KRISP NEWS
A visit by the Mastercard Foundation offered an opportunity to hear directly from African STARS fellows about their journeys, ambitions, and the impact of the programme on their academic and professional development.
Emerging infectious diseases do not appear in isolation. They emerge through complex interactions between humans, animals, ecosystems, climate, and environmental change. For Prof Carla Mavian, Programme Director for One Health at the Centre for Epidemic Response and Innovation (CERI), those connections are central to preventing future outbreaks.
CERIs new Social Science Unit will integrate social science into health research, strengthening community engagement, policy translation, and transdisciplinary collaboration across Africa.
The Silos to Synergy workshop introduced African STARS fellows to transdisciplinary research principles, stakeholder engagement, and creative methods for producing meaningful, context-specific research impact.
For Dr Monique Barnard-Matthee, some of the most important work in vaccine development happens in the systems behind the science: the workflows, infrastructure, automation platforms, and quality control processes that determine whether a promising scientific breakthrough can actually become a reliable public health solution. She believes that work must happen in Africa, led by African scientists, using African expertise.
A connection made at SWEAT Africa 2026 led to a role at Nanosene within weeks, offering a clear example of how the event creates the conditions for real opportunities to emerge.
KRISP SCIENTIFIC PUBLICATIONS
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
Hunt M, Hinrichs A, Anderson D, Karim L, Dearlove B, Knaggs J, Constantinides B, Fowler P, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego L, Amuzu D, Avaro M, Awandare G, Ayivor-Djanie R, Barkham T, Bashton M, Batty E, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers S, Campos J, Carr R, Chen Y, Cuba F, Dattero M, Dejnirattisai W, Dilthey A, Duedu K, Endler L, Engelmann I, Francisco N, Fuchs J, Gnimpieba E, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao N, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki K, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige G, Mashe T, Mongkolsapaya J, Montes B, Mora J, Moranga C, Mvula B, Nagarajan N, Nelson A, Ngoi J, da Paixão J, Panning M, Poklepovich T, Quashie P, Ranasinghe D, Russo M, San J, Sanderson N, Scaria V, Screaton G, Sessions O, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson R, Williamson C, Zair X, Biere B, Dürrwald R, Mache C, Oh D, Schulze J, Wedde M, Wolff T, Fuchs S, Semmler T, Paraskevopoulou S, Kerber R, Kröger S, Haas W, Bode K, Corman V, Erren M, Finzer P, Grosser R, Haffner M, Hermann B, Kiel C, Krumbholz A, Lorentz T, Meinck K, Nitsche A, Petzold M, Schwanz T, Szabados F, Tewald F, Tiemann C, de Oliveira T, Peto T, Crook D, Corbett-Detig R, Iqbal Z, Nature Methods (2026), 23:653-662.
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, 20222023.
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), :.
Spatiotemporal disease suitability prediction for Oropouche virus and the role of vectors across the Americas.
Poongavanan J, Dunaiski M, Dor 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.:.
KRISP VIDEOS
COVID-19 | News sub-variant being monitored closely
By: Tulio De Oliveira and CERI and KRISP teams
KRISP BIOINFORMATICS TOOLS
Genome Detective Coronavirus Typing Tool
Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
Genome Detective Dengue Virus Typing Tool
This is a beta version of our Dengue Virus Typing tool. For the mean time, this tool should be used for evaluation only. Please send feedback to Tulio de Oliveira.
Genome Detective Zika Typing Tool
This is the first version of the Zika typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.
Genome Detective Chikungunya Typing Tool
This is the first version of the Chikungunya typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.
Genome Detective Yellow Fever Virus Typing Tool
This is the first version of the Yellow Fever typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.
This is the first version of our Arbovirus typing tool for Chikungunya, Dengue, Yellow Fever and Zika
REGA HIV Subtyping Tool V3 - Belgium Mirror
Phylogenetic tool to identify the HIV-1 subtypes and recombinants. Query sequences are analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).
MORE TOOLS
KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).
Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira