NEWS SPOTLIGHT



the gem



the gem



CERI news

KRISP NEWS


Postdoctoral Research Fellowship

We invite applications from ambitious postdoctoral scientists to undertake research in a flagship program focused on the impact of extreme weather events on the mental health of vulnerable populations in Africa. Ideal candidates should have a background in quantitative methods, which may include expertise in thematic analysis and software such as NVivo or ATLAS.ti. Experience with participatory research is preferred, and candidates should demonstrate strong skills in high-quality research and data analysis.


New Funding Opportunity for Scientific Exchange: Genomics for Health in Africa (GHA-SciEX)

Apply now for the GHA-SciEX scientific exchange program, offering early-career researchers from Africa and Europe the chance to participate in short-term research visits focused on genomics and health. Don't miss this opportunity to boost your skills and foster international collaboration!


the gem: genomics, epidemics & microbes - Aug/Sep 2024

the gem is a monthly magazine produced by CERI at Stellenbosch University, KRISP at UKZN and SACEMA. The objective is to provide stories of world class African science that impact lives and train the next generation of scientists in Africa.


Oropouche Virus - a new virus associated with climate change emerge in Brazil

A new virus emerge from the Amazon Forest Basin and is spreading in Latin America text: Iani et al. medRXiV, 2024.08.02.24311415v2


28th VEME is delivered as a successful workshop in Brazil 2024

The world’s most advanced genomics and bioinformatics training on virus evolution and molecular epidemiology (VEME) was hosted in Brasília in parnership with FioCruz, Brazilian Ministry of Health, PAHO & CERI


CLIMADE Keynote Summit at Global Pandemic Preparedness Summit

The second Global Pandemic Preparedness Summit (GPPS), held in Rio de Janeiro, Brazil, from July 29 to 30, 2024, brought together leading experts and global leaders to confront the growing challenges posed by pandemics in an era of climate change.


CERI & KRISP expands partnership with AIMS & Google DeepMind

As we graduated the first batch of MSc students and continue to support PhD AI students, our partnership with AIMS and Google Deep-Mind expands


PUBLICATIONS SPOTLIGHT


Science


Nature Medicine


Nature

KRISP SCIENTIFIC PUBLICATIONS


The third era of genomics is at risk of being dismantled across the Global South.
de Oliveira T, Science (2024), 386(6718):eadt4843. doi: 10.1126/science.adt4843.:.



A new lineage nomenclature to aid genomic surveillance of dengue virus.
Hill V, Cleemput S, Pereira JS, Gifford RJ, Fonseca V, Tegally H, Brito AF, Ribeiro G, de Souza VC, Brcko IC, Ribeiro IS, De Lima ITT, Slavov SN, Sampaio SC, Elias MC, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, Lima ARJ, de Oliveira T, Grubaugh ND., PLoS Biology (2024), 22(9):e3002834. doi: 10.1371/journal.pbio.3002834.:.



Impacts of climate change-related human migration on infectious diseases.
Tsui JLH, Pena RE, Moir M, Inward RPD, Wilkinson E, San JE, Poongavanan J, Bajaj S, Gutierrez B, Dasgupta A, de Oliveira T, Kraemer MUG, Tegally H, Sambaturu P , Nature Climate Change (2024), 14, 793–802 (2024). https://doi.org/10.1038/s41558-024-02078-z:.



Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours.
Godwe C, Goni OH, San JE, Sonela N, Tchakoute M, Nanfack A, Koro FK, Butel C, Vidal N, Duerr R, Martin DP, de Oliveira T, Peeters M, Altfeld M, Ayouba A, Ndung'u T, Tongo M, Virus Evolution (2024), 10(1):veae070. doi: 10.1093/ve/veae070:.



Understanding the Transmission Dynamics of the Chikungunya Virus in Africa.
Ramphal Y, Tegally H, San JE, Reichmuth ML, Hofstra M, Wilkinson E, Baxter C, Climade Consortium, de Oliveira T, Moir M, Pathogens (2024), 13(7):605. doi: 10.3390/pathogens13070605:.



Sustained Human Outbreak of a New MPXV Clade I Lineage in the Eastern Democratic Republic of the Congo.
Vakaniaki EH, Kacita C, Kinganda-Lusamaki E, O'Toole Á, Wawina-Bokalanga T, Mukadi-Bamuleka D, Amuri-Aziza A, Malyamungu-Bubala N, Mweshi-Kumbana F, Mutimbwa-Mambo L, Belesi-Siangoli F, Mujula Y, Parker E, Muswamba-Kayembe PC, Nundu SS, Lushima RS, Makangara-Cigolo JC, Mulopo-Mukanya N, Pukuta-Simbu E, Akil-Bandali P, Kavunga H, Abdramane O, Brosius I, Bangwen E, Vercauteren K, Sam-Agudu NA, Mills EJ, Tshiani-Mbaya O, Hoff NA, Rimoin AW, Hensley LE, Kindrachuk J, Baxter C, de Oliveira T, Ayouba A, Peeters M, Delaporte E, Ahuka-Mundeke S, Mohr EL, Sullivan NJ, Muyembe-Tamfum JJ, Nachega JB, Rambaut A, Liesenborghs L, Mbala-Kingebeni P, Nature Medicine (2024), doi: 10.1038/s41591-024-03130-3:.



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