KRISP NEWS
On the first ever Health Day at a COP, a new report on climate change and epidemics was released. This report, which was compiled by over one hundred scientists and policy makers, highlights how climate change is fuelling new epidemics across the world, particularly in countries from the Global South.
Welcome to another edition of the CERI/KRISP monthly newsletter. In this issue, we are excited to highlight the remarkable efforts on advancing climate and health research taking place across Africa in the realm of pathogen surveillance and research capacity building. Our dedicated team of scientists has been making outstanding contributions to this critical field, garnering well-deserved recognition for their exceptional research endeavors.
Stellenbosch University's Research & Innovation Excellence Awards held on October 30, 2023, was a night to remember as the institution celebrated the exceptional contributions of its researchers and innovators ...
The South African Portuguese Chamber of Commerce (SAPCC) & ABSA Business Excellence Gala Awards 2023 held at The Wanderers Club in Illovo, Johannesburg, celebrated outstanding businesses and individuals who've contributed to South Africa's business community.
The 2023 Nobel Symposium in Chemistry Tuberculosis and Antibiotic Resistance From Basic Drug Discovery to Clinic was hosted at Stellenbosch University.
The Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University recently concluded an intensive RNA sequencing training program from October 16th to 23rd.
The recent Data Science for Biology Workshop Series in Durban, South Africa, showcased the intersection of data science and biology, emphasizing the importance of capacity building and fostering collaboration among participants.
KRISP SCIENTIFIC PUBLICATIONS
An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal .
Padane A, Tegally H, Ramphal Y, Ndiaye S, Sarr M, Diop M, Diedhiou CK, Mboup A, Diouf N, Souare A, Diagne ND, Aza-Gnandji M, Dabo NA, Dia YA, Diaw NA, Leye N, Diaw PA, Ambroise A, Cisse B, Diallo AS, Diop O, Diallo AA, Ndoye S, Sanko TJ, Baxter C, Wilkinson E, James SE, Tshiabuila D, Naidoo Y, Pillay S, Lessells R, Cisse K, Leye A, Mbaye A, Kania D, Traore I, Kagone ST, Tinto B, Ouedraogo A, Lourenco J, Giovanetti M, Giandhari J, de Oliveira T, Mboup S, medrxiv (2023), MEDRXIV-2023-298527v1:.
Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil.
Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi AC, Tscha M, Soares G, Dorl GG, Marques AEML, Sousa R, Adelino TER, Xavier J, de Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonça AF, de Macêdo IL, Ribeiro de Sousa DE, Rodrigues de Toledo Costa G, Botelho de Castro M, de Souza Andrade M, de Abreu FVS, Campos FS, Iani FCM, Pereira MA, Cavalcante KRLJ, de Freitas ARR, Campelo de Albuquerque CF, Macário 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, Oliveira de Moura NF, Fabri A, Dos Santos Rodrigues CD, Dos Santos CC, Barreto de Almeida MA, Dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, Mayoral Pedroso da Silva G, Soares MRF, de Castilhos MMS, de Souza E Silva JC, Bisetto Junior A, Pouzato EG, Tanabe LS, Arita DA, Matsuo R, Dos Santos Raymundo J, Silva PCL, Santana Araújo Ferreira Silva A, Samila S, Carvalho G, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, de Almeida Medeiros DB, Cruz ACR, Venâncio da Cunha R, Van Voorhis W, Bispo de Filippis AM, Almiron M, Holmes EC, Ramos DG, Romano A, Lourenço J, Alcantara LCJ, Duarte Dos Santos CN, Science Advances (2023), 9(35):eadg9204. doi: 10.1126/sciadv.adg9204:.
Will climate change amplify epidemics and give rise to pandemics?.
de Oliveira T, Tegally H, Science (2023), 381,6660, DOI: 10.1126/science.adk4500:.
Genomic epidemiology of the cholera outbreak in Malawi 2022-2023.
Chabuka L, Choga WT, Mavian CN, Moir M, Tegally H, Wilkinson E, Naidoo Y, Inward R, Morgenstern C, Bhatt S, Wint WGR, Khan K, Bogoch II, Kraemer MUG, Baxter C, Tagliamonte M, Salemi M, Lessells RJ, Mitambo C, Chitatanga R, Bango JB, Chiwaula M, Chavula Y, Bukhu M, Manda H, Chitenje M, Malolo I, Mwanyongo A, Mvula B, Nyenje M, de Oliveira T, Kagoli M, medRxiv (2023), https://doi.org/10.1101/2023.08.22.23294324:.
Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern.
Tegally H, Wilkinson E, Tsui JL, Moir M, Martin D, Brito AF, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells RJ, Faria NR, Kraemer MUG, de Oliveira T, Cell (2023), S0092-8674(23)00641-4. doi: 10.1016/j.cell.2023.06.001:.
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1.
Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O'Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, COVID-19 Genomics UK (COG-UK) consortium¶, Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MUG, Science (2023), 381(6655):336-343. doi: 10.1126/science.adg6605.:.
Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages.
Subramoney K, Mtileni N, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Maharaj A, Tshiabuila D, Tegally H, Wilkinson E, de Oliveira T, Fielding BC, Treurnicht FK, Viruses (2023), 15(5):1194. doi: 10.3390/v15051194:.
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