the gem: genomics, epidemics & microbes - Oct/Nov 2024

number 7 - volume 9 Oct/Nov 2024

genomics, epidemics & microbes

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Third era of genomics A Science article exploring the transformative potential of genomics

MSc & PhD scholarships in Mathematics, Statistics, Epidemiology, Data Science & Computer Science read it online

The art of grant writting Writing successful grants is not a oneman/woman show. It takes teamwork

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summary

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Africa in the World

Third era of genomics

A new Denguegenomic system

The festival brings together some of the brightest minds from across Africa, showcasing expertise and innovation across all fields of human endeavor.

In an expert commentary article in Science, Tulio de Oliveira explores the transformative potential of what he calls the “third era of genomics.”

The new nomenclaure system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals.

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

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Data Science & Bioinformatics

MSc & PhD scholarships available

Mastering the art of grant writting

The Advanced Data Science & Bioinformatics for Genomic Epidemiology Workshop was attended by over 20 fellows from various countries, who gained advanced skills in data analytics, including epidemiological modeling, phylogenetics, metagenomics, data visualization, AI, and bash scripting.

We seek motivated individuals with backgrounds in Mathematics, Statistics, Epidemiology, Biostatistics, Global Health, Data Science, Computer Science, or other related quantitative fields.

In the world of research, deadlines are relentless, and competition for funding is fierce.

Without strong grant writing skills, even the most innovative ideas can fall through the cracks.

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editorial

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he last few months have been a blast!

Spring has arrived in South Africa, bringing many friends and colleagues to visit.

We participated in several events, including Africa in the World, one of my all-time favourites. This event brings together politicians, business leaders, artists, journalists and scientists to advance the agenda of African excellence. Too-often, Africa is viewed as backward, poor and inefficient but this generalization is both wrong and unjust.

Despite many challenges, Africa has the potential to contribute meaningfully to solving global issues. One of the highlights was sharing the stage with a good South African friend, Professor Salim Abdool Karim, who recently won the Lasker Award, which is often called “America’s Nobel Prize” for its high prestige in honouring medical scientists.

In this edition of the GEM, we highlight our opinion piece in Science on the third age of genomics, a new era poised to bring substantial global benefits. However, for this to become a reality, we need to make sure that recent investment in genomics in the Global South are maintained and expanded. This new era also requires major investments in training and capacity building in data sciences, bioinformatics and AI. In September, we hosted an advanced Data Science Workshop, selecting 20 fellows from over 2,700 applicants across Africa. We continue to expand our capacity-building programmes, recruiting multiple new MSc, PhD and postdoctoral candidates, as well as organizing additional hands-on workshops, including an upcoming laboratory-based training on library preparation in partnership with Roche.

I hope you enjoy reading this edition of the GEM as much as we enjoyed creating it. May spring in the Southern Hemisphere bring new energy and excitement for the pursuit of excellence

text: Tulio de Oliveira

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Festival

Africa in the World text: Tul io de Ol ive ir a photo : Africa in the World

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he ‘Africa in the world’ festival has the world’s brightest on the African continent engage in all fields of human endeavour.

From September 4-7, the Africa In the World festival returned to Stellenbosch, bringing together global and continental leaders in a collaborative dialogue aimed at addressing Africa’s challenges.

Founded by Pulitzer Prize winner Dele Olojede in 2019, the festival promotes vibrant discussions among a diverse group of thinkers, innovators, and changemakers across various fields. Dele Olojede, welcomed guests to “my ancestral home, Stellenbosch”.

The 2024 lineup features distinguished speakers, including renowned scientists tackling major health issues like HIV, Ebola, and Malaria, as well as leaders from notable businesses and political figures such as South Africa’s Cape Town mayor.

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The multi-awarded speakers billed for the 2024 festival include scientists Prof Sir Adrian Hill, Dr Ally Olotu, Prof Tulio de Oliveira and Prof Salim Abdool Karim.

Among them they have tackled HIV/Aids, Dengue, SARSCoV-2, Zika, Yellow Fever Virus, Ebola and Malaria.

The festival’s second session, a conversation between Profs Salim Karim and Tulio de Oliveira, spoke to the power of coalition and collaboration, of scientists, activists and principled administrators marching in lockstep. Karim and De Oliveira are globally acclaimed SA epidemiologists. They have been at the forefront of fighting multiple infectious diseases, from HIV to Covid-19. Despite the subject’s seriousness, there was a joy in listening to the interplay between two virtuosos who’ve been at the forefront of influencing some of the world’s most powerful people.

In the third section, leaders in business include Standard Bank group chair Nonkululeko Nyembezi; founder and CEO of Onafriq Daré Okoudjou; and founder and CEO

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Africa in the World opening at Stellenbosch Town Hall. The festival included scientists, jornalists, business leaders, politicians, artists and poets united by their desire to improve Africa and the world.

of Africa Climate Ventures James Irungu Mwangi discussed about climate change, economy and governance.

There’s also the Nigerian minister of communications, innovation and digital economy Dr Bosun Tijani and Cape Town mayor Geordin Hill-Lewis in this panel discussion.

Each speaker arrived with their tools of trade — genetic sequencing, stanzas, cashflows and compositions — seemingly disconnected, but united by their desire to improve the world.

The festival delivered on inspiration and brilliance, fostering a collaborative spirit dedicated to progress on the African continent.

More info on the coverage of Africa in the World on Business Day:

Between the scientists and business builders stood Afrikaans and San poets Antjie Krog and Nunke Kadimo. Among others, they recited The Broken String. First recorded in the 1870s, it laments the destruction wrought by colonialism. It concludes, “they have broken the bow’s string for me and the old places are not sweet any more for what they did”.

- https://www.wantedonline.co.za/voices/2024-09-25-onbettering-african-lives/

Musician and intellectual Neo Muyanga accompanied by soprano Tina Mene, gave a mind blowing performanceof Africa and Opera: A Revelatory Journey (See photo of their performance at the editorial comments, page 2).

- https://www.youtube.com/watch?v=gK4C-Ghh3ns

- https://www.wantedonline.co.za/voices/2024-09-04-africa-in-the-world-festival-kicks-off/ Youtube: Africa In the World 2024 Festival Highlights:

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Publication

The third Era of Genomics Science 2024, DOI: 10.1126/science.adt4843

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he first era of genomics started with the publication of Watson and Crick’s notable work on the description of the DNA double helix in 1953. This era lasted 50 years, until the publication of the human genome in April 2003. The second era is associated with the period between the completion of the human genome and the present day. I argue that, with the discontinuity caused by the COVID-19 pandemic and the spread and increased use of genomics to every corner of the world, we are entering a new, third era of genomics that provides major opportunities to advance the health of humans, animals, and the planet. However, this can only happen if the capacity that has greatly expanded in recent years is maintained and expanded further rather than left to atrophy, particularly across the global south.

The first era was mostly led by research. It involved major basic science discoveries and the development of scientific methods to first visualize, describe, and then sequence DNA. This era was characterized by small-scale

sampling and the characterization of genes, mutations and genomes of pathogens, parasites, and uni- and multicellular model organisms. As DNA sequencing technologies matured, the concept of sequencing the human genome evolved, and the Human Genome Project began. Launched in 1990, it took more than 20 years to complete and cost billions of dollars. Close to its completion, a new technology called shotgun, or short-read, sequencing emerged, allowing genomes to be sequenced more rapidly and economically. This launched the second era of genomics, often referred to as the postgenomic period, that progressed beyond the gene-centered approach of the previous era and unlocked the power of genomics to produce thousands of genomes of different organisms.

The postgenomic era also linked these data to functional studies and converted the knowledge into practical solutions, such as the identification of drug resistance mutations in microorganisms and the understanding of disease emergence, transmission, and evolution. During this era, genomic information was also used to design and

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ine-tune diagnostics, therapies, and vaccines for human, animal, and plant organisms. Despite massive developments in the postgenomic era, such as “next generation” sequencing technologies, the process to develop solutions was still costly, with long turnaround times and the time from initial sequencing to the development of an intervention normally taking several years. Most were sequenced in centralized facilities, such as the Wellcome Sanger Institute, the Beijing Genomics Institute, and the BROAD Institute of MIT/Harvard.

The development of hand-held sequencers, the decrease of sequencing costs, and the use of genomics in the COVID-19 pandemic was a watershed moment to genomics and brought untold advantages. Not only did it allow the field of genomics surveillance to advance rapidly, but it also brought it to the attention of the world. For the first time in the history of genomics, whole genomes of viruses were produced within days of sampling. Originally restricted to rich countries, this capacity to sample and sequence whole virus genomes in a matter of days moved into the global south. During the COVID-19 pandemic, SARS-CoV-2 genomic data were public within minutes of being produced and could be analyzed everywhere. Highly effective genomics citizen science efforts arose, with nontraditional genomics researchers, such as high school teachers. Data production advanced to a new level, and more than 17 million genomes of SARS-CoV-2 were generated and are shared through the Global Initiative on Sharing All Influenza Data. This created a profound acceleration in sequencing. High-throughput DNA sequencers were set up in every corner of the globe, finally providing access to genomics to developing countries. In addition, the COVID-19 pandemic turbocharged the use of genomic data to develop diagnostics, therapeutics, and vaccines.

Development of vaccines from a genome that formerly would take years can now be done in days or months. The discovery of COVID-19 variants in the United Kingdom, South Africa, Brazil, and India generated a series of rapid changes, some of which were very positive, such as bivalent vaccines and diagnostics that had been rapidly adapted to the new variants. This led to the belief that ambitious programs, such as the 100 Days Mission to make effective vaccines, therapeutics, and diagnostics within 100 days of identification of any pathogen, were not science fiction but a reality.

Trust between scientists, policy makers, industry, and the public will be essential to advance the new age of genomics. Impact will be measured

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in terms of the interaction between public health, pharma, and discovery research to translate the results into action and products that can control an epidemic or better treat a genetic disease with precise therapies within days of its discovery. The recent characterization of Oropouche virus reemergence from the Amazon Basin allowed Brazilian health authorities to develop and implement diagnostics rapidly to detect and control outbreaks in multiple states. The same happened with Mpox in Africa, as a new clade (i.e., variant) was discovered in 2024, a health emergency was called by the World Health Organization and Africa Centres for Disease Control and Prevention, and finally, vaccines are being made available on the continent. The third era of genomics will also need to advance conservation genomics and precision breeding, particularly focused on developing resilient, higher-yield, and drought-resistant plants, crops, and animals.

We need to conserve the natural environment and maintain food production with less harm to the planet so that we can survive and thrive in the time of climate change.

To allow genomics to thrive in a more unpredictable and rapidly evolving world and to achieve the ambitious objectives and unleash an era of extreme potential for genomics, decision makers and politicians have a choice to make on whether to support and expand the genomics infrastructure and expertise that were developed during the COVID-19 period. Unfortunately, this capacity is at risk of being dismantled in many global settings. If not careful, the investment in the global south can vanish in a few years as equipment gets older and is not replaced and as funding for reagents and personnel dry up. If capacity in the global south plateaus or degrades, then many of the trained scientists there may emigrate to the global north.

We also need to ensure that the health benefits that can arise from these investments and efforts are truly widespread and evenly spread. The third era of genomics can provide huge opportunities if we invest and embrace it, supporting global development. Alternatively, it can increase disparities if the use of genomics turbocharges access to interventions in the global north that are unaffordable in the global south. Will the whole world see the benefit of the third area of genomics? Time will tell.

Link to publication: https://www.science.org/doi/10.1126/science. adt4843

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Will the whole world see the benefit of the third era of genomics?

Time will tell.

Tulio de Oliveira, Science, 2024.

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Global Collaboration

A new lineage nomenclature to aid genomic surveillance of dengue virus Publication in PLoS Biology, new website & tools to better classify Dengue genomes for public health response.

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he new nomenclaure system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals.

The system aims to provide additional spatial and temporal resolution with which to discuss the large genetic diversity of dengue virus. Specifically, it splits up existing genotypes into smaller groups and provides a standardized, neutral naming system.

Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules, but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. We designated an initial set of lineages based on all publicly available whole genome sequences with coverage greater than 70% in mid-2023.

We envision two ways of generating new lineage suggestions. The first is through community effort via a github repo, which is what this page is designed to help

with. Here, members of the dengue research/public health community can suggest new lineages to help with their surveillance efforts. These will be reviewed with some regularity and given a “putative” name.

The second method is an annual review, where all publicly available whole genome data is run through custom scripts to ensure that all new lineages have been identified, including appropriate putative ones suggested throughout the year. These will then be reviewed by an advisory board and assignment tools are updated.

Open Publication: - Hill et al. PLoS Bioology 2024 https://ceri.org.za/publication/?token=465 Website with classification system & sequencing protocols: - https://dengue-lineages.org/ Bioinformatics Tools: - https://www.genomedetective.com/app/typingtool/dengue/ - https://github.com/giffordlabcvr/Dengue-GLUE - https://clades.nextstrain.org

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CLIMADE

Mosquito-borne diseases are surging in Europe — how worried are scientists?

Nature News coverage of our work and how climate sensitive pathoges are becoming increasingly common as the insects that spread them move north. text: Tu l io de Ol ive ir a sum m a ry photo : James Gathany/CDC via Smith Collection/Gado/ Getty

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esearchers warn that climate change is transforming Europe into a breeding ground for mosquito-borne diseases, with elongated summers, higher temperatures, and increased rainfall creating ideal conditions for mosquito populations. This year, the European Centre for Disease Prevention and Control (ECDC) reported 715 locally acquired cases of West Nile virus (WNV) across 15 European countries, exceeding last year’s figures and the 10-year average, with 51 fatalities recorded as of September 2024.

WNV can lead to West Nile fever, characterized by symptoms like fever and fatigue, and severe complications in vulnerable populations, particularly the elderly. The primary vector, the Culex pipiens mosquito, has historically inhabited Europe, but climate change has expanded its transmission capabilities into previously unaffected regions.

According to Rachel Lowe, a climate and health scientist, the spread is associated with both climate shifts and increased travel following the COVID-19 pandemic.

Moreover, the Asian tiger mosquito (Aedes albopictus), responsible for transmitting dengue and chikungunya, has established itself in 13 European countries, resulting in reported cases in Italy and France this summer.

As mosquitoes proliferate in line with warmer, wetter conditions, researchers advocate for preventive

measures, such as using repellents, wearing suitable clothing, and eliminating standing water to decrease breeding sites. Additionally, there’s growing concern over asymptomatic donors possibly contaminating blood supplies with WNV. With the rise of these diseases prompting urgent calls for surveillance and preparedness in both endemic and non-endemic areas, experts emphasize the interconnectedness of global health challenges and the need for comprehensive strategies to combat the emerging risks.

Researchers say people who live in areas where outbreaks have been reported should take precautions to avoid mosquito bites.

“We are faced with a problem where new places could become hotspots of transmission that were not prepared for this before,” says Houriiyah Tegally, a genomic epidemiologist at Stellenbosch University in South Africa.

A July preprint from Ethiopian Public Health Institute and Addis Ababa University, KRISP and CERI, on which Tegally is a co-author, found that dengue virus strains in Ethiopia closely resemble those in Italy’s 2023 outbreak. “It’s impossible to prove the directionality of this movement,” says Tegally. But this “tells us that the world is very connected, and Europe could at one point, if not already, act as a source of these arboviruses as well, because there’s local transmission”.

Stay Safe: Rising MosquitoBorne Diseases Demand Precautions As mosquito-borne diseases increase in previously uncommon areas, researchers emphasize the importance of taking protective measures against mosquito bites. It’s recommended to use repellent, wear long-sleeved, light-coloured clothing, and install mosquito screens on windows. Reducing stagnant water in urban environments—such as in gardens, plant pots, and flower vases—can also minimize potential breeding sites. The Asian tiger mosquito, identifiable by its black-andwhite-striped legs, is a key concern.

Scientists warn of the risk posed by asymptomatic carriers who may unknowingly contaminate blood banks with diseases like WNV and Dengue Virus. Although testing mitigates this risk, it could impact the availability of blood and organ supplies; recent data showed that 190 blood donors in the U.S. tested positive for WNV this year.

These emerging risks underscore the necessity for vigilant surveillance of mosquito-borne diseases, even in non-endemic regions.

News piece at Nature: - https://www.nature.com/articles/ d41586-024-03031-y Preprint: - Abera, A. et al. Preprint at medRxiv 2024, https://doi. org/10.1101/2024.07.10.24310195

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DATA SCIENCE & BIOINFORMATICS FELLOWS CA PACIT Y BUI LDI NG FOR GENOMI C E PI DEM I OLOGY text: Maambele Khosa photo: Maambele Khosa

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ver four days, more than 20 fellows from nine countries gained advanced skills in data analytics, including epidemiological modeling, phylogenetics, metagenomics, data visualization, AI, and bash scripting.

CERI recently hosted a Data Science & Bioinformatics for Genomic Epidemiology Workshop, reaffirming the institution’s commitment to capacity building in Africa. held at STIAS. The participants gained advanced skills in data analytics, including epidemiological modeling, phylogenetics, metagenomics, data visualization, AI, and bash scripting.

Supported by The Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH and The Rockefeller Foundation, the workshop brought together expert trainers from Genome Detective, SACEMA, Nextstrain, the University of Sydney, and CERI. These leaders in the field guided participants through intensive, hands-on training aimed at empowering the next generation of researchers. The participants joined over 500 fellows who have been trained at Stellenbosch University in the past two years.

The commitment shown by both the trainers and the fellows underscores the necessity of such capacity-building efforts.”

Reflecting on the training, Dr. Bamlak Kassahun from Addis Ababa University & Animal Health Institute shared, “During my tenure at Stellenbosch University, I gained profound insights into bioinformatics and data science, both indispensable for infectious disease modeling. Investing in bioinformatics is crucial for advancing research into tropical diseases and improving public health outcomes.”

Another participant, Betselot Zerihun Ayano, a bioinformatics analyst from Ethiopia, said, “The workshop equipped me with invaluable tools to enhance genomic research at my institute. It was a rewarding experience to engage with experts and peers dedicated to advancing genomic epidemiology.”

As CERI continues its dedication to building research capacity, the success of this workshop highlights the power of collaboration and training in addressing global health challenges. More workshops are on the horizon, ensuring that Stellenbosch University remains a leader in genomic epidemiology.

Dr. Houriiyah Teagally, Head of Data Science at CERI, Stellenbosch University, highlighted the importance of this initiative: “Workshops like this allow us to bridge critical knowledge gaps in data science and bioinformatics, fostering collaboration and driving impactful genomic research across the continent.

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Data science & bioinformatics

Fellows

Hithesh Kumar

Andrew Ajang

Andrew Ajang Othow is a Medical Laboratory Scientist at the National Public Health Laboratory (Department of Molecular Virology) in South Sudan, specializing in Microbiology. He holds a master’s degree in medical laboratory science, with a focus on Medical Diagnostics and Microbiology. With five years of experience in performing molecular diagnostic techniques and providing technical support in outbreak detection and response, his dissertation at Mbarara University of Science and Technology addressed non-mycobacteria among TB-suspected patients and their susceptibility patterns.

Hithesh Kumar holds an MSc in Biotechnology from Kuvempu University, a PGD in Bioinformatics from SIT, India, and a Ph.D. in Bioinformatics from Vellore Institute of Technology, Tamil Nadu, India.

With five years of experience as a Bioinformatics Scientist in leading genomics companies, he has contributed to over 100 whole genome projects. His expertise spans whole genome analysis, hybrid WGS, transcriptomics, variant calling, metagenomics, methylation studies, insert characterization, and molecular docking and simulations. Currently serving as a Computational Biologist at Jivanu Therapeutics Pvt. Ltd., Bangalore, his research focuses on antimicrobial resistance (AMR), virulence factors in pathogenic bacteria.

Sibusiso Mahlangu

Sibusiso Mahlangu holds an MSc in Zoology from the University of Johannesburg, focusing on DNA barcoding and eDNA metabarcoding of estuarine macrobenthos. He joined the WWF Environmental Leaders Graduate Programme and worked at SANBI, enhancing his genomic analysis skills. He also completed an internship in Norway through the BioDATA Advanced Project. Sibusiso aims to apply machine learning to biodiversity genomics and pursue a PhD

Training funded by: The Deutsche Gesellschaft für Internationale Zusammenarbeit GmbH (GIZ), The World Bank and The Rockefeller Foundation.

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Chaima Hakimi

Chaima HAKIMI is a Ph.D. student in Bioinformatics at the Laboratory of Bioinformatics, Biomathematics, and Biostatistics (BIMS) at the Institut Pasteur of Tunis (IPT). Chaima is a bioinformatician with a biological background. Her research focuses on developing integrative computational approaches and applying machine learning to predict host-pathogen protein-protein interactions. In addition to her primary work, Chaima actively contributes to several international and national projects funded

by IPT, NIH, DAAD, and the Ministry for Europe and Foreign Affairs, demonstrating her expertise and dedication to collaborative research in bioinformatics.

Dr. Bamlak Kassahun Ruth Boniface

Ruth is a junior researcher focused on genomics surveillance, holding a Bachelor’s in Biotechnology from Sokoine University (2017) and a Master’s in Bioinformatics from the University of Nairobi (2024). She began her career with the HALI project, conducting molecular diagnostics for zoonotic virus surveillance in Tanzania. Since 2018, Ruth has served as a Tutorial Assistant at Muhimbili University’s Department of Biochemistry and Molecular Biology.

She also contributes to the Molecular Surveillance of Malaria in Tanzania (MSMT) project at the National Institute for Medical Research, where her work has been pivotal in mapping malaria parasite distribution and highlighting malaria’s impact in Tanzania.

Dr. Bamlak Kassahun holds a strong academic background in veterinary medicine and a Master’s degree in Tropical Infectious Diseases.

Currently leading a research project on antimicrobial resistance (AMR) as Principal Investigator, he applies his interdisciplinary expertise to address complex health challenges.

With extensive experience in data analysis, Dr. Bamlak derives meaningful insights from diverse datasets to inform research and policy.

Passionate about bioinformatics and data science, he seeks opportunities to integrate his veterinary knowledge with advanced computational techniques to drive impactful research and innovative solutions.

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PA N D E M I C

FOOTBALL MODEL FOR SCIENCE? Can global health learn from FIFA’s benefit sharing model? text: Ch e ryl B a xte r sum m a ry il l ustr a tio n: Midjourney.

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new proposal draws inspiration from FIFA’s benefitsharing model to support fair reward systems in global health, especially in pandemic preparedness. Following the COVID-19 pandemic, global health experts recognized the critical role played by scientists, particularly those in the Global South, who identified and provided vital data about the Omicron variant. However, these scientists, like Botswana-based virologist Sikhulile Moyo and South African bioinformatics scientist Tulio de Oliveira, were the last to benefit from the treatments developed due to geopolitical constraints, even facing travel bans and threats for their contributions.

Gabriel Butin, head of global health at an international forum, spearheaded a study exploring how FIFA’s solidarity model might offer a framework for fair compensation in global health. In soccer, FIFA’s system mandates that clubs compensating players’ training clubs with solidarity payments for each transfer, providing long-term benefits to smaller clubs involved in

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player development. This “solidarity mechanism” has led to substantial financial returns across players’ careers, like when Sporting CP and Manchester United received payments from Cristiano Ronaldo’s transfers.

Inspired by this model, global health advocates such as Spring Gombe suggest that a similar framework could address inequities in how health benefits and resources are distributed. A centralized clearinghouse, like FIFA’s, could track contributions from scientists worldwide and distribute resources fairly. This system could benefit the researchers and institutions contributing to pandemic data, thus sustaining research efforts in low-resource regions that often bear the brunt of epidemic responses.

The proposal is timely, as ongoing pandemic treaty negotiations with the World Health Organization (WHO) seek equitable frameworks for data sharing and benefit distribution. An approach akin to FIFA’s could streamline processes, automate benefit distribution, and establish accountability mechanisms that safeguard contributors from retaliatory actions like

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travel bans. Although differences in global health governance complicate direct implementation, integrating a centralized clearinghouse and digital platform could enhance collaboration and resource sharing.

Critics, however, caution that such a model might favour wealthier nations or organizations, much like how FIFA’s structure benefits richer clubs.

This risk of inequality underscores the need for flexibility and alignment with existing regulations, such as the International Health Regulations (IHR).

Still, supporters argue that the pressing need for fairer pandemic preparedness systems makes FIFA’s model a valuable reference.

Ultimately, a benefit-sharing model for global health could foster international solidarity by ensuring fair rewards for pandemic data providers, fortifying research infrastructure worldwide, and building trust—elements essential for effective, equitable global health responses.

LInk to DEVEX article: - https://www.devex.com/news/soccer-and-science-can-global-health-learnfrom-fifa-s-benefit-sharing-108261

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COULD A FIFA-INS BE USED TO EF REWARD SCI PREVENT PA

DEVEX, 2

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SPIRED MODEL FFECTIVELY IENTISTS & ANDEMICS?

2024.

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GLOBETROTTERS Inspiration, collaboraion and innovation around the world.

AFRICA CDC SACEMA and international members of NeoNet Africa, including representatives from the Africa CDC, convened in Addis Ababa on 15 and 16 October 2024. The meeting aimed to solidify a partnership between NeoNet Africa and Africa CDC, focusing on areas critical to neonatal sepsis management, including improving clinical practices, conducting applied research, leveraging data for public health decisionmaking, and enhancing bacterial isolate biobanking.

UNAIDS SACEMA leads the coordination of the UNAIDS Reference Group on Estimates, Modelling, and Projections (www.epidem. org), which provides guidance to UNAIDS on the development of modelling tools that generate key HIV estimates to nearly all countries globally (www.aidsinfo.unaids.org). This year’s in-person meeting was held in Addis Ababa, Ethiopia from 29 July to 1 August, focusing on topics such as the estimation of advanced HIV disease and causes of AIDS deaths, antiretroviral treatment interruption, and improving the reporting accuracy of people receiving treatment.

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GLOW The Global Women’s Research Society Conference (GLOW) took place on 23-24 September 2024 at the stunning McEwan Hall in Edinburgh. The conference theme, Rising to the Challenge: Women and Newborn Health in the Context of Global Crises. The conference opened with a compelling joint keynote by Professor Angela Dramowski, an infectious disease specialist and paediatrician from Tygerberg Hospital, and Dr. Larisse Bolton, a researcher from the South African Centre for Epidemiological Modelling and Analysis (SACEMA).

Their talk, titled Partnerships and Innovations to Tackle Antimicrobial-Resistant Infections in African Newborns.

BMGF IDM Jeremy Bingham, a Junior Researcher at the South African Centre for Epidemiological Modelling and Analysis (SACEMA), recently participated in the prestigious Bill and Melinda Gates Foundation’s Infectious Disease Modelling (IDM) Annual Symposium held on October 1-2. The event gathered leading experts in infectious disease modelling and public health professionals, creating a dynamic platform for knowledge exchange and collaboration. Funded by the Bill and Melinda Gates Foundation, Bingham delivered a compelling 15-minute presentation focused on the latest advancements in wastewater modelling.

LINGANISA II On 14 October 2024, SACEMA senior researcher Dr. Cari van Schalkwyk, and junior researcher, Lauren Brown, participated in the Linganisa II Annual Meeting. Funded by the Bill & Melinda Gates Foundation (BMGF), the multi-faceted project focuses on using advanced HIV and TB modelling to inform South Africa’s health strategies and interventions.

Collaborating with partners, including the Human Sciences Research Council (HSRC), PEPFAR, and NICD, ensures that the models developed are grounded in real-world data and can be translated into meaningful health outcomes.

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YOUTUBE VIDEOS

Carlin & AI Story Meet Carlin, a graduate of the ‘AI for Science’ Master’s program, utilizing machine learning to address diseases like Dengue fever and Zika, with an emphasis on enhancing disease tracking in Africa. Supported by the Google DeepMind Scholarship, Carlin’s research exemplifies efforts to increase diversity in AI by providing equitable access to education.

Google DeepMind partners with 26 universities globally and has committed $4.5M to launch the AI for Science Master’s program at AIMS, fostering AI research talent across Africa.

Special shoutout to Dr. Houriiyah Tegally and CERI for their supervision and support.

Microbes & Climate The “Microbes and Climate Change” event, held at the stunning Kirstenbosch National Botanical Garden on August 21, brought together over 200 high school learners, teachers, and community leaders for a unique exploration of these microscopic marvels.

Hosted by the International Society for Microbial Ecology (ISME), the Centre for Epidemic Response and Innovation (CERI) and Faculty of Science at Stellenbosch University, this event was more than just a science lesson—it was an invitation to see how microbes connect us all and how understanding them could help us tackle one of the biggest challenges of our time: climate change.

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Epidemiology in Humanitarian Operations In the recent #CERIseminar, Dr. Amrish Y. Baidjoe, Director of MSF-LuxOR, presented innovative models for establishing sustainable partnerships in humanitarian efforts. He highlighted the crucial roles of data, diagnostics, and applied epidemiology in improving the effectiveness of humanitarian work. By showcasing these elements, Dr. Baidjoe aimed to strengthen collaboration among stakeholders and enhance outcomes in crisis situations, demonstrating how strategic partnerships can lead to impactful solutions in global health challenges.

the Vaginal Microbiome In this #CERIseminar, In this seminar, two expert speakers explored the significance of the microbiome. Caroline Mitchell, Associate Professor at the University of Maryland, discussed the potential of leveraging the vaginal microbiome to enhance health outcomes, while Jacques Ravel, Act Director of the Institute for Genome Sciences, presented amazing bioinformatics software for microbiome analysis. Their insights highlighted the importance of understanding microbial communities in improving health and well-being.

Innaugural Lecture Prof. Thulani Makhalanyane delivers his thought-provoking inaugural lecture titled “Unveiling the Hidden World Within Us: What Environmental Microbiomes Can Teach Us About Ourselves” at Stellenbosch University. He explores the profound impact of microbial communities—essential yet invisible—on the health of our planet and humanity. Prof.

Makhalanyane discusses how environmental changes affect microbial diversity and functionality, emphasizing their critical role in ecological processes. Join us as he shares insights on the importance of safeguarding these communities for a sustainable future, aligning his research with global challenges and Sustainable Development Goals.reprate volutenes simus,

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Award at mass SRC reunion Professor Tulio de Oliveira was honored with the 2024 Honorary Award at Stellenbosch University’s Mass SRC Reunion, celebrating his significant impact on South African society.

With 270 esteemed alumni in attendance, de Oliveira shared powerful stories from his pioneering bioinformatics work, including his vital role in the COVID-19 Omicron variant research and humanitarian efforts in Libya. This inspiring event marked 20 years since the last reunion, celebrating SU alumni’s leadership and service to society.

Brazilian PhD Student, Débora de La-Roque, reflects on her time in South Africa Six months can make a world of difference, especially when spent in a hub of scientific excellence. This was certainly the case for Débora Glenda Lima de LaRoque, a PhD student from the University of São Paulo (USP) in Brazil, who came to Stellenbosch University’s Centre for Epidemic Response and Innovation (CERI) to enhance her research in dengue virus phylogenetics and phylodynamics.

“My PhD project is about dengue phylogenetics and phylodynamics, and CERI has some of the biggest experts in the area,” Débora explains. “I wanted to learn how to present my findings in a way that is relevant to my field.” Her work focuses on dengue virus evolution in a small endemic area, driven by her passion for studying viruses and the local impact of dengue in her home city As part of the fellowship, the Sigal Lab hosted Debora at the Africa Health Research Institute (AHRI). During her stay, Débora trained in virus isolation and neutralization assays to advance her research on dengue virus phylogenetics and phylodynamics. It’s always exciting to be part of these collaborations, where the exchange of knowledge and skills strengthens our ability to tackle emerging viral infections.

For anyone considering a short-term fellowship at CERI, Débora’s advice is simple: fully engage. “They have so much to teach, and the most valuable lessons come from daily interactions and meetings,” she says. As she heads back to Brazil, Débora is excited to apply her newfound skills and carry the fond memories from her time in South Africa with her.

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genomics, epidemics & microbes

Election to the Academy of Science of South Africa We extend our heartfelt congratulations to Professor Frank Tanser, Director of SACEMA and the Population Health Group at CERI, for being recognized as oone of the 44 distinguished scholars and scientists recently inaugurated as members of the Academy of Science of South Africa (ASSAf). Prof. Tanser was inaugurated as a Member of ASSAf at the Academy’s annual Awards Ceremony on October 23, 2024. We are honored to have esteemed CERI leaders among ASSAf’s distinguished members, including Prof. Thulani Makhalanyane and Prof.

Tulio de Oliveira. ASSAf, South Africa’s official academy, honors the nation’s most distinguished scholars across disciplines, recognizing their outstanding

KRISP at UKZN hosts Schools for Science Week As part of the National Science Week 2024, the team at KRISP hosted 50 students from Chesterville Secondary School and KwaMathanda High School in Durban.

Through the Ikamva Youth NGO program, these grade 10 and 11 learners came for a tour of the genomics laboratory and an introduction to the world of omics research. It was also an opportunity for the students to think about potential career paths available to them and admission

requirements to the university.

Lloyd Mnyandu, Branch Intern and mentor at the Chesterville branch of Ikamva Youth, emphasised that outings like these were important to show the learners that there is more to studying and life than what they see in the townships. “They get to view the world in a different light and get some much needed exposure to different professions,” he said.

Wellcome funded WEMA kick-off between CERI, SACEMA & AHRI The impact of extreme weather events on the mental health of vulnerable populations in Africa (WEMA project) held its inaugural meeting in October. The goal of this initiative is to highlight the direct impact of extreme weather events on the development of common mental disorders in vulnerable populations across

Burkina Faso, Kenya, Mozambique, and South Africa. The team has built on existing partnerships and formed new collaborations to create a transdisciplinary group, including community members, climate scientists, psychiatrists, epidemiologists, and social scientists.

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YOUR the gem TITLE (master page)

OPPORTUNITY

MSC AND PHD SCHOLARSHIPS Building the next generation of epidemiological modellers: Scholarships available for masters, doctoral and postdoctoral positions

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uilding the next generation of epidemiological modellers: Scholarships available for masters, doctoral and postdoctoral positions.

Are you passionate about using data and modelling to address critical public health challenges?

Stellenbosch University (SU) is firmly committed to the pursuit of knowledge, research, and innovation, in service of society. We provide a world-class centre for learning and development, globally relevant yet rooted in the upliftment and transformation of our local communities. Join the SACEMA, at CERI in advancing health through innovative epidemiological modelling.

SACEMA is recruiting for 2025! Scholarships available

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SACEMA supports postgraduate studies at the masters, doctoral and postdoctoral levels within the Faculty of Science and the Faculty of Medicine and Health Science, at Stellenbosch University. We seek motivated individuals with backgrounds in Mathematics, Statistics, Epidemiology, Biostatistics, Global Health, Data Science, Computer Science, or other related quantitative fields.

Our programs offer a hands-on, collaborative approach, and our students work on impactful projects that address real-world challenges.

New projects for 2025 Our diverse range of projects allows students to engage in various aspects of epidemiological modelling.

Here are some of the exciting topics we’re focusing on in 2025: • HIV epidemic dynamics: Studying inter provincial differences in the HIV epidemic in South

genomics, YOURepidemics TITLE (MASTER & microbes PAGE)

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Africa.

Hepatitis b prevention: Evaluating prevention strategies to reduce the burden of hepatitis B in South Africa.

Wastewater surveillance: Optimizing surveillance for polio, measles, influenza, and hepatitis E. HPV and cancer prevention: Developing models to prevent HPV infection and associated cancers in South Africa.

Population immunity estimation: Assessing immunity levels against polio and measles in South Africa and other African countries.

Health system optimization: Improving health systems in West, East, and Southern Africa for managing HIV and co-morbidities.

Childhood cancer epidemiology: Analyzing the epidemiology of childhood cancer in South Africa.

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broaden research perspectives.

Contributions to high-impact publications.

Professional development through workshops, training programs, and seminars.

Access to travel support for external workshops and conferences.

• How to apply If you have a strong quantitative background and are interested in joining our mission to improve health outcomes through modelling, apply now!

Information at: https://www.sacema.org/opportunities/ postgraduate-bursaries/

• Why Join SACEMA? We offer an exciting and dynamic environment where researchers from various disciplines collaborate to solve pressing health issues. Our mission is to build capacity for epidemiological modelling and public health research in Africa, equipping the next generation of scientists with the skills they need to drive impact in their communities and beyond.

Application Deadline: 31 October 2024.

Minimum requirements: • Proficiency in English, both oral and written.

• Some experience in coding in R, C++, or any other similar language.

In addition, • Masters Degree: requires an Honours or Structured Masters Degree in a relevant field.

• PhD Degree: requires a Research masters degree in a relevant field.

• Postdoctoral Fellows: requires a PhD in a relevant field obtained within the last 5 years, along with a track record of publications (with several high-quality publications as a first author).

At SACEMA, students benefit from: • Mentorship from experienced researchers and leading experts.

• International collaboration opportunities to

Visit our website to learn more: https://www.sacema.org/ opportunities/postgraduate-bursaries/ For further enquiries, contact SACEMA’s Training Coordinator, Faikah Bruce, at faikah@sun.ac.za.

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Call for Applications: Postdoctoral Research Fellowship (2-Year, Tax-Free) Stellenbosch University (SU) is firmly committed to the pursuit of knowledge, research and innovation, in service of society. We provide a world-class centre for learning and development, which is globally relevant, yet rooted in the upliftment and transformation of our local communities. The Centre for Epidemic Response and Innovation (CERI) at SU invites applications from dedicated postdoctoral scholars for a 2-year fellowship to contribute to a transdisciplinary research project:

"The Impact of Extreme Weather Events on the Mental Health of Vulnerable Populations in Africa."

Project Overview: This project employs mixed methods to explore the effects of extreme weather events (EWEs) on mental health among vulnerable populations in Burkina Faso, Kenya, Mozambique, and South Africa. The qualitative component utilizes a participatory approach, with digital storytelling as the primary data collection method. Community members will actively engage in research design, data generation, and analysis. Civil society stakeholders will also collaborate to interpret the findings and develop intervention strategies. By partnering with affected communities, civil society, and the media, the research aims to drive impactful advocacy and policy change.

Key Responsibilities: • • • • • • •

Produce high-quality research outputs and documentation.

Lead qualitative and participatory research, including data generation and analysis.

Combine qualitative results with clinical, demographic, and geographic data for integrative analysis.

Manage project administration across multiple sites.

Facilitate communication among project teams and community partners.

Support digital media efforts in creating digital stories to amplify research findings.

Deliver an online training program to upskill the research team.

Minimum requirements for the Postdoctoral research fellowships: • • • • •

PhD in a relevant social science field (completed within the last 5 years).

Strong publication record as first or senior author.

Expertise in thematic analysis and software like NVivo or ATLAS.ti.

Experience with participatory research preferred.

Demonstrated skill in high-quality research and data analysis.

How to apply: • Deadline for applications: 15 November 2024 • Click here to apply /use this link [https://t.ly/o4x3w] •32 For more information, contact Dr. Astrid Treffry-Goatley astrid222@sun.ac.za • Start date is January 2025 but can be flexible based on candidate needs.

genomics, epidemics & microbes

Call for Applications: Roche KAPA DNA Library Preparation in Genetics and Oncology Training

Date: 21 - 22 November 2024

Location: Centre for Epidemic Response & Innovation (CERI), Biomedical Research Institute, University of Stellenbosch, Cape Town, South Africa

The Centre for Epidemic Response and Innovation (CERI) in collaboration with Roche Diagnostics is excited to announce a specialized two-day training programme on DNA Library Preparation focused on Genetics and Oncology.

Training Overview This programme is designed to provide participants with both theoretical knowledge and practical skills in the latest Next-Generation Sequencing (NGS) DNA library preparation workflow. The training will include: • • •

Introduction to NGS DNA library preparation processes.

Hands-on laboratory training using the KAPA EvoPlus Kit V2, covering enzymatic fragmentation and 33 automatable workflows.

Exploration of clinical research applications in Genetics and Oncology

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Microbiome

INNAUGURAL LECTURE Prof. Thulani Makhalanyane Delivers Inaugural Lecture on “Microbiome Scientists: Healers of a Sick Planet” text: Ma a m be l e K ho sa photo : Ignus Dreyer

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icrobial communities, though invisible to the naked eye, shape the world in profound ways. These communities –composed of bacteria, fungi, viruses, and other microorganisms–are essential to the health of our planet and ourselves. From the air we breathe to the food we eat, microbes are involved in sustaining life, driving ecological processes, and even influencing human health. This was the backdrop against which Prof.

Thulani Makhalanyane delivered his thought-provoking inaugural lecture on October 8th, 2024, at Stellenbosch University.

Marking his first year at the university, Prof. Makhalanyane’s lecture, titled “Unveiling the hidden world

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within us: What environmental microbiomes can teach us about ourselves,” explored how these microbial communities are active, essential contributors to ecosystems and human health. His research focuses on how environmental changes impact the diversity and functionality of these microbes, which are critical to processes like carbon cycling, nutrient exchange, and even human digestion.

In his opening remarks, Prof.

Makhalanyane offered a powerful metaphor: “The planet is a sick patient, and microbiome scientists are its healers.” This vivid image highlights the urgency of understanding and safeguarding microbial communities to heal the damage caused by human activity. His work on microbial ecosystems, particularly in the Southern Ocean, contributes

to addressing pressing global challenges, aligning with Sustainable Development Goals (SDGs) such as SDG 14—Life Below Water.

Through his research, Prof.

Thulani Makhalanyane shows that microbiome scientists are indeed the healers of this planet, offering hope and solutions to some of the most critical issues facing our world today. In understanding microbes, we begin to understand ourselves and the delicate balance required to sustain life on Earth.

Youtube video of full lecture: - https://www.youtube.com/ watch?v=vHzydF5P_AA

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MASTERING THE ART OF GRANT WRITING Lessons from the Public Square Workshop

text : Maa mb el e Kho sa p h oto: The Dol l i e House ph otog r a phy

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genomics, epidemics & microbes

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n the world of research, deadlines are relentless, and competition for funding is fierce.

Without strong grant writing skills, even the most innovative ideas can fall through the cracks.

Writing a compelling grant proposal is an essential skill that determines whether a project will flourish or fade into obscurity. Recognizing this, researchers, scientists, and scholars gathered on the 15th of October for an insightful lecture and workshop on grant writing, hosted

by Stellenbosch University’s Public Squares initiative.

This initiative, managed by Stellenbosch University’s Division for Research Development (DRD) and led by Dr. Astrid Treffry-Goatley, is designed to foster researcher capacity in collaboration, develop bold and creative ideas, and support the pursuit of competitive grant proposals. The workshop was led by Professor Tulio de Oliveira, Director of the Centre for Epidemic Response and Innovation (CERI), who has an

extensive track record in securing large-scale research grants. His message was clear: successful grant writing is not a solitary endeavor-it takes teamwork, preparation, and persistence.

Dr. Astrid Treffry-Goatley, who leads the SU Public Squares initiative, emphasized the importance of equipping researchers with these skills: “The grant writing masterclass is a key part of our strategy to help transdisciplinary teams turn their innovative ideas into impactful, fundable projects.”

Professor de Oliveira further noted that grant writing isn’t just about securing funding; it’s about aligning research goals with funders’ priorities, learning how to communicate complex ideas effectively, and building a strong collaborative network. He stressed, “Writing successful grants is not a one-man show. It takes teamwork.”

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Key Takeaways from the Workshop 1. Start with a Strong Idea A successful grant application begins with a focused, innovative research idea. “Don’t try to solve all the world’s problems in one grant,” de Oliveira advised. He emphasized the importance of a hypothesis-driven proposal with achievable aims, designed to lay the foundation for further research.

2. Align with the Funder’s Goals To increase the chances of success, applicants must ensure their proposals align with the strategic goals of the funding body. Whether applying for national (NRF, SAMRC) or international (Wellcome Trust, EDCP) grants, understanding the specific requirements and objectives of the funder is crucial.

3. Plan and Build a Team Grant writing takes time and collaboration. De Oliveira encouraged participants to plan months in advance, involve co-investigators early, and seek feedback from both scientific and non-scientific peers.

“Don’t submit a half-baked application—reviewers will remember your bad applications,” he warned, stressing the importance of quality over quantity.

4. Learn from Rejection Rejection is an inevitable part of the process, but it shouldn’t discourage applicants. Instead, de Oliveira encouraged researchers to seek feedback, reassess their strategies, and enhance future applications.

5. Master the Details Grant writing goes beyond the research plan. Supporting documents like CVs, letters of support, budgets, and data-sharing plans must be meticulously prepared. De Oliveira advised researchers to “become experts” in all aspects of the grant submission process, from formatting to budget justification.

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6. Building a Diversified Funding Portfolio In a post-pandemic world, securing multiple streams of funding has become more important than ever.

De Oliveira encouraged researchers to diversify their funding sources, reducing reliance on a single grant.

Voices from the Workshop Several attendees shared their reflections on the workshop and how it has enhanced their understanding of grant writing.

left the workshop with a clearer understanding of what it takes to succeed in the competitive world of grant applications.

Grant writing is an essential skill for researchers looking to make a lasting impact, and as Professor de Oliveira aptly put it: “Think like a reviewer—imagine you’re tired, grumpy, and hungry, and then review your application.

Make it easy for them to say yes.”

Amina Abdullah, a project manager from the Division of Health Systems and Public Research, reflected on her challenges with grant writing: “I have worked on a grant for a month and not submitted it. Indeed, it’s not a one-man job. I take with me that one should plan ahead. It was also amazing to have an expert willingly and freely sharing their grant sources.”

Hamond Motsi, from the Soil Science department, highlighted the importance of time management and teamwork: “To enhance grant writing skills, I learned new techniques in writing and searching for grants. It’s a team effort, and I also learned the best way to use feedback to improve.”

Liezel Smith, a senior scientist at the Division of Molecular Biology and Human Genetics , appreciated the sense of community fostered by the workshop: “It’s good to hear an expert sharing about failure and rejection; this process is daunting and can be lonely. From this lecture, I also realized that mentorship is key even in this regard.”

The Public Square workshop underscored the necessity of mastering grant writing, not just as a technical skill but as a strategic tool for career development. Whether it’s learning to navigate the complexities of funders’ requirements or building a collaborative team, researchers

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Writing successful grants is not a one-man show.

It takes teamwork.

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SACEMA

South African Centre for Epidemiology and Modeling Analysis

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

SACEMA

South African Centre for Epidemiology and Modeling Analysis

SCHOOL

for Data Science and Computational Thinking

krisp