the gem: genomics, epidemics & microbes - Aug/Sep 2024

volume 7 - number 8 September 2024

genomics, epidemics & microbes

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Global Summit Keynote Global summit in Brazil with WHO on what is needed to prevent pandemics

ISME in Africa DNA borgs, inclusivity & equitable opportunities for African microbiome read it online

VEME 28th edition World’s long lasting and most advanced genomics & bioinformatics training

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summary

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editorial

global summit keynote

isme19-a 1st in africa

August has been a busy but very productive month, our team went to Brazil to present CLIMADE and to run the VEME workshop. We host over 1,500 people in Cape Town for ISME19 and produced great science that drove the epidemic response of Mpox and Orpouche.

Prof. de Oliveira presented a keynote adress at the second Global Pandemic Preparedness Summit, held in Rio de Janeiro, Brazil, from July 29 to 30, 2024.

The Summit brought together leading experts and global leaders to confront the growing challenges posed by pandemics in an era of climate change.

The International Symposium on Microbial Ecology (ISME) was hosted for the first time in Africa.

Held in Cape Town, South Africa, from August 18 to 23, 2024, this landmark event drew more than 1,500 scientists from over 70 countries. the conference featured over 1,100 poster presentations and more than 320 oral presentations.

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: Maambele Khosa, Vagner Fonseca, Paul Harris; linkedin: https://www.linkedin. com/company/ceri-su/; websites: https://ceri.org.za/ https://www.krisp.org.za/, https://www.sacema.org/; Twitter: @CERI_news, @KRISP_news ;Youtube: https://www.youtube.com/@krisp-ceri

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veme workshop in brazil

climate, migration & infectious diseases

Oropouche virus

The 28th edition of the Virus Evolution and Molecular Epidemiology (VEME) workshop took place in Brasília, Brazil, from 4-9 August 2024 and included participants from 33 countries.

In an expert comment in Nature Climate Change , researchers from the University of Oxford and CERI explore the specific pathway through which migration impacts infectious diseases. The authors highlight the urgent need for an integrated and equitable global response to the intersecting crises of climate change, migration, and infectious diseases.

Brazil has experienced a significant surge in oropouche virus cases, with over 7,000 reported by mid-2024. The CLIMADE Consortium highlights the need for robust surveillance systems at national and continental levels.

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editorial elcome to this month’s edition of the gem. August has been a busy but very productive month, our team went to Brazil to present CLIMADE as the keynote talk of the Global Pandemic Preparedness Summit in Rio de Janeiro, where the Director General of the WHO, the Africa CDC and multiple Health ministers gathered to plan ahead to the prevent and respond to new epidemics and pandemics, many of them being amplified by climate change. In addition, we worked with Brazilian scientists to identify a new variant of Oropouche Virus, which for the first time expanded beyond the Amazon Forest to cause global outbreaks. We also worked with the Brazilian Minister of Health, FioCruz & WHO/PAHO to host the 28th edition of the most advanced genomics and bioinformatics training in the world, the Virus Evolution and Molecular Epidemiology (VEME) that trained 150 researchers from 33 countries in advanced genomics analysis.

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Back in SA, we hosted the historic 19th International Symposium on Microbial Ecology (ISME19) held in Africa for the first time ever! Our involvement included having the chair of the conference, Prof Thulani Makhalanyane, hosting the “Microbes and Climate Change” event at Kirstenbosch, engaging Gen Z in critical discussions about microbiome. Leading up to the symposium, we also played a role in offering two workshops focusing on Oxford Nanopore Metagenomics and Bioinformatics to advance skills in microbial ecology.

SACEMA at CERI was recognised as a finalist for the National Research Foundation’s Social Impact Award! We also hosted many international visitors, including Prof Jeanne Marrazzo, director of NIH’s National Institute of Allergy and Infectious Diseases (NIAID), During her visit to South Africa, Prof Marrazzo visited several research groups including CERI and gave an open seminar on the NIH/NIAID's vision.

e dito r ia l te a m Tulio de Oliveira, Maambele Khosa and Cheryl Baxter

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CLIMADE

GLOBAL PANDEMIC PREPAREDNESS SUMMIT Global Summit reinvigorates efforts to prepare for future pandemics highlighting the crucial role of genomic surveillance in detecting and controlling disease outbreaks

text: Ma a m be l e K ho sa Vide o : C EPI pr ov ide d CEPI

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he second Global Pandemic Preparedness Summit (GPPS), held in Rio de Janeiro, Brazil, from July 29 to 30, 2024, brought together leading experts and global leaders to confront the growing challenges posed by pandemics in an era of climate change. Convened by the Coalition for Epidemic Preparedness Innovations (CEPI) and cohosted by Brazil’s Ministry of Health and Fiocruz, one of the world’s oldest public health institutions, the summit served as a critical platform for discussing advancements and strategies in pandemic preparedness.

One of the keynote speakers, Professor Tulio de Oliveira, Director of the Centre for Epidemic Response and Innovation (CERI), emphasized the crucial role of genomic surveillance in detecting and controlling disease outbreaks. In his address, he warned that the world remains dangerously unprepared for future pandemics, particularly as climate change continues to drive the spread of infectious diseases.

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“Over half of pathogens are being amplified by climate change. With the global circulation of pathogens, there is a larger risk for transmission across different continents,” Professor de Oliveira cautioned. He stressed the importance of enhancing global genomic surveillance systems to detect emerging threats early and prevent widespread transmission.

The two-day summit featured a series of keynote speeches, plenary panels, and in-depth discussions, bringing together experts from various countries to share insights and experiences. Topics ranged from the latest advancements in medical countermeasures to the lessons learned from recent health emergencies.

Participants highlighted the urgent need for broader research and international collaboration to better prepare for the next pandemic. Leaders from across the world, representing diverse fields such as public health, science, and policy, underscored the importance of addressing the interconnected challenges of climate change and epidemic preparedness.

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Watch the keynote at GPPS here: https://youtu.be/3If2hxfsVCc

The Global Pandemic Preparedness Summit underscored the pressing need for a unified global response to the emerging threats posed by climate change and pandemics, with a particular focus on strengthening genomic surveillance and international cooperation. As the world faces the increasing risks of global disease outbreaks, the summit highlighted the critical importance of being better prepared to protect public health on a global scale

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Over half of pathogens are being amplified by climate change. With the global circulation of pathogens, there is a larger risk for transmission across different continents.

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Artificial Intelligence

CERI expands partnership with AIMS & Google DeepMind

As we graduated the first batch of MSc students and continue to support PhD AI students, CERI's partnership with AIMS and Google Deep-Mind expands

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ood security, healthcare and exploring the cosmos are among the ways students of a new pan-African Master’s program aspire to apply AI At Google DeepMind, we’re committed to supporting the next generation of artificial intelligence (AI) leaders to help build a stronger, more diverse and inclusive global AI community. This includes increasing access to AI and science through education.

Last year, we partnered with the African Institute for Mathematical Sciences (AIMS), Africa’s first network of centers of excellence in mathematical sciences, to launch an AI for Science Master’s program, with a $4.5M grant from Google DeepMind.

With such stellar scientific neighbours, the program benefits from the expertise of the Square Kilometre Array Observatory (SKAO) and its South African partner, the South African Radio Astronomy Observatory (SARAO), the Centre for Epidemic Response and Innovation (CERI), and the South African Centre for Epidemiological Modelling and Analysis (SACEMA).

This funding helps AIMS provide full scholarships, equipment and compute to talented local students, giving them access to advanced studies in mathematics, AI and machine learning from world-class academics

at AIMS South Africa. Students have the opportunity to accelerate scientific discovery, with mentoring and support from Google DeepMind’s researchers and engineers.

This summer, the first cohort of students graduated at a ceremony at the AIMS campus in Cape Town, South Africa. As the next generation of AI leaders in Africa, Béria Chingnabé Kalpélbé, Olivier Mahumawon Adjagba and Diffo Mboudjiho Annette Dariose shared their experiences in pioneering AI research and what they’re hoping to achieve with their work.

Béria: Innovating for better food security Sustainability is a top priority for Béria, originally from Chad. “I hope to develop solutions for sustainable agricultural development that will benefit both people and the planet by integrating principles of renewable energy, precision farming, and ecological preservation in my work,” he says.

“Beyond agriculture, AI offers significant potential to enhance the resilience of Africa’s natural environments,” Béria adds. “By implementing AI-powered monitoring and decision-support systems, we can safeguard Africa’s precious green areas and biodiversity for future generations.”

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Olivier: Pioneering virus transmission research through the lens of climate change Olivier’s passion for applying mathematics to complex problems led him to AIMS South Africa: “Throughout my academic journey, I’ve been fascinated by the power of mathematics, particularly in addressing real-world challenges through AI,” he says. “A solid foundation in mathematical sciences is crucial for driving progress in areas such as healthcare, climate science and technology — and I’m eager to be at the forefront of these advancements.”

Originally from Benin, Olivier now looks to apply this approach to data from African countries to help understand the spread of dengue fever. “Using advanced AI techniques, I hope to create more accurate prediction models to inform public health strategies and interventions, ultimately contributing to the control and prevention of this viral disease.”

Olivier researhc work is part of the Climate Amplified Diseases and Epidemics (CLIMADE), a global program that is led by CERI. Discussing the personal impact of his scholarship, Olivier recounts, “Without it, pursuing advanced studies at such a prestigious institution would have been financially unattainable for me. This support enabled me to fully immerse myself in AIMS’ rigorous academic environment, so I could engage deeply in coursework, collaborate with professors and peers, and contribute meaningfully to research projects.”

Producing the next generation of AI specialists in Africa to fight epidemics, climate change and explore the outer space As a home for AI research, Stellenbosch University (SU) is one of only three universities across Africa with scholarships from Google DeepMind, a world leader in artificial intelligence (AI) research and its application in the real world.

SU is also a founding and degree-issuing partner of the African Institute for Mathematical Sciences, where the first cohort of students graduated from the new panAfrican master’s program, AI for Science. Of 16 students that graduated, 11 graduated from SU. The Centre for Epidemic Response and Innovation (CERI) at SU were the focal point for five of the students, exposing them to advanced genomics, epidemiological and climate change large datasets to track and predict epidemics and pandemics.

“This first cohort of AI students in Africa were phenomenal, they have been trained by the top experts in the world and applied their knowledge to some of the biggest global challenges, like climate change and epidemics” commented Prof Tulio de Oliveira, director of CERI at SU. “One of the challenges that we put to the students was how to use AI to better detect and predict where and how new variants of pathogens will emerge, so we can make Africa and the world safer” Prof de Oliveira team detected the Omicron variant and now use AI to predict and track new pathogens.

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Olivier Mahumawon Adjagba wants to use AI to create more accurate prediction models for the spread of dengue fever

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Google DeepMind featured three of our SU graduates in a blog as they brought cutting-edge AI to scientific challenges in food security, health care, and outer space. Featured in this Google DeepMind blog post are Béria Chingnabé Kalpélbé from Chad, Olivier Mahumawon Adjagba from Benin, who worked at CERI tracking pathogens, and Diffo Mboudjiho Annette Dariose from Cameroon.

The university became the first African university to be awarded scholarships from Google DeepMind for postgraduate students in STEM in 2020. From 2022, SU’s Department of Applied Mathematics offers a structured MSc in Machine Learning and AI with further scholarships from Google DeepMind. In the Faculty of Engineering, Leanne Nortje is supported by a Google DeepMind PhD scholarship under the guidance of Prof Herman Kamper, working on AI specifically for local languages.

More information on the The AI for Science Master’s program at AIMS South Africa AI for Science is a stream in AIMS South Africa’s Master’s degree in Mathematical Science, made possible through a partnership with Google DeepMind. The program sits at the exciting intersection of AI and the Sciences. This exciting program started with its first intake of students in September 2023. It is a fully residential one-year taught masters with a research component. Applications are open

to students from across Africa who are passionate about mathematics, artificial intelligence and machine learning.

We are looking for students who gaze at the stars and the world around them in wonder, and who want to use their talents to accelerate scientific discovery.

A Google DeepMind donation funds 40 scholars per year for the four years starting September 2023. The funding covers full scholarships, equipment and computation costs for students. Our scholars are Google DeepMind scholars, and have opportunities to connect with Google DeepMind’s researchers and engineers for mentoring and support.

Beyond scholarships, the program will draw on Google DeepMind’s world-leading expertise in AI for Science.

It is an exciting time for science in Africa. On our doorstep, the Square Kilometre Array will be the largest radio telescope ever built and will produce science that changes our understanding of the universe. The first detection of the Beta and Omicron Covid-19 variants happened close to our institute in Muizenberg.

More info: https://ai.aims.ac.za & https://deepmind.google/discover/blog/a-new-generation-of-african-talent-brings-cutting-edge-ai-to-scientificchallenges/

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Microbial Ecology

ISME 19 First Time in Africa in Over 40 Years: from borgs, to climate change and African microbiome network, a historic event happens in South Africa: The 19th International Symposium on Microbial Ecology (ISME19)

text: Maambele Khosa photo : Charlie Sperring

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or the first time in over 40 years, the International Symposium on Microbial Ecology (ISME) has made its way to Africa. Held in Cape Town, South Africa, from August 18 to 23, 2024, this landmark event drew more than 1,500 scientists from over 70 countries, with a record-setting 200 researchers from Africa alone.

The symposium kicked off with a remarkable plenary session revealing a groundbreaking discovery: a new ‘life organism’ that lies somewhere between a virus, a bacterium, and a bacteriophage. Prof. Jillian Banfield from University of Carlifonia Berkeley took the stage, unveiling her team’s groundbreaking discovery:

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a mysterious new genetic element dubbed “DNA Borgs.” These massive sequences of DNA, discovered while sifting through mud samples from her own backyard in California, left the audience in awe. Inspired by her Trekkie son, Banfield named these unusual elements after the “Borg” from Star Trek—cybernetic aliens that assimilate other species.

Banfield explained that these Borgs are unlike anything seen before, with features that don’t neatly fit into known categories like viruses or bacteria. Found in methane-oxidising archaea, they are large, linear strands of DNA—some nearly a million bases long—containing genes that are largely novel. These DNA Borgs have the potential to enhance the metabolic capacity of their host

microbes, including methane consumption, which has significant implications for both ecology and climate research. Banfield’s talk left the audience buzzing with excitement, as she proposed that Borgs could be a new class of giant viruses or even genomic parasites, marking a remarkable leap forward in microbial ecology. It was the perfect start to a symposium full of surprises and innovation.

This year's symposium was chaired by South African scientist Prof. Thulani Makhalanyane from Stellenbosch University. In his passionate address, Prof. Makhalanyane emphasised the crucial role of African scientists in advancing microbiome research.Makhalanyane, the Chair of the local organising committee, emphasised the importance

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of collaborative work with African scientists, stating, "By having this symposium here, we can encourage partnerships with and on the African continent," highlighting the need for more accessible and equitable science globally". He further highlighted the potential of creating a network of African laboratories to unlock the benefits of microbiome studies, which could drive innovations such as drought-resistant plants, dietary supplements, and therapies for diseases prevalent on the continent

Another keynote presenter was Prof. Tulio de Oliveira, who presented the work of the Climate Amplified Diseases and Epidemics (CLIMADE) consortium. Among many examples of diseases that are being amplified by climate change, the emergence

of a new virus, the Ouropouche virus, that left the Amazon forest and caused an epidemic in Brazil, Colombia and Cuba draws attention to how deforestation may have enabled mosquitos to move to the cities and carry new pathogens with them. Prof, de Oliveira also highlighted the adventurous work on the CLIMADE consortium, which involves putting DNA sequencing laboratories in boats and exploring the big rivers in Brazil in the Pantanal and Amazon to characterize new pathogens before they emerge.

The 19th edition of the International Symposium on Microbial Ecology (ISME19) was a historic first on the African continent.

As the premier global conference in microbial ecology, ISME19 attracted over 1,500 scientists from more than 70 countries to discuss cutting-edge research in the field. With 1,564 abstracts submitted, the conference featured over 1,100 poster presentations and more than 320 oral presentations, making it a significant event for the scientific community.

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It is great to see this international conference coming to Africa, the home of all.

Prof. Thulani Makhalanyane, -Chair ISME19 local organising committee

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Left figure: The cover of Nature shows an artist’s interpretation of Borgs, a novel kind of extrachromosomal element described by Jillian Banfield and her colleagues.

Right figure: Prof. Jillian Banfield was the first keynote speech at ISME19.

Below: figure Opening cerimony of ISME19, attracted over 1,500 scientists from more than 70 countries to discuss cutting-edge research in the field.

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Virus Evolution

VEME 2024 The world’s most advanced genomics and bioinformatics training on virus evolution and molecular epidemiology (VEME) was hosted in Brasília in parnership with FioCruz, Brazilian Ministry of Health, PAHO & CERI

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he 28th edition of the Virus Evolution and Molecular Epidemiology (VEME) workshop took place in Brasília, Brazil, from 4-9 August 2024. VEME was hosted by the Fundação Oswaldo Cruz (Fiocruz), the Pan American Health Organization (PAHO) and CERI. It was such an enriching week of intensive training and collaboration in genomics, bioinformatics, and public health.

The Netherlands, Serbia, Italy etc.

Comprehensive

Curriculum

The workshop's curriculum is designed to equip researchers with the latest tools and methodologies to tackle pressing bioinformatics challenges. The program consists of four core modules: • Phylogeny Inference • Evolutionary Hypothesis Testing • Next Generation Sequencing • Genomic Surveillance for Public Health

A Global Convergence of Expertise The VEME workshop, held in 18 countries over its 28 editions, has earned a reputation as one of the world's most advanced and intense training programs. This year, it had participants from 33 countries and instructors from 12 countries, ensuring a diverse and comprehensive learning experience.

Some of the countries that have hosted the VEME workshop include Belgium, Brazil, Finland, Greece, Portugal, the USA, South Africa,

These modules covered the current methods used to analyze the vast data generated by modern DNA sequencing technologies, providing participants with both practical skills and theoretical knowledge. The workshop included lectures and practical sessions where students had an opportunity to analyze their own research data. Students also presented posters about their research

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with both practical skills and theoretical knowledge. Students also presented posters about their research.

Keynote Highlights and Networking The opening ceremony featured keynotes from leading experts in the field. Dr. Jairo Mendez-Rico, Regional Advisor for Viral Diseases at PAHO, emphasized the critical need for timely access to national and regional reference laboratories for detecting and characterizing new epidemic agents. He stated, “Timely access to these laboratories is crucial for managing emerging and re-emerging viral threats.”

Prof. Tulio de Oliveira, a renowned figure in bioinformatics, highlighted the significant impact of climate change on pathogen outbreaks. He noted, “Over half of known pathogen outbreaks will increase due to climate change, underscoring the need for enhanced surveillance and response strategies.”

The official opening was not only a platform for speeches but also an excellent opportunity for networking. Participants and teachers engaged in discussions, forging connections that will undoubtedly lead to fruitful collaborations throughout the week and beyond.

Poster presentations At VEME, over 80 diverse research topics were displayed, highlighting the global efforts in disease tracking and prevention, showcasing the latest advancements in public health genomics. Among the many compelling posters, a select few were recognized as the best in their respective modules. David Martins, who won the award for the NextGeneration Sequencing Analysis module, emphasized the importance of clarity and visual appeal in effective scientific communication.

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“It’s crucial to be very concise, accurate, and visually appealing,” said Martins. His winning poster, titled

CrAssphage distribution analysis in an Amazon River based on metagenomic sequencing data and georeferencing, delves into the use

of CrAssphages as biomarkers for faecal contamination in water bodies.

Gratitude to Sponsors and Teachers We extend our heartfelt thanks to all the sponsors and teachers whose support and expertise are essential in making this training a success. Their collective efforts ensure a collaborative and impactful experience for all participants. Special thanks to Prof.

Anne-Mieke Vandamme for her exceptional contributions in organizing VEME workshops from 1994 to 2019. Her dedication has been instrumental in establishing the workshop as a leading event in public health. We look forward to #VEME2025 in Senegal next year.

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Timely access to these laboratories is crucial for managing emerging and re-emerging viral threats.

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Dr. Jairo Mendez-Rico, Regional Advisor for Viral Diseases at PAHO, at the opening of VEME 2024

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#2MINUTES POSTERPITCH

We challenged our fellows to summarize their work in 2 minutes! https://www.youtube.com/@krisp-ceri

Harriet Ng’ombe on cholera vaccine and strain validation, Zambia

Dr. Andrew Musyoki, SMU on Antimicrobial resistance, South Africa

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Emmanuel Lokilo on the discovery of clade Ib of Mpox in DRC

Gaspary Mwanyika on Dengue outbreaks and genomes in Tanzania

Luis Janssen the Yellow Fever explosive outbreaks in Brazil

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GENOMICS AFRICA & CLIMADE FELLOWS:

Alhagie Papa Sey is the LIS Manager at the National Health Laboratory Services of the Ministry of Health, The Gambia.

Dr. Andrew Waititu is a pharmacist and researcher currently serving at the Ministry of Health in Nigeria.

With a strong commitment to improving patient outcomes and medication safety, he has been actively involved in the field of pharmacogenomics, focusing on how genetic variations affect individual responses to medications.

His work aims to enhance personalized medicine approaches in healthcare.

Fellowship sponsors: the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), the World Bank and the EDCTP.

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With a major in Information Systems (Computer Science) and a focus on Bioinformatics, he is part of the MoH-ICT Core implementation team as a system analyst. He is interested in developing programs and tools for analyzing genomics data to support public health decisions and interventions.

Fellowship sponsors: the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), the World Bank and the EDCTP.

Mokgerwa Zacharia Monama is a Bioinformatics lecturer and researcher at the University of Limpopo (UL) in South Africa, under the New Generation of Academics Programme (nGAP).

Mr Monama received his Genomics and Structural Bioinformatics training from Rhodes University.

His research focuses on drug resistance in Mycobacterium tuberculosis and SARS-CoV-2 related proteins, with an interest in developing software tools for molecular data analysis.

Fellowship sponsors: the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), the World Bank and the EDCTP.

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Omotayo Anick J. Bara is a PhD student at the Centre de Recherches Médicales de Lambaréné (CERMEL) in Gabon.

Her research focuses on the transmission flow of Plasmodium falciparum genotypes from infected human hosts to mosquito vectors. As a biologist, she seeks to deepen her knowledge of genomics applications to infectious diseases and develop her skills in bioinformatics.

Fellowship sponsors: the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), the World Bank and the EDCTP.

Andile Khumalo is a medical virologist from eSwatini, currently a final-year NHLS intern medical scientist and pursuing a Public Health Postgraduate Diploma at the University of Pretoria.

Graca Kamba Kandanda is a Biotechnologist and MSc student in Biotechnology, also serving as a Research Assistant at the Namibia University of Science and Technology With a strong foundation in molecular biology, microbiology, and genomics, their research focuses on wastewater-based epidemiology for genomic surveillance of antimicrobial resistance. Graca is dedicated to scientific literacy and mentorship, guiding secondary school, undergraduate, and graduate students in Namibia.

Her research includes HIV drug resistance, occult Hepatitis B Virus, and respiratory infections.

With experience in characterizing HIV drug resistance mutations, she is passionate about genomics and bioinformatics. She aims to advance public health and collaborate on impactful research to benefit the people of eSwatini.

Fellowship sponsors: the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), the World Bank and the EDCTP.

Fellowship sponsors: the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), the World

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Capacity Building

SHINNING A LIGHT ON CAPACITY BUILDING IN THE GLOBAL SOUTH 2 1 WO R KS HOPS I N 2024 AND A LOT MOR E TO COME TO MAK E THE GLOBA L S O UTH LEAD I N SCI ENCE & I NNOVATI ON text: Tu l io de Ol ive ir a a nd C he ryl B a xte r photo : Tu l io de Ol ive ir a , M idJo ur ney

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n 2024, we decided to invest heavily in training and capacity building.

CERI, KRISP and SACEMA partnered with AIMS, Separations, Illumina, DIPLOMICS and FioCruz Foundation to deliver 21 training workshops, with over 90% were hosted in our facilities at BMRI at Stellenbosch University and the Nelson R Mandela School of Medicine. In these workshops, we received over 1,000 participants, most for hands-on training. In addition, we hosted over 100 fellows who spend weeks, months and sometimes years with us to further advance their skills and careers. Below is a list of workshops delivered and planned so far for 2024.

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16-28 June - MMED with SACEMA 15-19 July - Genomic Fellowships 22-26 July - Bioinformatics Fellowships 23-25 July - Separations Training Academy - WGS Workshop 1-20 Aug - SEAMS (Software Engineering in Mathematical Sciences) 4-9 Aug 28th I n te r n a t i o n a l Bioinformatics & Virus Evolution & Molecular Epidemiology (VEME) 13-15 Aug - Separations Training Academy - Metagenomics Workshop 16-18 Aug- ISME / DIPLOMICS – ONT WGS workshop

04-08 March - Introduction to data management with R

16-17 Aug- ISME bioinformatics workshop - Microbiome training

12-14 March- Separations Training Academy - Metagenomics Workshop

19 Aug- Separations Training Academy - WGS workshop

April-June- Introduction to Epidemiology & Research Methodology

10-12 Sep- Separations Training Academy - WGS workshop

15-18 April- ISO accreditation training

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7-10 May- Illumina NGS library prep training 10-14 June- MedPH Program (part of Biomath Honours Course/ AIMS S t r u ct u r e d M a s te r s )

Sep Science

Ad va n c e d Wo r k s h o p

8-10 Oct- Separations Training Academy - RNA Sequencing workshop 11 Nov - Separations Training Academy - Bioinformatics workshop

25-27 May - Separations Training Academy - RNA Sequencing workshop

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CLIMADE

EXPERT COMMENT: HOW CAN WE ADDRESS THE NEXUS OF CLIMATE CHANGE, MIGRATION, AND INFECTIOUS DISEASES? text: O x fo r d Unive r sity & C ER I , SU photo : Claudiad, Getty Images.

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limate change and its associated impacts have been closely linked to increased risks of infectious disease transmission, with projections indicating that these risks will further intensify the global burden of infectious diseases and lead to substantial disruptions in human societies. This situation is further complicated by a significant rise in the number of internally displaced persons (IDPs), which increased from 33.3 million to 71.1 million between 2013 and 2022, reflecting the extensive human displacement driven by various factors such as conflicts, violence, and natural disasters.

In a recent perspective piece in Nature Climate Change, our team of researchers — an international collaboration between researchers from the Department of Biology and the Pandemic Sciences Institute at the University of Oxford and Stellenbosch University’s Centre for Epidemic Response and Innovation (CERI) — came together to deepen our understanding of the impacts of the interrelated crises of climate change, migration, and infectious diseases and to explore their potential implications for research and policy.

This work is part of the broader initiative to address the pressing concerns around climate-sensitive diseases as part of the Climate Amplified Diseases and Epidemics (CLIMADE) consortium.

Our review and analyses show that high-income countries that have contributed the most to global emissions face a lower infectious disease burden and are less vulnerable to the added impacts of climate change.

On the other hand, low- and middleincome countries (LMICs) in Africa

and Asia, that have made the least contribution to the global emission of greenhouse gasses, have continued to experience the greatest burden from infectious diseases and the highest vulnerability towards climate change. Most of the internal displacements as a result of weather-related hazards occurred in Asia and Africa.

Meanwhile, a large number of high-income nations, such as Portugal and Hungary, with high rates of outward migration are less vulnerable to climate change in comparison to the majority of low- and middle-income nations with high rates of inward migration such as Kenya and Uganda. This emphasizes the need for assessing the health effects of migration in LMICs to ensure a more equitable approach to lowering the health effects of climate change. In recognition of the critical link between climate change and human health, COP28 for the first time introduced a dedicated Health Day, spotlighting clear, evidencebased pathways that illustrate how climate change directly affects human health.

We explore the specific pathway through which migration impacts infectious diseases. Migration, whether forced or voluntary, could alter the epidemiological landscape by introducing pathogens into new areas or by exposing migrants to diseases to which they have little or no immunity (acquired either through vaccination and/or exposure). The examples of Cholera and Hepatitis E outbreaks in refugee camps in Kenya, following severe droughts in the Horn of Africa in 2011, starkly illustrates how displacement can precipitate public health crises. These highlight the need for targeted interventions that address the vulnerabilities of displaced populations, particularly in LMICs.

To enhance the effectiveness of adaptation measures, it is essential to integrate climate risk assessments into national health planning, particularly in LMICs. This includes improving surveillance systems for infectious diseases, strengthening healthcare infrastructure, and ensuring that health facilities are resilient to climate impacts. Furthermore, the development and dissemination of early warning systems for climate-related health risks should be a priority.

For instance, monitoring changes in disease vector populations and environmental conditions can help predict the spread of vectorborne diseases, allowing for preemptive actions to reduce transmission. We call for context-specific and multidisciplinary approaches to designing and implementing adaptation strategies to reduce the impact of migration on infectious disease spread. However, the implementation of these strategies remains a significant challenge, particularly in regions with limited resources.

In conclusion, our comprehensive analysis of the complex interplay between climate change, migration, and infectious diseases reiterates the urgent need for an integrated and equitable global response to these intersecting crises and to address the gaps in current approaches. The path forward requires a concerted effort to enhance global health security, promote climate justice, and build resilient communities capable of withstanding the dual threats of climate change and infectious diseases.

The perspective ‘Impacts of climate change-related human migration on infectious diseases’ has been published in Nature Climate Change.

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CLIMADE

OROPOUCHE VIRUS A new virus emerged from the Amazon Forest Basin and is spreading in Latin America

text: I a n i e t a l . m e dR XiV, 2 0 2 4 . 08 .0 2 .2 4 3 1 1 4 1 5 v 2

razil has experienced a significant surge in Oropouche virus cases, with over 7,000 reported by mid-2024. Recent genomic analyses reveal a rapid north-tosouth spread of the virus from the Amazon Basin into historically nonendemic regions. This study, conducted as part of the CLIMADE consortium, also reports the first fatal cases of Oropouche virus infection.

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from regions outside the Amazon and the first recorded fatal cases.

Oropouche virus, first identified in Trinidad and Tobago in 1955 and later in Brazil in 1960, has historically caused around 30 outbreaks, primarily within the Amazon Basin. The virus circulates among forest animals and is transmitted to humans by the midge Culicoides paraensis.

The rapid spatial expansion and the first reported fatalities underscore the need for enhanced surveillance of this evolving pathogen. Factors such as viral adaptation, deforestation, and climate change may have contributed to the virus’s spread beyond the Amazon Basin.

In collaboration with Central Public Health Laboratories across Brazil, researchers integrated epidemiological metadata with genomic analyses of recent cases. This effort resulted in the generation of 133 whole genome sequences from the virus’s three genomic segments (L, M, and S), including the first genomes

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All 2024 genomes form a monophyletic group with sequences from the Amazon Basin sampled since 2022.

The analyses revealed 21 reassortment events and a rapid viral movement from the Amazon Basin into new regions. However, it remains unclear if the virus’s genomic evolution has enabled it to adapt to local ecological conditions and evolve new phenotypes of public health importance.

The spread of Oropouche virus into regions more than 3,500 km from the Amazon Basin, coupled with genome reassortment events, suggests the virus is adapting to new environments.

This evolution could lead to new viral phenotypes, affecting vector efficiency and disease outcomes, and highlights the need for robust surveillance systems at national and continental levels.

genomics, epidemics & microbes

Figure 1: Spread of Orpoupoche in Brazil and the world.

Full Open paper: https://www.medrxiv.org/content/10.1101/2024.08.02.24311415v2

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“We are not scared and are working to detect new pathogens before they emerge” “Partnering with FioCruz, and the Brazilian Navy to take genomics surveillance to the most remote forests and popultations”

Profs. Luiz Alcantara & Tulio de Oliveira on behalf of CLIMADE. 30

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The NIH director visit CERI and give an open seminar Prof Jeanne Marrazzo, director of NIH’s National Institute of Allergy and Infectious Diseases (NIAID), During her visit to South Africa, Prof Marrazzo visited several research groups including CERI and gave an open seminar on the NIH/NIAID's mission and impactful infectious diseases research.

The seminar was attended by over 100 participants at the BMRI faclity and co-hosted by CERI and the Faculty of Medical and Health Sciences (FMHS) at the Tygerberg campus.

The full video of the seminar is available here https://www.youtube.com/ watch?v=rnE8Sx2DHoA

Oropouche virus 101: A guide to a little-known virus that’s raising concern this year Summary of the article at NPR: The Oropouche virus, first identified in 1955 in Trinidad, is gaining attention due to an increase in cases and its potential to spread beyond its traditional confines in the Amazon Basin. The Pan American Health Organization (PAHO) has issued an alert, emphasizing the need for enhanced prevention and surveillance. The virus, transmitted by mosquitoes and midges, is typically associated with mild symptoms such as fever, rash, and muscle aches, lasting about a week. However, recent spikes in cases—rising from 832 in Brazil in 2023 to over 7,284 in 2024—along with reports from Bolivia and Cuba, raise concerns.

Researchers attribute the virus’s emergence to climate change, which creates more favorable conditions for the insects that spread it. Deforestation in the Amazon has displaced wildlife, leading these vectors to seek human hosts. Alarmingly, 2024 has seen two deaths of healthy young women in Brazil attributed to Oropouche, increasing scrutiny on the virus’s potential severity. There are also concerning reports of congenital transmission, with some infants born with defects and others not surviving.

While Brazilian public health officials are actively managing the situation, there is apprehension regarding the virus’s global spread, especially in regions less equipped to handle arboviral outbreaks.

Full article at NPR: https://www.npr.org/sections/goats-and-soda/2024/08/15/ nx-s1-5074058/virus-oropouche-brazil-mosquitoes-midges-dengue

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genomics, epidemics & microbes

Exchange grants between UKZN, Stellenbosch & Europe for ARUA/The Guild CoRE The CoRE-GHA consortium provides funding for short research stays (up to 90 days). Young researchers will have the chance to explore the fields of rare and infectious diseases, particularly focusing on the genomics aspects of disease and health. This opportunity is limited to researchers at institutions that are partners in the consortium. .

Target Group: Early Career Researchers/postdocs at a home institution belonging to the CoRE-GHA consortium For more about the program or to submit an application, visit: https://www.genomicsforhealthinafrica.org /consortium)

The surge of mpox in Africa: a call for action The WHO’s declaration of mpox as a public health emergency of internatonal concern highlights the critical situation in Africa, where the virus continues to spread unchecked.

The global community’s previous neglect of the disease in Africa has now led to a resurgence that poses a threat beyond the continent. The WHO’s call to action aims to mobilize resources, enhance surveillance, and support research efforts to control and eventually eliminate mpox.

The CERI and KRISP teams have been central in raising awareness about the ongoing Mpox outbreaks and stress the urgent need for a comprehensive and collaborative approach to tackle the mpox crisis in Africa and prevent its further spread globally.

In addition to conducting multiple interviews, CERI has contributed to the paper titled “The Surge of Mpox in Africa: A Call for Action,” published in The Lancet Global Health.

Open manuscript at: https://doi.org/10.1016/ S2214-109X(24)00187-6 Opinion piece published in the Conversation Africa piece at: https://theconversation.com/ mpox-outbreak-in-africa-was-neglected-it-could-now-turn-into-thenext-global-pandemic-236893

Understanding the Transmission of Chikungunya in Africa The paper “ ,” published in Pathogens, provides a comprehensive review of the epidemiology, genetic diversity, and transmission dynamics of the Chikungunya virus (CHIKV) in Africa. The authors call for ongoing surveillance,

research, and collaboration to mitigate the burden of CHIKV in Africa and improve public health outcomes. link: https://www.mdpi. com/2076-0817/13/7/605

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2 0 2 4 N R F Aw a r d s

SACEMA SACEMA is recognized by the NRF as a finalist for Societal Impact Award

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he National Research Foundation (NRF) acknowledged the South African Centre for Epidemiological Modelling and Analysis (SACEMA) at Stellenbosch University as one of three finalists (out of 35 research centres) for the prestigious Societal Impact Award at a ceremony held on 22 August 2024 at Sun City Resort, North West Province.

This esteemed recognition highlights SACEMA’s remarkable contributions over the past 18 years to understanding and controlling infectious diseases such as HIV, tuberculosis (TB), human papillomavirus (HPV), and, more recently, the COVID-19 pandemic. SACEMA is a national centre of excellence which has been funded by the NRF since its inception in 2006 until April 2024. It is the forefront institution in epidemiological modelling on the African continent and its mission is to improve population health in Africa through effective use of modelling.

Prof. Frank Tanser, Director

of SACEMA, expressed immense gratitude and pride in this achievement: “Being named a finalist for the NRF Societal Impact Award is a massive honour for SACEMA. It not only demonstrates the high regard in which our work is held but also underscores the substantial societal impacts we have made over nearly two decades. Through its activities SACEMA has exemplified the NRF’s commitment to advancing research with impactful societal benefits.”

SACEMA’s research has led to groundbreaking methods, such as the Kassanjee method for HIV incidence estimation, adopted by the US CDC, and significant contributions to global HIV modelling and estimation. The centre also played a crucial role in the COVID-19 response, providing pivotal forecasts that informed public health strategies in South Africa and beyond. In addition, SACEMA is passionate about building South African and African capacity in epidemiological modelling. To date SACEMA has graduated over 200 students, published over 500 scientific articles and together with its partners delivered intensive short courses in infectious disease

modelling and epidemiology to over 1000 participants.

Lynnemore Scheepers, Deputy Director of Operations at SACEMA, emphasized the importance of collaboration in their success: “This recognition is a testament to the incredible teamwork and partnerships we’ve fostered over the years. Our achievements are deeply rooted in our collaborations with national and international organizations, which have been instrumental in translating our research into meaningful real-world impact.”

Prof. Sibusiso Moyo, Deputy Vice-Chancellor for Research, Innovation, and Postgraduate Studies at Stellenbosch University, lauded SACEMA’s achievement: “SACEMA’s recognition by the NRF is a significant milestone for Stellenbosch University. It highlights the vital role that cutting-edge research plays in addressing global health challenges and reinforces our commitment to advancing knowledge that benefits society.”

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PU B L I C E NG AG EM ENT Microbes and Climate Change Event at Kirstenbosch Botanical Garden 36

tex t: M a a m be l e K h o sa ph oto : Hen k O e ts ph otog r a phy

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key highlight of the 19th

International Symposium on Microbial Ecology (ISME19) was its emphasis on public engagement, showcased by a science outreach event titled “Microbes and Climate Change.” This event, held at Kirstenbosch National Botanical Garden on 21 August, was organized by the International Society for Microbial Ecology (ISME) in collaboration with the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University. It drew an audience of over 150 high school learners, teachers, community leaders, and members of the public, offering an opportunity to explore the vital role of microbes—including bacteria, fungi, protists, and viruses—in relation to climate change.

The event began with an opening address by Thulani Makhalanyane and Phi Hugenholts, ISME presidentl,

They each set the stage by emphasizing the importance of bridging the gap between science and society in addressing global challenges.

This was followed by welcoming remarks from Prof. Wim de Villiers, Vice-Chancellor and Rector of Stellenbosch University, who highlighted the university’s commitment to promoting scientific literacy and environmental stewardship.

Attendees were then treated to presentations from a distinguished lineup of speakers. Dr. Raquel S. Peixoto from King Abdullah University of Science and Technology (KAUST), and the newly appointed president of ISME, shared her groundbreaking work on marine microbiomes. “After assiduously searching underwater for three months, we discovered the perfect place to build the first probiotic coral ‘village,’” she explained. “We now have a permanent underwater laboratory where experts and principal investigators can develop and carry out their research. It’s a magical place, isolated, protected,

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Next, Dr. Joana Falcao Salles from the University of Groningen provided insights into terrestrial and soil microbiomes. She highlighted that soils are the foundation of life on Earth, with soil microorganisms playing a crucial role in sustaining ecosystems and keeping our planet healthy. “Conventional agricultural practices may aim for higher yields, but they often come at a cost to both the environment and farmers, due to the heavy reliance on external inputs such as fertilizers and pesticides,” she noted.

Dr. Luis Pedro Coelho from Queensland University of Technology then discussed the human microbiome and its connection to climate change. He emphasized the unique yet interconnected nature of microbial communities, stating, “Microbes are different, but they are connected—they respect temperatures but not borders. However, there is hope in microbiome research, which can lead to innovative solutions.”

The event also featured a mediated panel discussion, led by Alwin Mabuza, Individual and Regular Giving Fundraiser at Stellenbosch University’s Development and Alumni Relations division. This session provided a platform for rich engagement between the speakers and the audience, culminating in a lively Q&A that fostered environmental stewardship and further discussion on actionable strategies for climate change mitigation.

Through this event, ISME19 highlighted the significant interactions between microbial ecosystems and climate change, aiming to foster greater public understanding and inspire actionable strategies for environmental conservation.

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“ Microbes are different, but they are connected— they respect temperatures but not borders

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Dr. Luis Pedro Coelho Queensland University of Technology

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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

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