KRISP NEWS
the gem is a monthly magazine produced by CERI, SACEMA and the Data School at Stellenbosch University and KRISP at UKZN. The objective is to provide stories of world class African science that impact lives and train the next generation of scientists in Africa. In this first issue of 2025, we partner with the Mastercard Foundation and the Institute Pasteur de Dakar to launch the African STARS Fellowship.
Join the cutting-edge research team at the Centre for Epidemic Response and Innovation (CERI), Stellenbosch University! We are offering three postdoctoral fellowships in pathogen phylodynamics, disease ecological modeling, and machine learning for infectious diseases. Collaborate with top scientists, analyze large-scale genomic datasets, and develop innovative solutions to tackle infectious diseases at the intersection of genomics, epidemiology, and data science. This competitive, tax-free fellowship is based in South Africa, with opportunities for international collaborations.
UKZN 2024 Research Awards Dinner: Celebrating Excellence in Research. This much-anticipated occasion highlights UKZN's unwavering commitment to fostering research excellence and its profound impact on local and global communities.
Members of the KRISP (KwaZulu-Natal Research Innovation and Sequencing Platform) team recently had the privilege of hosting undergraduate students from UKZN and the University of Limpopo as part of the HIV Cure Workshop.
Roche Diagnostics and the Centre for Epidemic Response and Innovation (CERI) hosted a two-day training on advanced DNA Library Preparation at Stellenbosch University's Biomedical Research Institute (BMRI).
Released at COP29 in the WHO Pavillion. Baku, Azerbaijan. On the final day of COP29, an international team of over 100 scientists and policymakers released the 2024 edition of the Climate Change and Epidemics report at the WHO Pavilion.
By Prof Tulio de Oliveira - New York Times, 19 Nov 2024. As a virus scientist in South Africa, Ive been watching with dread as H5N1 bird flu spreads among animals in the United States.
KRISP SCIENTIFIC PUBLICATIONS
Hybrid versus vaccine immunity of mRNA-1273 among people living with HIV in East and Southern Africa: a prospective cohort analysis from the multicentre CoVPN 3008 (Ubuntu) study.
Garrett N, Tapley A, Hudson A, Dadabhai S, Zhang B, Mgodi N, Andriesen J, Takalani A, Fisher L, Kee J, Magaret C, Villaran M, Hural J, Andersen-Nissen E, Ferarri G, Miner M, Le Roux B, Wilkinson E, Lessells R, de Oliveira T, Odhiambo J, Shah P, Polakowski L, Yacovone M, Samandari T, Chirenje Z, Elyanu P, Makhema J, Kamuti E, Nuwagaba-Biribonwoha H, Badal-Faesen S, Brumskine W, Coetzer S, Dawson R, Delany-Moretlwe S, Diacon A, Fry S, Gill K, Ebrahim Hoosain Z, Hosseinipour M, Inambao M, Innes C, Innes S, Kalonji D, Kasaro M, Kassim P, Kayange N, Kilembe W, Laher F, Malahleha M, Maluleke V, Mboya G, McHarry K, Mitha E, Mngadi K, Mda P, Moloantoa T, Mutuluuza C, Naicker N, Naicker V, Nana A, Nanvubya A, Nchabeleng M, Otieno W, Potgieter E, Potloane D, Punt Z, Said J, Singh Y, Tayob M, Vahed Y, Wabwire D, McElrath M, Kublin J, Bekker L, Gilbert P, Corey L, Gray G, Huang Y, Kotze P, Badal-Faesen S, Baepanye K, Bailey V, Baloyi-Oseh K, Booley M, Botha J, Brown Y, Brown V, Bunts L, Coetzer S, Cohen M, Collie S, Dawson R, Deb P, El Sahly H, El-Khorazaty J, Engelbrecht A, Gildea M, Govender D, Hanke J, Harris J, Hendricks S, Hopkinson N, Howell H, Ketter N, Khuto K, Laher Omar F, Katsidzira L, Linton K, Ludwig J, Mabilane B, Malefo M, Mamushiana N, Margineantu D, May J, Mayat F, Molitor C, Naidoo Y, Nebergall M, Nguyen A, Nikles S, Noronha B, Peda M, Phiri T, Pillay S, Pillay S, Proulx-Burns L, Rinn L, Sanders L, Sopher C, Sripathy S, Stirewalt M, Tegally H, Thiebaud S, Toledano A, Van Wyk S, Whitby S, Wilcox S, Wilkinson E, Wilvich H, Wiysonge C, Xaba N, Xulu N, eClinicalMedicine (2025), 80():103054. doi: 10.1016/j.eclinm.2024.103054.:.
Dynamics and ecology of a multi-stage expansion of Oropouche virus in Brazil.
Tegally H, Dellicour S, Poongavanan J, Mavian C, Dor G, Fonseca V, Tagliamonte M, Dunaiski M, Moir M, Wilkinson E, de Albuquerque C, Frutuoso L, , Holmes E, Baxter C, Lessells R, Kraemer M, Lourenço J, Alcantara L, de Oliveira T, Giovanetti M, (2024), ():. doi: 10.1101/2024.10.29.24316328.:.
Dengue virus importation risks in Africa: a modelling study.
Poongavanan J, Lourenço J, Tsui J, Colizza V, Ramphal Y, Baxter C, Kraemer M, Dunaiski M, de Oliveira T, Tegally H, The Lancet Planetary Health (2024), 8(12):e1043-e1054. doi: 10.1016/s2542-5196(24)00272-9.:.
Using HIV and Hepatitis C Molecular Epidemiology to Investigate Assisted Partner Services Recruitment Among People Who Inject Drugs in Kenya.
Kingston H, Chohan B, Mbogo L, Bukusi D, Monroe-Wise A, Sambai B, Omballa V, Tram K, Guthrie B, Giandhari J, Masyuko S, Bosire R, Sinkele W, de Oliveira T, Scott J, Farquhar C, Herbeck J, AIDS Research and Human Retroviruses (2024), ():. doi: 10.1089/aid.2024.0036.:.
SARS-CoV-2 Infections in a Triad of Primary School Learners (Grades 1-7), Their Parents, and Teachers in KwaZulu-Natal, South Africa: Protocol for a Cross-Sectional and Nested Case-Cohort Study.
Dassaye R, Chetty T, Daniels B, Gaffoor Z, Spooner E, Ramraj T, Mthethwa N, Nsibande D, Pillay S, Bhana A, Magasana V, Reddy T, Mohlabi K, Moore P, Burgers W, de Oliveira T, Msomi N, Goga A, JMIR Research Protocols (2024), 13():e52713. doi: 10.2196/52713.:.
The COVID-19 pandemic in BRICS: Milestones, interventions, and molecular epidemiology.
van Wyk S, Moir M, Banerjee A, Bazykin G, Biswas N, Sitharam N, Das S, Ma W, Maitra A, Mazumder A, Karim W, Lamarca A, Li M, Nabieva E, Tegally H, San J, Vasconcelos A, Xavier J, Wilkinson E, de Oliveira T, PLOS Global Public Health (2024), 4(12):e0003023. doi: 10.1371/journal.pgph.0003023.:.
Alignment-Free Viral Sequence Classification at Scale.
van Zyl D, Dunaiski M, Tegally H, Baxter C, , de Oliveira T, Xavier J, (2024), ():. doi: 10.1101/2024.12.10.627186.:.
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