B.1.351 may sound sweet to a molecular epidemiologist, but what is the alternative, other than stigmatizing geographical names? News piece at NY Times highlighting our work with WHO on a new nomenclature system for COVID-19 variants
A variant of concern first identified in Brazil has now been found in the UK. Public health officials are investigating the six cases and are deploying more testing to see if it has spread to more people. Some variants, like this one, appear to be more contagious and there are concerns vaccines may not work quite so well against them.
A new SARS-CoV-2 variant, which has dominated Covid-19 infections in Uganda and Rwanda, has been detected in South Africa. The announcement was made by Professor Tulio de Oliveira, director of the KRISP lab. However, de Oliveira told Health24 that is not a variant of concern, and that genome surveillance will monitor this and other variants
Scientists worldwide have been closely monitoring the emergence of coronavirus variants. Although there are a large number of variants, some of them have turned out to be more alarming. Professor Tulio de Oliveira provided an update on the spread of three of these, and said that two more have been placed on the WHO's watchlist.
South Africas pause of its rollout of the Oxford/AstraZeneca vaccine in response to concern about a local coronavirus variant sparked global debate and shone a spotlight on how the countrys science has become vital to understanding where the pandemic may go next.
Evidence that a variant of the coronavirus identified in South Africa might compromise immunity sparks concerns about vaccine effectiveness.
Efforts to track SARS-CoV-2 sequences have helped identify worrying variants - but researchers are blind to emerging mutations in some regions.
Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil.
Iani FCM, Giovanetti M, Fonseca V, Souza WM, Adelino TER, Xavier J, Jesus JG, Pereira MA, Silva MVF, Costa AVB, Silva EC, Mendes MCO, Filippis AMB, Albuquerque CFC, Abreu AL, Oliveira MAA, Alcantara LCJ, Faria NR., Infect Genet Evol (2021), S1567-1348(21)00082-4:.
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma.
Wibmer CK, Ayres F, Hermanus T, Madzivhandila M, Kgagudi P, Oosthuysen B, Lambson BE, de Oliveira T, Vermeulen M, van der Berg K, Rossouw T, Boswell M, Ueckermann V, Meiring S, von Gottberg A, Cohen C, Morris L, Bhiman JN, Moore PL, Nature Medicine (2021), https://doi.org/10.1038/s41591-021-01285-x:.
Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes.
Torres MC, Lima de Mendonça MC, Damasceno dos Santos Rodrigues C, Fonseca V, Ribeiro MS, Brandão AP, Venâncio da Cunha R, Dias AI, Santos Vilas Boas L, Felix AC, Alves Pereira M, de Oliveira Pinto LM, Sakuntabhai A, Bispo de Filippis AM, on behalf of ZikAction Consortium., Viruses (2021), 13(2), 349:.
Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa
.
Madhi SA, Baillie VL, Cutland CL, Voysey M, KoenAL, Fairlie L, Padayachee SD, Dheda K, Barnabas SL, Bhorat QE, Briner C, Kwatra G, Ahmed K, Aley P, Bhikha S, Bhiman JN, Bhorat AE, du plessis J, Esmail A, Groenewald M, Horne E, Hwa S-H, Jose A, Lambe T, Laubscher M, Malahleha M, Masenya M, Masilela M, McKenzie S, Molapo K, Moultrie A, Oelofse S, Pate Fl, Pillay S, Rhead S, Rodel H, Rossouw L, Taoushanis C, Tegally H, Thombrayil A, van Eck S, Wibmer C, Durham NM, Kelly EJ, Villafana T, Gilbert S, Pollard AJ, de Oliveira T, Moore PL, Sigal A, Izu A, NGS-SA, Wits VIDA COVID vaccine trial group
, medRxiv (2021), https://doi.org/10.1101/2021.02.10.21251247:.
Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil.
Xavier J, Fonseca V, Bezerra JF, Do Monte Alves M, Mares-Guia NA, Claro IM, De Jesus R, Adelino T, Araujo E, Cavalcante KRLJ, Tosta S, De Souza TR, Moreira Da Cruz FE, De Araujo Fabri A, de Oliveira EC, De Moura NFO, Do Carmo Said RF, De Albuquerque CFC, Azevedo V, de Oliveira T, De Filippis AMB, Venancio Da Cunha R, Luz KG, Giovanetti M, Alcantara L, IJID (2021), S1201-9712(21)00037-0:.
Sixteen novel lineages of SARS-CoV-2 in South Africa.
Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Gottberg A, Walaza S, Fonseca V, Allam M, Ismail A, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Pettruccione F, Sigal A, Gazy I, Hardie D, Hsiao M, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenco J, Alcantara LCJ, de Oliveira T, Nature Medicine (2021), https://doi.org/10.1038/s41591-021-01255-3:.
Escape of SARS-CoV-2 501Y.V2 variants from neutralization by convalescent plasma.
Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Balazs AB, Gosnell BI, Hanekom W, Moosa MYS, NGS-SA, COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A, medRxiv (2021), 250224v1-Sigal:.
New concerns raised over South African variant of COVID-19
By: CBS News
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).
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