Detection of a SARS-CoV-2 variant of concern in South Africa.
Houriiyah Tegally,Eduan Wilkinson,Marta Giovanetti,Marta Giovanetti,Arash Iranzadeh,Vagner Fonseca,Vagner Fonseca,Jennifer Giandhari,Deelan Doolabh,Sureshnee Pillay,Emmanuel James San,Nokukhanya Msomi,Koleka Mlisana,Anne von Gottberg,Sibongile Walaza,Mushal Allam,Arshad Ismail,Thabo Mohale,Allison J. Glass,Susan Engelbrecht,Gert U. van Zyl,Wolfgang Preiser,Francesco Petruccione,Alex Sigal,Alex Sigal,Diana Hardie,Gert Marais,Nei yuan Hsiao,Stephen N.J. Korsman,Mary-Ann Davies,Lynn Tyers,Innocent Mudau,Denis York,Caroline Maslo,Dominique Goedhals,Shareef Abrahams,Oluwakemi Laguda-Akingba,Arghavan Alisoltani-Dehkordi,Arghavan Alisoltani-Dehkordi,Adam Godzik,Constantinos Kurt Wibmer,B.T. Sewell,José Lourenço,Luiz Carlos Junior Alcantara,Luiz Carlos Junior Alcantara,Sergei L Kosakovsky Pond,Steven Weaver,Darren P. Martin,Richard J Lessells,Richard J Lessells,Jinal N. Bhiman,Carolyn Williamson,Carolyn Williamson,Tulio de Oliveira,Tulio de Oliveira,Tulio de Oliveira +55 more
TLDR
A newly arisen lineage of SARS-CoV-2 (designated 501Y.V2) was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province.Abstract:
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data-which show rapid expansion and displacement of other lineages in several regions-suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape6-8.read more
Citations
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Features, Evaluation and Treatment Coronavirus (COVID-19)
TL;DR: The effects of the epidemic caused by the new CoV has yet to emerge as the situation is quickly evolving, and world governments are at work to establish countermeasures to stem possible devastating effects.
Journal ArticleDOI
Mechanisms of SARS-CoV-2 entry into cells.
TL;DR: In this article, structural and cellular foundations for understanding the multistep SARS-CoV-2 entry process, including S protein synthesis, S protein structure, conformational transitions necessary for association of the spike (S) protein with ACE2, engagement of the receptor-binding domain of the S protein with ACS, proteolytic activation of S protein, endocytosis and membrane fusion are provided.
Journal ArticleDOI
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.
Nuno R. Faria,Thomas A. Mellan,Charles Whittaker,Ingra Morales Claro,Darlan da Silva Candido,Darlan da Silva Candido,Swapnil Mishra,Myuki A E Crispim,Flavia C. S. Sales,Iwona Hawryluk,John T. McCrone,Ruben J.G. Hulswit,Lucas A M Franco,Mariana S. Ramundo,Jaqueline Goes de Jesus,Pamela S Andrade,Thais M. Coletti,Giulia M. Ferreira,Camila A. M. Silva,Erika R. Manuli,Rafael Henrique Moraes Pereira,Pedro S. Peixoto,Moritz U. G. Kraemer,Nelson Gaburo,Cecilia da C. Camilo,Henrique Hoeltgebaum,William Marciel de Souza,Esmenia C. Rocha,Leandro Marques de Souza,Mariana C. Pinho,Leonardo José Tadeu de Araújo,Frederico S V Malta,Aline B. de Lima,Joice do P. Silva,Danielle A G Zauli,Alessandro C. S. Ferreira,Ricardo P Schnekenberg,Daniel J Laydon,Patrick G T Walker,Hannah M. Schlüter,Ana L. P. dos Santos,Maria S. Vidal,Valentina S. Del Caro,Rosinaldo M. F. Filho,Helem M. dos Santos,Renato Santana Aguiar,José Luiz Proença-Módena,Bruce Walker Nelson,James A. Hay,Melodie Monod,Xenia Miscouridou,Helen Coupland,Raphael Sonabend,Michaela A. C. Vollmer,Axel Gandy,Carlos A. Prete,Vitor H. Nascimento,Marc A. Suchard,Thomas A. Bowden,Sergei L Kosakovsky Pond,Chieh-Hsi Wu,Oliver Ratmann,Neil M. Ferguson,Christopher Dye,Nicholas J. Loman,Philippe Lemey,Andrew Rambaut,Nelson Abrahim Fraiji,Maria Perpétuo Socorro Sampaio Carvalho,Oliver G. Pybus,Oliver G. Pybus,Seth Flaxman,Samir Bhatt,Samir Bhatt,Ester Cerdeira Sabino +74 more
TL;DR: In this article, the authors used a two-category dynamical model that integrates genomic and mortality data to estimate that P.1 may be 1.7-to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.
Journal ArticleDOI
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
TL;DR: The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function as discussed by the authors , highlighting the rapid spread in regions with high levels of population immunity.
Journal ArticleDOI
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.
Erik M. Volz,Swapnil Mishra,Meera Chand,Jeffrey C. Barrett,Robert Johnson,Lily Geidelberg,Wes Hinsley,Daniel J. Laydon,Gavin Dabrera,Áine O'Toole,Roberto Amato,Manon Ragonnet-Cronin,Ian Harrison,Ben Jackson,Cristina V. Ariani,Olivia Boyd,Nicholas J. Loman,Nicholas J. Loman,John T. McCrone,Sónia Gonçalves,David Jorgensen,Richard M. Myers,Verity Hill,David K. Jackson,Katy A. M. Gaythorpe,Natalie Groves,John Sillitoe,Dominic P. Kwiatkowski,Seth Flaxman,Oliver Ratmann,Samir Bhatt,Samir Bhatt,Susan Hopkins,Axel Gandy,Andrew Rambaut,Neil M. Ferguson +35 more
TL;DR: In this paper, the authors show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing.
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