The BRICS Network for Genome Surveillance (NGS-BRICS) was established in 2021 and generates and investigates sequence data of viral pathogens of public health importance, such as COVID-19. In the interest of increasing bioinformatics and experimental expertise within BRICS countries. Applications close on 1st of August 2022.
This intensive, hands-on workshop will use microbiome data as a backdrop to learn R. The workshop will feature morning & afternoon sessions taught by expert faculty and technical assistants. All participants will acquire fundamental computational skills, bioinformatics best practices, exploratory data analysis, and modeling techniques. Deadline for application - 7 Aug 2022.
Please find CERIs & KRISPs newsletter June/July issue of 2022. This months edition is a celebration of more awards and recognition of the tireless efforts of our teams towards the global pandemic response; but also a reflection on the future, not only of the evolution of COVID-19 sub-variants and their repercussions, but also the emergence or continuation of other viral threats. Another area of interest is the evolution of Monkey Pox to a global health emergency and what that means for the African continent.
The Stellenbosch University has received a grant from the International Bank for Reconstruction and Development (IBRD) for Accelerating Genomics-based Surveillance for COVID-19 Response in South Africa (P177439) and intends to apply part of the proceeds to eligible payments for goods and consulting services to be procured under this project.
Presenter: Dr.Suzanne McCluskey, Assistant Professor, Harvard Medical School, Date: 10 Aug 2022, Locations: KRITH seminar Room (K2), University of KwaZulu-Natal or virtually
Stakeholder Engagement includes the process of engaging stakeholders for a clear purpose to achieve agreed outcomes. It is now also recognized as a fundamental accountability mechanism since it obliges an organization to involve stakeholders in identifying and understanding of the specific program/project and responding to issues and concerns raised by the stakeholders for decisions, actions, and hence improving program/project performance.
The Africa Centres for Disease Control and Prevention (Africa CDC) has since welcomed the decision made by WHO chief Dr Tedros Adhanom Ghebreyesus, but added that the continent had battled the virus before.
Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection..
Khan K, Karim F, Ganga Y, Bernstein M, Jule Z, Reedoy K, Cele S, Lustig G, Amoako D, Wolter N, Samsunder N, Sivro A, San JE, Giandhari J, Tegally H, Pillay S, Naidoo Y, Mazibuko M, Miya Y, Ngcobo N, Manickchund N, Magula N, Karim QA, von Gottberg A, Abdool Karim SS, Hanekom W, Gosnell BI; COMMIT-KZN Team, Lessells RJ, de Oliveira T, Moosa MS, Sigal A, Nature Communications (2022), doi: 10.1038/s41467-022-32396-9:.
Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment.
Juma J, Fonseca V, Konongoi SL, van Heusden P, Roesel K, Sang R, Bett B, Christoffels A, de Oliveira T, Oyola SO, BMC Genomics (2022), 23(1):520. doi: 10.1186/s12864-022-08764-6:.
HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy.
Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK, mBio (2022), 13(3):e0026922. doi: 10.1128/mbio.00269-22:.
Adherence measured using electronic dose monitoring is associated with emergent antiretroviral resistance and poor outcomes in patients co-infected with HIV/AIDS and multidrug-resistant tuberculosis.
Bateman M, Wolf A, Chimukangara B, Brust JCM, Lessells R, Amico R, Boodhram R, Singh N, Orrell C, Friedland G, Naidoo K, Padayatchi N, O'Donnell MR, Clin Infect Dis. (2022), ciac232. doi: 10.1093/cid/ciac232:.
Low-frequency HIV-1 drug resistance mutations in antiretroviral naive individuals in Botswana.
Maruapula D, Seatla KK, Morerinyane O, Molebatsi K, Giandhari J, de Oliveira T, Musonda RM, Leteane M, Mpoloka SW, Rowley CF, Moyo S, Gaseitsiwe S, Medicine (Baltimore) (2022), 101(28):e29577. doi: 10.1097/MD.0000000000029577:.
Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021.
Subramoney K, Mtileni N, Bharuthram A, Davis A, Kalenga B, Rikhotso M, Maphahlele M, Giandhari J, Naidoo Y, Pillay S, Ramphal U, Ramphal Y, Tegally H, Wilkinson E, Mohale T, Ismail A, Mashishi B, Mbenenge N, de Oliveira T, Makatini Z, Fielding BC, Treurnicht FK, J Med Virol. (2022), 4(8):3676-3684. doi: 10.1002/jmv.27797:.
Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa..
Davies MA, Kassanjee R, Rousseau P, Morden E, Johnson L, Solomon W, Hsiao NY, Hussey H, Meintjes G, Paleker M, Jacobs T, Raubenheimer P, Heekes A, Dane P, Bam JL, Smith M, Preiser W, Pienaar D, Mendelson M, Naude J, Schrueder N, Mnguni A, Le Roux S, Murie K, Prozesky H, Mahomed H, Rossouw L, Wasserman S, Maughan D, Boloko L, Smith B, Taljaard J, Symons G, Ntusi NAB, Parker A, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Arendse J, Kariem S, Moodley M, Wolmarans M, Cloete K, Boulle A, Trop Med Int Health (2022), 27(6):564-573. doi: 10.1111/tmi.13752:.
Prof. de Oliveira says the world has entered an age of epidemics and pandemics
By: Tulio de Oliveira
Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
This is the first version of the Zika typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.
This is the first version of the Chikungunya typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.
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
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).
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).