NEWS SPOTLIGHT

KRISP NEWS

CERI and GIZ Launch Next Phase of Genomic Surveillance Partnership to Boost South Africa’s and Europe’s Epidemic Preparedness

The Centre for Epidemic Response and Innovation (CER) and GIZ have launched the second phase of their genomic surveillance partnership in Cape Town, securing ZAR 12 million to expande pathogen monitoring, capacity building, and data-sharing across Africa. This phase will broaden surveillance to influenza, RSV, H5N1 and emerging COVID-19 variants while strengthening laboratory infrastructure and integrating genomic insigths into public-health policy.

Join the Next #CERIseminar on Building a South African Clinical Metagenomics Platform

The CERI seminar on 30 July 2025 will showcase Dr Gert JK Marais’s work developing tailored software and wet-lab protocols to make clinical metagenomics affordable and practical in South African diagnostic labs. Attendee, both in person and online, will learn how these innovations are lowering barriers to comprehensive infectious-disease testing in resource-limited settings.

AI & Pathogen Spillover Prediction by Dr. Houriiyah Tegally

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

Honouring The Youth, Inspiring the Future: Reflections from KRISP's Young Professionals

This June, as South Africa commemorated Youth Day, we at KRISP took a moment to reflect on the importance of this day—not just in remembrance of the past, but in celebration of the present and the promise of the future. Youth Day marks a powerful moment in our nation’s history, honouring the courage of the 1976 student uprisings and reminding us of the role young people continue to play in driving change.

CERI's Strategic Trip to the UK

In June 2025, Prof Wim de Villiers and Dr Richard Gordon visited the UK (London and Cambridge) to explore a number of collaboration opportunities. These included the pharmaceutical sector (Glaxo Smith Kline), funding agencies (Wellcome Trust, Children’s Innovation Fund Foundation (CIFF)) as well as several UK funding agencies such as UK Research and Innovation (UKRI) and Foreign, Commonwealth & Development Office (FCDO).

Harriet Ng'ombe Showcases Cholera Genomics Research at 12th EDCTP Forum in Kigali

Harriet Ng’ombe, a PhD student at Stellenbosch University and researcher at the Centre for Infectious Disease Research in Zambia (CIDRZ), presented work on genomic research at the 12th EDCTP Forum in Kigali, Rwanda.

Forbes Africa 30 Under 30 - Maambele Khosa

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

PUBLICATIONS SPOTLIGHT

KRISP SCIENTIFIC PUBLICATIONS

Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa.
Dor G, Wilkinson E, Martin DP, Moir M, Tshiabuila D, Kekana D, Ntozini B, Joseph R, Iranzadeh A, Nyaga MM, Goedhals D, Maponga T, Maritz J, Laguda-Akingba O, Ramphal Y, MacIntyre C, Chabuka L, Pillay S, Giandhari J, Baxter C, Hsiao NY, Preiser W, Bhiman JN, Davies MA, Venter M, Treurnicht FK, Wolter N, Williamson C, von Gottberg A, Lessells R, Tegally H, de Oliveira T, Nature Communications (2025), 28;16(1):4937. doi: 10.1038/s41467-025-60081-0:.

Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023.
Chabuka L, Choga W, Mavian C, Moir M, Morgenstern C, Tegaly H, Sharma A, Wilkinson E, Naidoo Y, Inward R, Bhatt S, WilliamWint G, Khan K, Bogoch I, Kraemer M, Lourenço J, Baxter C, Tagliamonte M, Salemi M, Lessells R, Mitambo C, Chitatanga R, Bitilinyu-Bango J, Chiwaula M, Chavula Y, Bukhu M, Manda H, Chitenje M, Malolo I, Mwanyongo A, Mvula B, Nyenje M, de Oliveira T, Kagoli M, Emerging Infectious Diseases (2025), 31(6):. doi: 10.3201/eid3106.240930.:.

Importance of outbreak response research in bridging knowledge gaps on emerging infectious diseases.
Breiman R, Osoro E, Reithinger R, Wang D, Diamond M, Van Voorhis W, Wasserheit J, Rabinowitz P, Mboup S, Hemingway-Foday J, de Oliveira T, Boon A, Schieffelin J, Sempowski G, Moody M, Vasilakis N, Hanley K, Nasimiyu C, Situma S, Ngere I, Kyobe Bosa H, Nyakarahuka L, Bakamutumaho B, Woodson S, Njenga M, BMJ Global Health (2025), 10(6):e018297. doi: 10.1136/bmjgh-2024-018297.:.

Artificial intelligence for modelling infectious disease epidemics.
Kraemer M, Tsui J, Chang S, Lytras S, Khurana M, Vanderslott S, Bajaj S, Scheidwasser N, Curran-Sebastian J, Semenova E, Zhang M, Unwin H, Watson O, Mills C, Dasgupta A, Ferretti L, Scarpino S, Koua E, Morgan O, Tegally H, Paquet U, Moutsianas L, Fraser C, Ferguson N, Topol E, Duchêne D, Stadler T, Kingori P, Parker M, Dominici F, Shadbolt N, Suchard M, Ratmann O, Flaxman S, Holmes E, Gomez-Rodriguez M, Schölkopf B, Donnelly C, Pybus O, Cauchemez S, Bhatt S, Nature (2025), 638(8051):623-635. doi: 10.1038/s41586-024-08564-w.:.

Spatiotemporal disease suitability prediction for Oropouche virus and the role of vectors across the Americas.
Poongavanan J, Dunaiski M, D’or G, Kraemer M, Giovanetti M, Lim A, Brady O, Baxter C, Fonseca V, Alcantara L, de Oliveira T, Tegally H, medRxiv (2025), doi: 10.1101/2025.02.28.25323068.:.

Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population.
Lugano D, Mwangi K, Mware B, Kibet G, Osiany S, Kiritu E, Dobi P, Muli C, Njeru R, de Oliveira T, Njenga M, Routh A, Oyola S, medRxiv (2025), doi: 10.1101/2025.03.03.25323296.:.

Unveiling novel features and phylogenomic assessment of indigenous Priestia megaterium AB-S79 using comparative genomics.
Adeniji A, Chukwuneme C, Conceição E, Ayangbenro A, Wilkinson E, Maasdorp E, de Oliveira T, Babalola O, Microbiology Spectrum (2025), doi: 10.1128/spectrum.01466-24.:.

KRISP VIDEOS

COVID-19 | News sub-variant being monitored closely
By: Tulio De Oliveira and CERI and KRISP teams

KRISP BIOINFORMATICS TOOLS