NEWS SPOTLIGHT

KRISP NEWS

Advances in AI can help prepare the world for the next pandemic

A new paper in Nature demonstrates how artificial intelligence (AI) can transform infectious disease research and pandemic preparedness by enhancing predictive modeling, outbreak tracking, and healthcare responses. Co-authored by a global network of scientists, the study emphasizes AI’s potential to save lives by identifying high-risk areas, accelerating vaccine development, and improving pathogen analysis. Experts from CERI at Stellenbosch University played a key role in this research, contributing advanced AI methodologies to epidemiology and public health. While AI presents remarkable opportunities, the authors stress the need for transparency, collaboration, and safety measures to ensure responsible implementation.

Scientific Seminar - From Bench to Bedside: Pioneering the Genital Inflammation Test for Women's Health

On Wednesday, 26 February 2025 (12:00-13:00 SAST), the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University will host a scientific seminar on the Genital Inflammation Test (GIFT), a pioneering diagnostic tool for women's health. Led by Professor Jo-Ann Passmore (NHLS, UCT), the session will explore how GIFT improves the detection of sexually transmitted infections and bacterial vaginosis while addressing its role in HIV risk assessment. The event will be held at BMRI Room 3073, SU Tygerberg Campus, with an online streaming option.

Call for Applications: The 29th International Workshop on Virus Evolution and Molecular Epidemiology (VEME2025)

VEME2025 will be organized in Dakar, Senegal, during August 4–8, 2025. The workshop comprises 6 full days of theoretical lectures, practical sessions and keynote presentations. VEME2025 will accept 150 participants in 4 modules.

Postdoctoral Research Fellowship in Biotechnology Commercialisation at CERI, Stellenbosch University

Join the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University! We're seeking a postdoc to help bridge academic innovation and industry by developing commercialisation pathways for biotech startups. Key areas include genetic engineering, recombinant protein production, and entrepreneurship training.

the gem: genomics, epidemics & microbes - Jan 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. In this first issue of 2025, we partner with the Mastercard Foundation and the Institute Pasteur de Dakar to launch the African STARS Fellowship.

Postdoctoral Fellowships at CERI – Stellenbosch University

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.

Top 10 Young Researcher Award: Dr Jennifer Giandhari - KRISP, UKZN

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.

PUBLICATIONS SPOTLIGHT

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