NEWS SPOTLIGHT



the gem





African STARS

KRISP NEWS


40 Publications During a PhD and Now Over 70: A Conversation with Dr. Houriiyah Tegally on Breaking Barriers and Leading Epidemic Response

Dr. Houriiyah Tegally, Head of Data Science at CERI, is a leader in epidemic response, with over 70 publications, including 40 during her PhD. She specializes in integrating AI and climate data into infectious disease modeling, shaping global health strategies. Her work, from tracking SARS-CoV-2 variants to forecasting emerging epidemics, highlights the power of data-driven public health.


Nikita Sitharam Awarded Prestigious Oppenheimer Memorial Trust Scholarship

Nikita Sitharam, PhD candidate at Stellenbosch University and CERI, is advancing viral genomics research in Africa. She recently received the prestigious Oppenheimer Memorial Trust Postgraduate Scholarship, securing full funding for her PhD. Her work emphasizes the importance of mentorship and early preparation in securing research funding.


the gem: genomics, epidemics & microbes - Feb 2025

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.


CERI & SANGER partner to strengthen global genomics surveillance

Top Genomics Labs partner with UK Foreign, Commonwealth & Development Office (FCDO) to strengthen surveillance of respiratory pathogens


Scientists On Video - the gem, Vol 8, Issue 2 - Feb 2025

Here, we present some of our recent videos and TV appearances highlighting the important aspect of science communication to the general public.


Virus Evolution & Molecular Epidemiology (VEME) 2025 workshop BACK IN AFRICA: APPLICATIONS OPEN!

Are you a scientist working in virus evolution, bioinformatics, or genomic surveillance? Don’t miss your chance to apply for the Virus Evolution & Molecular Epidemiology (VEME) 2025 workshop, one of the world’s most advanced training programmes in genomics and bioinformatics.


Dr. Houriiyah Tegally Receives Prestigious Grant to Investigate Climate Change’s Impact for CLIMADE

Dr. Houriiyah Tegally from the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, has been awarded a significant grant by the Global Science Summit Programme of the Novo Nordisk Foundation.


PUBLICATIONS SPOTLIGHT


Science


Nature Medicine


Nature

KRISP SCIENTIFIC PUBLICATIONS


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.:.



Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022–2023.
Abera A, Tegally H, Tasew G, Wilkinson E, Ali A, Regasa F, Bitew M, Belachew M, Chabuka L, Mwanyika G, Tshiabuila D, Giandhari J, Pillay S, Poogavanan J, Moir M, Kraemer M, Khan K, Huber C, Tollera G, de Wit T, Baxter C, Lessells R, Wolday D, Beyene D, de Oliveira T, , Emerging Infectious Diseases (2025), 31(3):. doi: 10.3201/eid3103.240996.:.



Infectious diseases in a warming world: A call for action.
Moir M, Baxter C, Tegally H, de Oliveira T, South African Journal of Science (2025), 121(3/4):. doi: 10.17159/sajs.2025/20722.:.



Travel-associated international spread of Oropouche virus beyond the Amazon.
de Melo Iani F, Pereira F, de Oliveira E, Rodrigues J, Machado M, Fonseca V, Adelino T, Guimarães N, Tomé L, Gómez M, Nardy V, Ribeiro A, Rosewell A, Ferreira ?, Silva de Mello A, Fernandes B, de Albuquerque C, dos Santos Pereira D, Pimentel E, Lima F, Silva F, de Carvalho Pereira G, Tegally H, Almeida J, Moreno K, Vasconcelos K, Santos L, Silva L, Frutuoso L, Lamounier L, Costa M, de Oliveira M, dos Anjos M, Ciccozzi M, Lima M, Pereira M, Rocha M, de Souza da Silva P, Rabinowitz P, de Almeida P, Lessells R, Gazzinelli R, da Cunha R, Gonçalves S, dos Santos S, de Alcântara Belettini S, Pedroso S, Araújo S, da Silva S, Croda J, Maciel E, Van Voorhis W, Martin D, Holmes E, de Oliveira T, Lourenço J, Alcantara L, Giovanetti M, Journal of Travel Medicine (2025), doi: 10.1093/jtm/taaf018.:.



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.



Genome Detective

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