TIME 100: The 100 Most Influential People of 2022 - Prof Tulio de Oliveira and Sikhulile Moyo

NEWS SPOTLIGHT



Science



Nature



The Guardian

KRISP NEWS


NGS-BRICS Viral Sequencing and Phylogenetics Workshop, 26-30 Sept 2022

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.


Workshop: Exploratory Data Analysis and Modelling in R with Microbiome Applications, 22-26 August 2022, Durban, South Africa

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.


General Procurement Notice for the Project Accelerating Genomics-based Surveillance for COVID-19 Response in South Africa

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.


CERI's Stakeholders Engagement Plan for the project Accelerating Genomics-based Surveillance for COVID-19 Response in South Africa

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.


Monkeypox is now a global health emergency - Here’s what it means for Africa

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.


The Network for Genomics Surveillance in South Africa (NGS-SA) received the NSTF-South32 Awards 2022 for Data Science

The prestigious 'Oscars' of the science, engineering and technology (SET) world took place on 21 July 2022. This, the 24th celebration of South African science, ingenuity, and innovation, is a shining light at a time when the world needs far more good news. The success stories that define this year’s Awards stand out for many reasons, but perhaps the most powerful is how they all showcase how science can play a significant role in driving sustainable development, improving quality of life, and connecting people and communities.


First case of antibody-avoiding Covid subvariant detected

The first case of Covid-19 attributed to a new antibody-avoiding subvariant, BA.2.75, has been detected in Thailand, but experts do not foresee it causing serious outbreaks, according to the Centre for Medical Genomics.


PUBLICATIONS SPOTLIGHT


Nature


Nature


Science

KRISP SCIENTIFIC PUBLICATIONS


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:.



Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa.
Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Moyo S, Amoako D, Althaus C, Anyaneji U, Kekana D, Viana R, Giandhari J, Maponga T, Maruapula D, Choga W, Mayaphi S, Mbhele N, Gaseitsiwe S, Msomi N, Naidoo Y, Pillay S, Sanko T, San J, Scott L, Singh L, Magini N, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht F, Venter M, Davids M, Chiloane G, Mendes A, McIntyre C, O'Toole A, Ruis C, Peacock T, Roemer C, Williamson C, Pybus O, Bhiman J, Glass A, Martin D, Rambaut A, Gaseitsiwe S, von Gottberg A, Baxter C, Lessells R, de Oliveira T, Nature Medicine (2022), https://doi.org/10.1038/s41591-022-01911-2:.



KRISP VIDEOS


Prof. de Oliveira says the world has entered an age of epidemics and pandemics
By: Tulio de Oliveira

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