Title: Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
Authors: Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenço J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T.
Journal: medRxiv,https://doi.org/10.1101/2020.12.21.20248640: (2020)
Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.
Citation: Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenço J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa medRxiv,https://doi.org/10.1101/2020.12.21.20248640: (2020).
Alarming COVID variants show vital role of genomic surveillance - Nature - 2021-01-17
Efforts to track SARS-CoV-2 sequences have helped identify worrying variants — but researchers are blind to emerging mutations in some regions.
Genome Detective Coronavirus variant typing tool - KRISP News - 2021-01-17
Phylogenetic identification of variants 501Y.V1, 501Y.V2, 501Y.V3 (B.1.1.7, B.1.351, P.1 / Nextstrain 20I, 20H, 20J). Tool also determines nucleotide (NT), amino acids (AA) and codon (CDS) mutations. The mutations list are provided in html and excel formats.
Answers to 9 crucial questions about the coronavirus variants spreading around the world - Business Insider - 2021-01-15
Experts worldwide are urgently studying three coronavirus variants to understand what risks they pose. One variant first identified in the UK, one in South Africa, and one in Japan are probably more contagious than the original strain. They have caused cases to surge and the three nations to lock down. Here are nine key questions about the variants, answered.
Will vaccines work against the new COVID variants? Scientists race to find out - Bhekisisa - 2021-01-15
One year later and the new coronavirus is still posing new questions for researchers. The recent emergence of new COVID-19 variants across the world has left scientists searching for answers once again as they try to understand what these changes mean for the pandemic — and vaccine roll-outs. As South Africa awaits the arrival of its first shipment of COVID vaccines there are growing concerns about a new coronavirus variant — known as 501Y.V2 — circulating in the country, and what the changes in the virus could mean for how well the jabs work.
As Coronavirus Mutates, the World Stumbles Again to Respond - The New York Times - 2021-01-15
A South African tip led to the discovery of mutations around the world. With infections skyrocketing, 'it’s a race against time.'. Doctors and nurses at a South African hospital group noticed an odd spike in the number of Covid-19 patients in their wards in late October...
‘A bloody mess’: Confusion reigns over naming of new COVID variants - Nature - 2021-01-15
As more lineages emerge, researchers are struggling with a patchwork of nomenclature.
Could new COVID variants undermine vaccines? Labs scramble to find out - Nature - 2021-01-14
Researchers race to determine why lineages identified in Britain and South Africa spread so quickly and whether they’ll compromise vaccines.
Third concerning coronavirus variant should be a 'wake up call' to the world, experts warn - The Telegraph - 2021-01-12
A variant identified in Japan in arrivals from Brazil shares 'concerning' characteristics with mutations detected in the UK and South Africa
WHO calls for new names for Covid variants to avoid country stigma - The Telegraph - 2021-01-12
Countries that conduct a lot of genetic sequencing are more likely to find new strains, say experts
The New Covid-19 Strain in South Africa: What We Know - The Wall Street Journal - 2021-01-11
Researchers warn that the new variant may spread faster and could reduce the efficacy of vaccines
As the coronavirus mutates, the world stumbles to respond - Brief on NY Times live blog - The New York Times - 2021-01-09
The coronavirus has evolved as it has made its way across the world, as any virus is expected to do. But experts have been startled by the pace at which significant new variants have emerged.
South African Covid variant may affect vaccine efficacy, warn scientists - Financial Times - 2021-01-06
Mutation reduces ability of antibodies to bind to virus and could make some shots less effective.
South African variant unlikely to fully negate COVID vaccines, scientist says - Reuters - 2021-01-06
JOHANNESBURG (Reuters) - A variant of the coronavirus first detected in South Africa is unlikely to completely negate the immunising effects of vaccines, a researcher studying it told Reuters.
Boris Johnson Tightens U.K. Lockdown, Citing Fast-Spreading Version of Virus - The New York Times - 2021-01-04
The variant is up to 70 percent more transmissible than earlier versions, officials said. People in southeast England, including London, were told to stay at home.
Fast-spreading virus variants raise alarms - Science - 2021-01-01
Scientists are scrambling to better understand effects of a series of worrisome mutations from in the U.K. and South Africa variants.
'Si nous permettons au virus de continuer à circuler librement, nous lui donnons une grande marge de manœuvre pour mieux s'adapter à la transmission chez l'homme', déclare Tulio de Oliveira, le Brésilien à l'origine de la découverte d'une nouvelle mutation "plus transmissible" du coronavirus qui suscite des inquiétudes dans le monde entier.
South Africa hits 1 million coronavirus cases as new variant spreads rapidly - The Guardian - 2020-12-27
President Cyril Ramaphosa expected to announce new restrictions in attempt to slow the surge
Coronavírus: brasileiro que descobriu mutação de covid-19 explica nova variante - BBC Brasil - 2020-12-24
Tulio de Oliveira, o brasileiro por trás da descoberta de uma nova mutação "mais transmissível" do coronavírus que vem causando preocupação ao redor do mundo, diz à BBC News Brasil que "se o vírus continuar circulando livremente, o risco dele se adaptar melhor aumenta".
In June, Ravindra Gupta, a virologist at the University of Cambridge, heard about a cancer patient who had come into a local hospital the month before with COVID-19 and was still shedding virus. The patient was being treated for a lymphoma that had relapsed and had been given rituximab, a drug that depletes antibody-producing B cells. That made it hard for him to shake the infection with SARS-CoV-2.
South African Covid-19 variant may be 'more effective at spreading - The Guardian - 2020-12-23
Research still to confirm threat posed but variant does not appear to provoke more serious symptoms
Got questions about the new Covid-19 variant in South Africa? Health department has lots of answers - Department of Health - 2020-12-19
The new variant of SARS-CoV-2 detected in SA has left scientists working round the clock to unravel its mysteries, the health department said on December 19 2020. The department of health issued a lengthy list of questions and answers on Saturday after announcing that the virus that causes Covid-19 has evolved into a new variant.
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).