NEWS SPOTLIGHT



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the gem



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KRISP NEWS


Postdoctoral Research Fellowship

We invite applications from ambitious postdoctoral scientists for a 3-year fellowship in partnership with the CLIMADE consortium at the Centre for Epidemic Response and Innovation (CERI). This transdisciplinary project focuses on leveraging satellite data, remote sensing, GIS, and climate modeling to advance spatial epidemiology research. The successful candidate will integrate genomic and geospatial data to develop predictive models that monitor and control infectious disease outbreaks influenced by climate change.


Africa in the World Festival

The ‘Africa in the world’ festival has the world’s brightest on the African continent engage in all fields of human endeavour.


Key Takeaways from the Grant Writing Workshop

Key learning points from Prof. Tulio de Oliveira on the Art of Grant Writing Workshop. Published at the gem: genomics, epidemics & microbes - Oct/Nov 2024


Mastering the Art of Grant Writing

Lessons from the Public Square Workshop. In the world of research, deadlines are relentless, and competition for funding is fierce. Without strong grant writing skills, even the most innovative ideas can fall through the cracks.


Prof. Thulani Makhalanyane Delivers Inaugural Lecture

This inaugural lectured titled on Unveiling the Hidden World Within Us: What Environmental Microbiomes Can Teach Us About Ourselves, explored how these microbial communities are active, essential contributors to ecosystems and human health.


KRISP at UKZN hosts Schools for National Science Week

As part of the National Science Week 2024, the team at KRISP hosted 50 students from Chesterville Secondary School and KwaMathanda High School in Durban.


Brazilian PhD Student, Débora de La-Roque, reflects on her time in South Africa

Six months can make a world of difference, especially when spent in a hub of scientific excellence. This was certainly the case for Débora Glenda Lima de LaRoque, a PhD student from the University of São Paulo (USP) in Brazil, who came to Stellenbosch University’s Centre for Epidemic Response and Innovation (CERI) to enhance her research in dengue virus phylogenetics and phylodynamics.


PUBLICATIONS SPOTLIGHT


Science


Nature Medicine


Nature

KRISP SCIENTIFIC PUBLICATIONS


Unraveling the Complexity of Chikungunya Virus Infection Immunological and Genetic Insights in Acute and Chronic Patients.
Fritsch H, Giovanetti M, Clemente L, da Rocha Fernandes G, Fonseca V, de Lima M, Falcão M, de Jesus N, de Cerqueira E, Venâncio da Cunha R, de Oliveira Francisco M, de Siqueira I, de Oliveira C, Xavier J, Ferreira J, Queiroz F, Smith E, Tisoncik-Go J, Van Voorhis W, Rabinowitz P, Wasserheit J, Gale M, de Filippis A, Alcantara L, Genes (2024), 15(11):1365. doi: 10.3390/genes15111365.:.



Integrated analyses of the transmission history of SARS-CoV-2 and its association with molecular evolution of the virus underlining the pandemic outbreaks in Italy, 2019-2023.
Cella E, Fonseca V, Branda F, Tosta S, Moreno K, Schuab G, Ali S, Slavov S, Scarpa F, Santos L, Kashima S, Wilkinson E, Tegally H, Mavian C, Borsetti A, Caccuri F, Salemi M, de Oliveira T, Azarian T, de Filippis A, Alcantara L, Ceccarelli G, Caruso A, Colizzi V, Marcello A, Lourenço J, Ciccozzi M, Giovanetti M, International Journal of Infectious Diseases (2024), ():107262. doi: 10.1016/j.ijid.2024.107262.:.



Fatal Oropouche Virus Infections in Nonendemic Region, Brazil, 2024.
Bandeira A, Pereira F, Leal A, Santos S, Barbosa A, Souza M, de Souza D, Guimaraes N, Fonseca V, Giovanetti M, Alcantara L, Lessa A, Saavedra R, Tomé L, Iani F, Barros R, Purificação S, de Jesus J, Fonseca R, Araújo M, Emerging Infectious Diseases (2024), 30(11):. doi: 10.3201/eid3011.241132.:.



North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic.
Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M, BMC Infectious Diseases (2024), 24(1):. doi: 10.1186/s12879-024-09658-6.:.



Detection of Multiple Human Viruses, including Mpox, Using a Wastewater Surveillance Approach in Brazil.
Calabria de Araujo J, Carvalho A, Leal C, Natividade M, Borin M, Guerra A, Carobin N, Sabino A, Almada M, Costa M, Saia F, Frutuoso L, Iani F, Adelino T, Fonseca V, Giovanetti M, Alcantara L, Pathogens (2024), 13(7):589. doi: 10.3390/pathogens13070589.:.



Insights into SARS-CoV-2 Surveillance among Prison Populations in Mato Grosso do Sul, Brazil, in 2022.
Ferreira da Silva L, Alcantara L, Fonseca V, Frias D, Umaki Zardin M, de Castro Lichs G, Esposito A, Xavier J, Fritsch H, Lima M, de Oliveira C, Castilho de Arruda L, Maziero L, Rodrigues Barretos E, Tsuha Oshiro P, Gimenes Mendes Menezes E, de Freitas Cardoso L, Ferreira Lemos E, Lourenço J, de Albuquerque C, do Carmo Said R, Rosewell A, Ferraz Demarchi L, Croda J, Giovanetti M, Maymone Gonçalves C, Viruses (2024), 16(7):1143. doi: 10.3390/v16071143.:.



Exploring Microorganisms Associated to Acute Febrile Illness and Severe Neurological Disorders of Unknown Origin: A Nanopore Metagenomics Approach.
Moreno K, de Andrade V, de Melo Iani F, Fonseca V, Lima M, de Castro Barbosa E, Tomé L, Guimarães N, Fritsch H, Adelino T, Oliveira Fereguetti T, Aspahan M, Gamarano Barros T, Alcantara L, Giovanetti M, Genes (2024), 15(7):922. doi: 10.3390/genes15070922.:.



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