessary to control the virus,” he explains.

Thanks to this approach, South Africa was able to prepare for Omicron, with minimal restrictions and lower death rates than in previous waves.

Beyond national efforts, De Oliveira’s work catalysed a shift in Africa’s scientific standing. South Africa was the second country in the world, after the United Kingdom, to launch a national genomic surveillance programme for SARS-CoV-2. Through partnerships with 42 African nations, his team coordinated datasharing efforts that resulted in groundbreaking publications1,2.

“We built a culture of collaboration, not competition,” he says. “We have trained over 660 African scientists in genomic surveillance and data analysis. This wasn’t just about COVID-19; it was about building a future in which Africa is at the forefront of global health security.”

The pandemic provided a blueprint for future epidemic preparedness. One of the most significant breakthroughs, De Oliveira explains, was the shift towards real-time data-sharing through platforms like the Global Initiative on Sharing All Influenza Data (GISAID). This enabled scientists around the world to track viral evolution, and develop diagnostics and vaccines, at an unprecedented pace.

To help sustain these advances, De Oliveira and his colleagues launched the Climate Amplified Diseases and Epidemics (CLIMADE) initiative. The partnership, spanning 40 African countries, is aimed at predicting and mitigating outbreaks fuelled by climate change.

The Genomic Surveillance Unit (GSU) of the Wellcome Sanger Institute also partnered with CERI, marking a major step in equitable global health collaboration. This collaboration will expand genomic research, bolster training programmes, and ensure that discoveries benefit all regions of the world. “This partnership is not about dependency,” De Oliveira stresses. “It’s about equitable exchange – leveraging Africa’s expertise and infrastructure while collaborating with global institutions. The days of African scientists being seen as mere participants in global research are over.”

Challenges remain, including the rise of vaccine nationalism, misinformation and funding cuts. De Oliveira has been vocal about these issues, arguing in the New York Times that global health leaders could learn from Africa’s coordinated, community-driven approach to disease surveillance.

Yet, his commitment to scientific transparency and innovation has never wavered. “This is not about individual recognition. It’s about building something greater – an Africa that leads in science, that protects its people, and that contributes meaningfully to global health,” he says.

References: 1 - Wilkinson, E. et al, Science 374, 423-431(2021).

2 - Tegally, H. et al, Science 378, eabq5358 (2022).

But he warns that the gains are fragile. “There’s a real risk of dismantling the genomic surveillance systems we built. Maintaining these capabilities is crucial, not just for COVID-19, but for emerging threats like Mpox, Marburg and climate-amplified epidemics.”

17

the gem

CERI Sequencing Core in Stellenbosch Univ.

18

genomics, epidemics & microbes

KRISP team at UKZN inspecting a flow cell.

19

the gem

Scientific Paper

TRAVEL-ASSOCIATED INTERNATIONAL SPREAD OF OROPOUCHE Iani et al. Journal of Travel Medicine 2025

text: A bst r a ct & C o ncl usio n photo : Figure 3, Iani et al. 2025

20

genomics, epidemics & microbes

O

ropouche virus (OROV), first detected in Trinidad and Tobago in 1955, was historically confined to the Brazilian Amazon Basin. However, since late 2022, an increasing number of OROV cases have been reported across various regions ofBrazilas well as in urban centers in Bolivia, Ecuador, Guyana, Colombia, Cuba, Panama and Peru.

In collaboration with Central Public Health Laboratories across Brazil, we integrated epidemiological metadata with genomic analyses from recent cases, generating 133 whole-genome sequences covering the virus’s three genomic segments (L, M, and S). These include the first genomes from regions outside the Amazon and from the first recorded fatal cases.

Phylogenetic analyses show that the 2024 OROV genomes form a monophyletic group with sequences from the Amazon Basin sampled since 2022, revealing a rapid northto-south viral movement into historically non-endemic areas.

We identified 21 reassortment events, though it remains unclear whether these genomic changes have facilitated viral adaptation to local ecological conditions or contributed to phenotypic traits of

public health significance. Our findings demonstrate how OROV has evolved through reassortment and spread rapidly across multiple states in Brazil, leading to the largest outbreak ever recorded outside the Amazon and the first confirmed fatalities.

Additionally, by analysing travelrelated cases, we provide the first insights into the international spread of OROV beyond Brazil, further highlighting the role of human mobility in its dissemination.

The virus’s recent rapid geographic expansion and the emergence of severe cases emphasize the urgent need for enhanced surveillance across the Americas. In the absence of significant human population changes over the past two years, factors such as viral adaptation, deforestation, and climate shifts-either individually or in combination-may have facilitated the spread of OROV beyond the Amazon Basin through both local and travel-associated transmission.

emerging arboviruses. Our findings, combined with recent research, underscore the need for continuous genomic surveillance to unravel the evolutionary and epidemiological patterns of OROV. Such efforts are crucial for anticipating and mitigating future outbreaks, ensuring timely and effective public health responses locally and globally. This comprehensive approach will be instrumental in managing the ongoing spread of OROV and preparing for future threats from similar pathogens.

Access full manuscript:

Iani et al. Journal of Travel Medicine 2025 - https://academic.oup.com/jtm/article/32/3/ taaf018/8046862

The interplay of climate change, ecological shifts, and human movement highlights the global implications of OROV emergence. The increasing frequency of arbovirus spillover events into previously unaffected areas necessitates coordinated international efforts to monitor and control OROV and other

21

the gem

Global Funding Crisis

IT IS A TIME FOR SOLUTIONS ON THE FACE OF US FUNDING CUTS text: Spotlight photo : Tulio de Oliveira, Midjourney

I

n light of the Trump administration’s decision to freeze foreign aid, Professor Tulio de Oliveira emphasizes that the U.S. may face greater losses than its 1% investment in foreign assistance. The non-partisan Pew Research Center notes that in 2023, approximately $71.9 billion was allocated for foreign aid, with significant portions directed toward combating diseases like HIV/AIDS and emerging public health threats. De Oliveira argues that investment in biosecurity is not merely an expense for the U.S., but a vital investment in global health that benefits Americans, especially considering the recent pandemic.

De Oliveira, a prominent bioinformatics professor, gained international recognition for his role in identifying the Beta and Omicron COVID-19 variants. He emphasizes the necessity of global scientific collaboration to address infectious diseases, stating that pathogens transcend borders. Current health threats, including influenza and outbreaks of Marburg and Ebola, underline the urgency for swift identification and control of diseases to protect global health.

22

The halt in U.S. aid has already affected numerous South African research institutions that rely on funding from U.S. entities like the NIH and CDC. This has led to the suspension of critical clinical trials and could have catastrophic consequences for public health initiatives. Notably, plans for significant studies related to HIV prevention might be jeopardized, while uncertainties increase with the appointment of Robert F. Kennedy as health secretary, who has focused on shifting priorities away from infectious diseases.

Despite these challenges, De Oliveira is optimistic about his institute’s future. At the Centre for Epidemic Response and Innovation (CERI), he asserts that while U.S. funding is dwindling, CERI is in an expansion phase, with diverse funding sources that mitigate reliance on a single donor. He highlights the importance of a well-rounded funding portfolio, which includes active grants from various international sources.

The potential withdrawal of U.S. leadership in global health funding raises questions about who might fill

genomics, epidemics & microbes

that void. De Oliveira suggests that countries like China could step in, alongside wealthy philanthropic foundations such as the Novo Nordisk Foundation, indicating that unexpected sources may emerge as new benefactors.

De Oliveira’s global influence was recognized in 2022 and 2024 when he was named among the world’s most influential people, though he downplays the impact of this recognition on funding acquisition.

He maintains a strong commitment to conducting research that positively affects global health, advocating for collaboration among investigators disseminating shared goals.

public health challenges.

As the discussion wraps up, De Oliveira articulates the broader implications of global environmental degradation and urbanization on the spread of infectious diseases, framing this moment as a pivotal time for scientific and medical research to pursue innovative solutions.

Access the full article at Spotlight: https://www.spotlightnsp.co.za/2025/02/24/it-is-a-timefor-solutions-says-prof-tulio-de-oliveira-in-face-of-usfunding-cuts/

Reflecting on the current landscape, he addresses the more vulnerable nations, such as Mozambique, that are heavily reliant on foreign aid for essential medicines.

The recent U.S. funding cuts threaten progress in developing an HIV vaccine and underscore the need for continuous investment in scientific research to address

23

the gem

A f r i c a n S TA R S

CLOSE TO 3,000 APPLICANTS FOR 40 FELLOWSHIPS! We concluded the first call for applications for the African STARS Fellow

24

genomics, epidemics & microbes

A

frica has the fastest-growing young population in the world, projected to make up nearly half of the global youth by 2100. Currently, young Africans have limited formal employment opportunities.

To address this urgent challenge, we must focus on building capacity and cultivating the next generation of young leaders in Africa who are well-prepared for employment, employ more Africans, and capable of addressing emerging and reemerging health crises.

The African STARS Fellowship Programme seeks to meet this need by enhancing African expertise in genomics, diagnostics and vaccine design, while also working to retain skilled professionals in the sector.

Initially funded by a generous award from the Mastercard Foundation, the programme’s vision is to expand employment opportunities for African youth, especially young African women in closely aligned with Mastercard Foundation objectives. This programme is also aligned with the Saving Lives and Livelihoods Phase II initiative to strengthen the continent’s health workforce

in preparation to respond to future epidemics.

The first call for applications for the Advanced and Translational Training (ATT) Fellowship (4 months) and the Young Professional Programme (YPP) Fellowship (12 months) received an overwhelming number of applications, highlighting the need for such a programme in the African continent.

The CERI and IPD teams are now evaluating the applications to select the first 40 Fellows; 20 for the ATT and 20 for YPP programmes. The results of the selection process will be released on 1 of May and the Fellowships will start by end of July 2025.

In the second semester of 2025, we will release the call for the Master of Business Administration (MBA) and the Master of Bioinformatics in Infectious Diseases (MSc) at Stellenbosch University.

For more information on the program, visit: https://starsfellows.africa

25

the gem

Scientific Paper

BUILDING PATHOGEN GENOMIC SEQUENCING CAPACITY IN AFRICA: A FELLOWSHIP EVALUATION Agboli et al. Tropical Medicine and Infectious Diseases 2025 An evaluation of a past fellowship programme at CERI by 36 fellows with diverse backgrounds from 16 countries.

26

genomics, epidemics & microbes

T

he World Health Organization African region has the greatest infectious disease burden in the world.

However, many African countries have limited capacity to rapidly detect, report, and respond to public health events.

The Centre for Epidemic Response and Innovation (CERI), KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) in South Africa, and global Climate Amplified Diseases and Epidemics (CLIMADE) consortium are investing in building the capacity of African scientists in pathogen genomics and bioinformatics.

A two-week long (11–21 April 2023) intensive training in wet-laboratory genomic data production, bioinformatics, and phylogenetic analyses of viral and bacterial pathogens was held in Cape Town, South Africa.

Training was provided to 36 fellows with diverse backgrounds from 16 countries, 14 of which were low- and middle-income African countries.

In this publication, the fellows reflected on their collective experiences and described how the learnt skills have been integrated into the operations of their home institutions to advance genomic surveillance capabilities. They identified the in-person and hands-on learning format of the

training, taught by genomics experts and field application specialists, as the most impactful elements of the training. Adaptation and miniaturisation of protocols to detect other pathogens was a great enhancement over the traditional method of using a single protocol for a pathogen.

Limitations and suggestions for improvement Twenty-six fellows identified the duration of the training as the largest limiting factor. Due to their diverse backgrounds, with fellows mostly having experience in either the computational or wet-laboratory component, having only two weeks to bring all fellows to the same level on both components was challenging.

This resulted in difficulties for some to follow a few sessions, particularly the computationally intensive bioinformatics sessions. They recommended ameliorating this challenge in the following ways: extending the training for bioinformatics to two weeks or the full training period up to four weeks, with more time for hands-on practice of methods; providing learning material on computational basics of bioinformatics to prepare in advance of the training; providing all learning materials (for both wet- and dry-lab) before the training; reducing the number of tools taught for the bioinformatics component to narrow the focus;

providing homework exercises for repeated practice and learning after contact sessions; and lastly, presenting the bioinformatics analysis in the mornings and schedule the activities that require less concentration in the afternoons.

Tying into this limitation was the recommendation that the knowledge needs of the fellows be assessed beforehand and that fellows be grouped based on their prior capabilities. The training content and schedule may then be tailored to the specific needs of the different groups of fellows so that more time may be spent on certain components where skills are lacking.

The Fellows also recommended that the training programme be designed collaboratively between trainers and trainees to reach a consensus on the content presented.

Full open article on the fellows evaluation of the programme can be accessed here: Abgoli et al. Trop. Med. Infect. Dis. 2025, 10(4), 90; https://www.mdpi. com/2414-6366/10/4/90.

27

the gem

Dr. Jennifer Giandhari Honored at Women Tech Dr. Jennifer Giandhari has been recognized for her contributions to science, technology and innovation at the Technology Innovation Agency’s (TIA) inaugural Women Technology Innovation Programme Launch, held on 26 March 2025 in Sandton, Gauteng. She was awarded a Certificate of Recognition, highlighting her outstanding work in the field of genomics.

Accompanied by her long-time friend and colleague, Dr. Sureshnee Pillay, Dr. Giandhari traveled to Gauteng to accept this prestigious honor. The event celebrated the achievements of women in technology and emphasized the importance of fostering innovation and inclusivity in the industry. Reflecting on this incredible honour, Dr, Giandhari said, “This recognition is not just mine, it belongs to the many mentors and colleagues who have guided me, especially at KRISP and UKZN.” She added that women’s presence in this field is very important for progress and innovation because diversity not only enriches our perspectives but also enhances the outcomes of our collective work. text: Paul Harris photo: Supplied

28

SACEMA Honored for Societal Impact The South African Centre for Epidemiological Modelling and Analysis (SACEMA) has been awarded the Societal Impact Award at the Cape Chamber of Commerce and Industry’s inaugural Academic Innovation Awards. This recognition, presented in partnership with the Cape Higher Education Consortium (CHEC), highlights SACEMA’s role in translating research into real-world impact.

For nearly two decades, SACEMA has been at the forefront of infectious disease modelling, informing public health policies on HIV, TB, COVID-19, and more.

Its work has shaped national and global strategies, influencing organisations like the World Health Organisation (WHO) and the Africa Centres for Disease Control and Prevention (Africa CDC). Beyond research, SACEMA has trained hundreds of postgraduate students and health officials across Africa, strengthening epidemiological expertise in the region.

“Innovation in understanding health and responding effectively to epidemics is not just a public health priority—it’s an economic necessity,” says Prof. Frank Tanser, SACEMA Director. “Our work ensures that policymakers and healthcare leaders have the data-driven insights needed to mitigate economic losses tied to disease outbreaks.”

“SACEMA plays a crucial role in improving public health policies by providing data-driven insights on HIV/AIDS and other infectious diseases. Its research helps optimize treatment programs, guiding the rollout of ART and PrEP to reduce transmission rates, this recognition is well deserved” said Prof. Eugene Cloete, CEO of CHEC.

genomics, epidemics & microbes

Multi-omics symposium and workshop in Oldenburg, Germany.

From March 3–7, 2025, post-doctoral fellow Nonsikelelo Hlongwa and PhD student Keith Dube attended the Anvi’o Workshop and EarlyCareer Researcher Symposium at the Helmholtz Institute for Functional Marine Biodiversity (HIFMB) in Oldenburg, Germany. The event provided advanced training in integrated microbial ‘omics using the Anvi’o software and offered a platform for early-career researchers to present their work, exchange ideas, and build professional networks within the microbial ecology research community.

Photo: Dr. Nonsikelelo Hlongwa (left) and Keith Dube (right) at the main entrance of the Helmholtz Institute for Functional Marine Biodiversity (HIFMB) in Oldenburg, Germany.

Prof Tulio de Oliveira selected for the African Leadership Initiative, Aspen Global Leadership Network Prof Tulio de Oliveira joins the African Leadership Initiative of the Aspen Institute. This is a two years fellowship program.

The ALI’s mission is to empower a number of leaders who are now shaping the continent in a positive light.

As the Africa Leadership Initiative (ALI) has a clear-cut objective to develop the next generation of valuesbased African leaders. These leaders will not only impart knowledge and share opinions, but also guide and lead their countries with integrity.

ALI forms part of the Aspen Global Leadership Network (AGLN). This network was established worldwide in collaboration with the Aspen Institute, and consists of other leadership initiatives similar to ALI.

exceptional group of individuals brings a wealth of experience and fresh perspectives to our network.

Class XV to the ALI SA network will work together to address South Africa’s most pressing challenges. https://africaleadership.net/fellows/ class-xv/

Prof de Oliveira joins the Class XV’s

29

the gem

H A R V E S T S T U DY

HARVEST TRIAL HIGHLIGHTS SOUTH - SOUTH COLLABORATION Trial evaluating TB treatment on HIV-positive and HIV-negative adults with TB meningitis

text: D r. R icha r d Le sse l l s photo : Dr Richard Lessells

D

r Richard Lessells visited the Infectious D i s e a s e s Institute (IDI) at Makerere University in Kampala, Uganda between Monday 24 February and Thursday 27 February. This was for the unblinding meeting for the HARVEST trial. This randomised controlled trial is evaluating whetherhigh-dose oral rifampicin improves survival in HIV-positive and HIVnegative adults with TB meningitis.

Richard travelled with the Durban study team, including Prof Kogie Naidoo and Dr Bongeka Hlabisa from CAPRISA, and Prof Yunus Moosa from UKZN Department of Infectious Diseases.

30

The trial is an excellent example of a South-South collaboration, involving teams in Uganda, Indonesia and South Africa, with Chief Investigators Prof David Meya from IDI, Uganda and Prof Rovina Ruslami from Bandung, Indonesia.

The study also benefited from strong support from long-standing collaborators at the University of Minnesota in the US and Radboud University in the Netherlands. In Durban, the trial was conducted at Prince Mshiyeni Memorial Hospital and Victoria Mxenge Hospital (formerly King Edward VIII Hospital).

After reviewing the results of the primary analysis, the team worked together to write the

manuscript reporting the main findings. This was done within three days, and the paper was submitted to the journal before we all left Kampala. A great example of teamwork in action!

Photos: Top: Dr. Richard Lessells in his traditional Ugandan attire, known as a Kanzu and other visiting clinicians during visit to Uganda.

genomics, epidemics & microbes

31

the gem

Communication

YOUTUBE VIDEOS Our engagement in videos and TVs.

From Data to Action On Wednesday, 26 March 2025, the seminar featured an insightful talk by Christina Riley, Director and Portfolio Lead at Akros, who discussed how geospatial data and genomics are strengthening public health interventions. With over 12 years of experience in malaria operational research and public health program implementation across Africa and Southeast Asia, Christina shared how data-driven approaches are transforming disease surveillance and response strategies.

Watch full video: https://youtu.be/ydL8CduNmNU?si=_7YcZoagTngKT4SO

From Bench to Bedside From Bench to Bedside: Pioneering the Genital Inflammation Test for Women’s Health by Professor Jo-Ann Passmore, Principal Medical Scientist (NHLS) and Professor of Medical Virology (UCT), as she discusses the development of the Genital Inflammation Test (GIFT)—a groundbreaking, affordable pointof-care diagnostic tool for sexually transmitted infections and bacterial vaginosis. Prof. Passmore will also share her research on genital tract inflammation and its impact on HIV risk in women.

Watch full video: https://www.youtube.com/watch?v=XHyE3m5v63Y

32

genomics, epidemics & microbes

Prof. de Oliveira on funding cuts on SA USA decision to permanently halt foreign aid is expected to significantly affect the future of research programmes at local universities. For years, U.S-funded initiatives have helped researchers at various institutions become leaders in addressing regional and global challenges.” Latashia N. from Newzroom Afrika visited our labs to chat with the director, Prof. Tulio de Oliveira regarding this matter.

View full video: https://www.youtube.com/watch?v=kwk8A0zOxSc

British High Commissioner on UK/SA collaboration In this short video the British High Commissioner to South Africa Antony Phillipson on the UK/SA partnership on genomics surveillance between CERI at Stellenbosch University and the GSU at the Wellcome Sanger Institute Watch full video: https://www.youtube.com/watch?v=QsKnYFd01Ec

Genomics in the UK and SA In this short video, Dr. Caroline Heywood. Head of Products and Research from the Genomics Surveillance Unit (GSU) of the Wellcome Sanger Institute talk about the Collaborative project for genomics surveillance in the UK and South Africa on respiratory pathogens.

Watch full video: https://youtu.be/_QiC9YDKqTk

33

the gem

Fund raising

PEDA L I N G FO R A P U R P O SE : CERI #Move4Maties Conquers the 109km Cape Town Cycle Tour to Help Bridge the Financial Gap for tex t : Maamb el e Kho sa ph oto: Supp l i ed

34

genomics, epidemics & microbe

E

ducation is a powerful force for change, but for many students at Stellenbosch University, financial constraints threaten to derail their academic dreams. These students, known as the “missing middle,” do not qualify for state financial aid (NSFAS) yet struggle to afford their education. As the economic climate worsens, more talented students face the prospect of dropping out.

Determined to make a difference, the Centre for Epidemic Response and Innovation (CERI) team participated in the 47th Cape Town Cycle Tour as part of the #Move4Maties campaign. This initiative turned their passion for cycling into a mission to create opportunities for students who need them most.

The event was more than just a race— it was a movement to support education and empower future leaders.

Making an Impact CERI’s participation in the race not only raised awareness but also mobilized essential funds to

support scholarships, resources, and student aid programs. Each pedal stroke contributed to a future where education is accessible to all, regardless of financial background.

A Community Effort Thanks to everyone who donated, shared, and supported the ride, the #Move4Maties campaign made a tangible impact. The funds raised will go directly toward assisting students who are #CaughtInTheMiddle, ensuring that they can continue their studies and build a better future.

Education is not just about textbooks and exams; it’s about unlocking potential and shaping a brighter tomorrow. By coming together, we have shown these students that they are not alone in their journey.

Looking Ahead The success of this campaign is a reminder that small actions can lead to significant change. While the race may be over, the mission continues. Those who still wish to contribute can do so by donating here: https://www.givengain.com/project/ ceri-raising-funds-for-stellenboschuniversity-south-africa-94947.

35

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