KRISP NEWS
An evening of storytelling, culture, and conversation brought African scientists, entrepreneurs, funders, and investors together in Cape Town, creating connections and exploring new opportunities for collaboration through SWEAT Africa.
CERI Team Wins International Award for AI Research into Infectious Diseases
Artificial intelligence is opening new possibilities for understanding infectious diseases and anticipating emerging health threats. An award-winning South African research team is developing approaches that could strengthen disease surveillance and public health responses in Africa and beyond.
Unlocking Africa's Microbial Wealth for Women's Health
Prof Jo-Ann Passmore on why African-led microbiome research, biobanking, and manufacturing are essential to developing better treatments for women.
Building Genomics Capacity That Lasts
Drawing on experiences in Brazil and Africa, a new publication offers ten practical rules for making genomics part of routine laboratory practice. At its heart is a message about the importance of people, collaboration, and continuous learning in building sustainable scientific capacity.
At an African STARS seminar, biotechnology entrepreneur Dominic Nicholas shared Immobazyme's journey towards commercial production and the lessons learned along the way.
Beyond PSA: Why Better Prostate Cancer Diagnosis Must Include Africa
New genetic research could help identify aggressive prostate cancers more accurately while reducing unnecessary investigations and treatment. Following a seminar hosted by CERI and SACEMA at Stellenbosch University on 8 October 2026, Professor Jyotsna Batra of Bond University, Australia, explains how advances in prostate-specific antigen (PSA) research could improve diagnosis and why African populations must be included in developing better diagnostic tools.
Tracing Rift Valley Fever's Journey Across Africa
New research reveals how a widespread lineage of Rift Valley fever virus emerged in southern Africa, travelled thousands of kilometres, and continued evolving during the years between major outbreaks.
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, Morang’a 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, 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), :.
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.:.
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 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 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 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.
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.
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