Network for Genomic Surveillance in South Africa: A network  established to rapidly respond to public health threats

NEWS SPOTLIGHT



The Atlantic



The New York Times



Wired

KRISP NEWS


Some Nations Could Wait Years for Covid Shots. That’s Bad for Everyone

While richer places, such as the U.S., hope to vaccinate most of their citizens within months, poorer countries, like Kenya, expect to reach just small fractions of their populations in that time.


Rare COVID reactions might hold key to variant-proof vaccines

Some people mount an immune response able to fend off a menagerie of coronavirus variants. Nature news covering four of our recent papers on the variant, neutralisation of plasma and Vaccines (Novavax and Astrazeneca)


What’s unique about the body’s response to the 501Y.V2 variant? Find out

New research from South Africa’s genomic surveillance network shows that people infected with the 501Y.V2 variant are also immune to other forms of the virus. The team found the protection against the 501Y.V2 variant could also extend to the original virus circulating the country and the variant first identified in Brazil.


We Now Can See a Virus Mutate Like Never Before

Tracking the coronavirus’s evolution, letter by letter, is revolutionizing pandemic science.In the beginning, there was one. The first genome for the virus causing a mysterious illness we had not yet named COVID-19 was shared by scientists on January 10, 2020. That single genome alerted the world to the danger of a novel coronavirus.


Antibodies from S Africa COVID variant may offer cross-protection

The 501Y.V2 variant reportedly produces a high number of antibodies, providing protection against infection by other variants. The findings in laboratory studies offer hope that COVID-19 vaccines based on the 501Y.V2 variant first identified late last year could protect against multiple variants circulating in different parts of the world


A Virus Variant by Any Other Name - Please

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


Covid variants: What are they and will vaccines work?

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.


PUBLICATIONS SPOTLIGHT


NEJM


Nature


NEJM

KRISP SCIENTIFIC PUBLICATIONS


Cross-Reactive Neutralizing Antibody Responses Elicited by SARS-CoV-2 501Y.V2 (B.1.351).
Moyo-Gwete T, Madzivhandila M, Makhado Z, Ayres F, Mhlanga D, Oosthuysen B, Lambson EB, Kgagudi P, Tegally H, Iranzadeh A, Doolabh D, Tyers L, Chinhoyi RL, Mennen M, Skelm S, Wibmer K C, Bhiman N J, Ueckermann V, Rossouw T, Boswell M, de Oliveira T, Williamson T, Burgers W, Ntusi N, Morris L, Moore P, NEJM (2021), DOI: 10.1056/NEJMc2104192:.



Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.
Engelbrecht S, Delaney K, Kleinhans B, Wilkinson E, Tegally H, Stander T, van Zyl G, Preiser W, de Oliveira T, Viruses (2021), 22;13(3):526. doi: 10.3390/v13030526:.



Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma..
Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Bernstein M, Balazs AB, Gosnell BI, Hanekom W, Moosa MS; NGS-SA; COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A., Nature (2021), DOI: 10.1038/s41586-021-03471-w:.



A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa.
de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P A P R R C, Freitas H R, Mufinda F, Tessema K S , Tegally H, San E J, Wilkinson E, Giandhari J, Pillay S, Giovanetti M, Naidoo Y, Katzourakis A, Ghafari M, Singh L, Tshiabuila D, Martin D, Lessells R, medRxiv (2021), :.



Appropriate names for COVID-19 variants.
Karim SSA, de Oliveira T, Loots G, Science (2021), http://science.sciencemag.org/content/371/6535/1215:.



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 , NEJM (2021), https://doi.org/10.1056/NEJMoa2102214:.



KRISP VIDEOS


New concerns raised over South African variant of COVID-19
By: CBS News

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