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.


CERI & KRISP Newsletter June/July 2022: Monkeypox, COVID-19 BA.4 and BA.5 lineages, Microbiome and phylogenetic training and much more.

Please find CERI’s & KRISP’s newsletter June/July issue of 2022. What an eventful and action-packed period it has been! In this issue we feature our recent paper on the real-time tracking of the 2022 Monkeypox outbreak, the renaming of Monkeypox to remove the geographic stigma, and our Nature Medicine publication that identified the BA.4 and BA.5 Omicron lineages and how they drove the 5th wave in South Africa.


Seminar: Digital Health Computing, Information Systems and Machine Learning for Public Health

Presenter: Professor Douglas Pires ,School of Computing and Information Systems at the University of Melbourne, Australia. Date: 22 June2022, Locations: STIAS, Manor House Library, Wallenberg Centre, Stellenbosch or *VIRTUALLY


Opportunities: Laboratory Technician at CERI, Tygerberg Campus

Laboratory Technologists (x2) at CERI in Stellenbosch University. The purpose of this position is to provide support to CERI's laboratory by conducting research, next generation sequencing and diagnostic tests to meet project deadlines and within allocated turnaround times.


Opportunity for Masters and PhD scholarship within KRISP at UKZN: 2023

Offered through CAPRISA DSI and NRF Centre of Excellence (CoE) in HIV Prevention The KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), the state of the art UKZN Research Centre has opportunities for Masters and PhD students with great potential and an ambition to pursue a career in research. Successful applicants will become part of a dynamic research team and they will get hands-on experience in the generation and analysis of genomic, epidemiological and clinical data.


PUBLICATIONS SPOTLIGHT


Nature


Nature


Science

KRISP SCIENTIFIC PUBLICATIONS


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:.



Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.
Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, ’Toole A, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T, Virological (2022), https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853:.



Tracking the 2022 monkeypox outbreak with epidemiological data in real-time.
Kraemer MUG, Tegally H, Pigott DM, Dasgupta A, Sheldon J, Wilkinson E, Schultheiss M, Han A, Oglia M, Marks S, Kanner J, O’Brien K, Dandamudi S, Rader B, Sewalk K, Bento AI, Scarpino SV, de Oliveira T, Bogoch II, Katz R, Brownstein JS, , The Lancet Infectious Diseases (2022), DOI:https://doi.org/10.1016/S1473-3099(22)00359-0:.



An early warning system for emerging SARS-CoV-2 variants.
Subissi L, von Gottberg A, Thukral L, Worp N, Oude Munnink BB, Rathore S, Abu-Raddad LJ, Aguilera X, Alm E, Archer BN, Attar Cohen H, Barakat A, Barclay WS, Bhiman JN, Caly L, Chand M, Chen M, Cullinane A, de Oliveira T, Drosten C, Druce J, Effler P, El Masry I, Faye A, Gaseitsiwe S, Ghedin E, Grant R, Haagmans BL, Herring BL, Iyer SS, Kassamali Z, Kakkar M, Kondor RJ, Leite JA, Leo Y, Leung GM, Marklewitz M, Moyo S, Mendez-Rico J, Melhem NM, Munster V, Nahapetyan K, Oh D, Pavlin BI, Peacock TP, Peiris M, Peng Z, Poon LLM, Rambaut A, Sacks J, Shen Y, Siqueira MM, Tessema SK, Volz EM, Thiel V, van der Werf S, Briand S, Perkins MD, Van Kerkhove MD, Koopmans MPG, Agrawal A, Nature Medicine (2022), https://doi.org/10.1038/s41591-022-01836-w:.



Infectious diseases science in Africa takes a leading place in the world.
de Oliveira T, The Lancet (2022), https://doi.org/10.1016/S0140-6736(22)00977-1I:.



Omicron infection enhances Delta antibody immunity in vaccinated persons.
Khan K, Karim F, Cele S, Reedoy K, San EJ, Lustig G, Tegally H, Rosenberg Y, Bernstein M, Jule Z, Ganga Y, Ngcobo N, Mazibuko M, Mthabela N, Mhlane Z, Mbatha N, Miya Y, Giandhari J, Ramphal Y, Naidoo T, Sivro A, Samsunder N, Kharsany A, Amoako D, Bhiman J, Manickchund N, Karim Q, Magula N, Abdool Karim SS, Gray G, Hanekom W, von Gottberg A, Milo R, Gosnell B, Lessells R, Moore P, de Olveira T, Moosa M-Y S, Sigal A, Nature (2022), https://doi.org/10.1038/s41586-022-04830-x:.



Effectiveness of the Ad26.COV2.S vaccine in health-care workers in South Africa (the Sisonke study): results from a single-arm, open-label, phase 3B, implementation study.
Bekker LG, Garrett N, Goga A, Fairall L, Reddy T, Yende-Zuma N, Kassanjee R, Collie S, Sanne I, Boulle A, Seocharan I, Engelbrecht I, Davies MA, Champion J, Chen T, Bennett S, Mametja S, Semenya M, Moultrie H, de Oliveira T, Lessells R, Cohen C, Jassat W, Groome M, Von Gottberg A, Le Roux E, Khuto K, Barouch D, Mahomed H, Wolmarans M, Rousseau P, Bradshaw D, Mulder M, Opie J, Louw V, Jacobson B, Rowji P, Peter JG, Takalani A, Odhiambo J, Mayat F, Takuva S, Corey L, Gray GE, Lancet (2022), 399(10330):1141-1153. doi: 10.1016/S0140-6736(22)00007-1:.



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