KRISP NEWS
Professor Tulio de Oliveira was invited by Dr. Tedros Adhanom Ghebreyesus (Director General WHO) and Dr. Chikwe Ihekweazu (Director of WHO pandemic Hub) to take a position on the leadership committee of the International Pathogen Surveillance Network (IPSN). Prof de Oliveira will be a panellist on the official launch of IPSN as part of the World Health Assembly on 30 May 2023 in Geneva.
Sophisticated genomic surveillance lab aims to keep one step ahead of outbreaks with effective tests, treatments and vaccines
Welcome to the April/May 2023 edition of our newsletter. April was an incredibly busy and exciting month for CERI and KRISP, centered around the launch of the CLIMADE (Climate Amplified Diseases and Epidemics) consortium and the inauguration of the R1.2 billion Biomedical Research Institute (BMRI) at Stellenbosch University. This events brought together leading experts and stakeholders from all over the world to celebrate this momentous occasion and the state-of-the-art facilities that will enable us to lead the way in genomic research.
The WHO Hub for Pandemic and Epidemic Intelligence was established in Berlin with the foundational investment of the Government of the Federal Republic of Germany in September 2021 to support countries, regions, and global actors to avert and manage public health threats more efficiently.
The fellowship is a tailored training opportunity intended to train a pathogen genomics and bioinformatics workforce with expertise to improve outbreak detection and disease surveillance in Africa.
A new coalition, CLIMADE, brings together some of the biggest names in public health to address climate-amplified diseases in Africa and Latin America.
Regarded as the pride of Africa, the facility has opened its doors to the continent and the world offering training and fellowships to those in the field of genomics.
KRISP SCIENTIFIC PUBLICATIONS
HIV-1 drug resistance in people on dolutegravir-based ART: Collaborative analysis of cohort studies.
Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, Monforte AD, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos R, medRxiv (2023), 5:2023.04.05.23288183. doi: 10.1101/2023.04.05.23288183:.
Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing.
Pillay S, San JE, Tshiabuila D, Naidoo Y, Pillay Y, Maharaj A, Anyaneji UJ, Wilkinson E, Tegally H, Lessells RJ, Baxter C, de Oliveira T, Giandhari J, PLoS ONE (2023), 18(4):e0283219. doi: 10.1371/journal.pone.0283219:.
Genomic epidemiology sheds light on the recent spatio-temporal dynamics of Yellow Fever virus and the spatial corridor that fueled its ongoing emergence in southern Brazil.
Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi A, Tscha M, Soares G, Dorl G, Marques AE, Sousa RS, Adelino TER, Xavier J, Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonca AF, de Macedo IL, de Souze DER , Costa GRT, de Castro MB, Iani FCM, Pereira MA, Cavalcante KRLJ, Freitas ARR, de Albuquerque CFC, Macario EM, dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, de Moura NFB, Fabri A, Rodrigues CDS, dos Santos CC, de Almeida MAB, dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, da Silva GMP, Soares MRF, de Castilhos MMS, Silva JCS, Junior AB, Pouzato EG, Tanabe LS, Arita DA, Matsuo RM, Raymundo JS, Silva PCL, Silva ASAF, Samila S, Pereira GC, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, Medeiros DBA, Cruz ACR, Cunha RV, Voorhis WV, de Filippis AMB, Almiron MA, Holmes EC, Ramos DG, Martins AP, Lourenco JL, Alcantara LCJ, dos Santos CND, medRxiv (2023), 2023.01.13.23284525v1:.
Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay.
Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FCM, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Junior Alcantara LC, medRXiV (2023), doi:10.1101/2023.04.16.23288635:.
SARS-CoV-2 Africa dashboard for real-time COVID-19 information.
Xavier JS, Moir M, Tegally H, Sitharam N, Abdool Karim W, San JE, Linhares J, Wilkinson E, Ascher DB, Baxter C, Pires DEV, de Oliveira T, Nature Microbiology (2023), 8(1):1-4. doi: 10.1038/s41564-022-01276-9:.
Advancing detection and response capacities for emerging and re-emerging pathogens in Africa.
achega JB, Nsanzimana S, Rawat A, Wilson LA, Rosenthal PJ, Siedner MJ, Varma JK, Kilmarx PH, Mutesa L, Tanner M, Binagwaho A, Forrest J, Mbala-Kingebeni P, Muyembe-Tamfum JJ, Ntoumi F, Zumla A, de Oliveira T, Mills EJ, Lancet Infect Dis. (2023), :S1473-3099(22)00723-X. doi: 10.1016/S1473-3099(22)00723-X:.
New nomenclature for mpox (monkeypox) and monkeypox virus clades.
Ulaeto D, Agafonov A, Burchfield J, Carter L, Happi C, Jakob R, Krpelanova E, Kuppalli K, Lefkowitz EJ, Mauldin MR, de Oliveira T, Onoja B, Otieno J, Rambaut A, Subissi L, Yinka-Ogunleye A, Lewis RF, Lancet Infect Dis. (2023), 23(3):273-275. doi: 10.1016/S1473-3099(23)00055-5:.
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