Authors
Steven A Kemp, Dami A Collier, Rawlings P Datir, Isabella ATM Ferreira, Salma Gayed, Aminu Jahun, Myra Hosmillo, Chloe Rees-Spear, Petra Mlcochova, Ines Ushiro Lumb, David J Roberts, Anita Chandra, Nigel Temperton, Clinical data collection De Bie Eckart MDD 3 Bunclark Katherine 3 Josipovic Masa 33 Mackay Michael 3 Rossi Sabrina 34 Selvan Mayurun 3 Spencer Sarah 14 Yong Cissy 34, Royal Papworth Hospital ICU Ansaripour Ali 24 Michael Alice 24 Mwaura Lucy 24 Patterson Caroline 24 Polwarth Gary 24, Addenbrooke’s Hospital ICU Polgarova Petra 22 di Stefano Giovanni 22, Cambridge & Peterborough Foundation Trust Fahey Codie 35 Michel Rachel 35, ANPC & Centre for Molecular Medicine & Innovative Therapeutics Bong Sze-How 36 Coudert Jerome D. 37 Holmes Elaine 38, Funding acquisition, leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis, software & analysis tools and visualization Robson Samuel C. 40, Funding acquisition, leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis and software & analysis tools Loman Nicholas J. 41 Connor Thomas R. 42 43, Leadership & supervision, metadata curation, project administration, samples & logistics, sequencing & analysis, software & analysis tools and visualization Golubchik Tanya 44, Funding acquisition, metadata curation, samples & logistics, sequencing & analysis, software & analysis tools and visualization Martinez Nunez Rocio T. 45, Funding acquisition, leadership & supervision, metadata curation, project administration and samples & logistics Ludden Catherine 46, Funding acquisition, leadership & supervision, metadata curation, samples & logistics and sequencing & analysis Corden Sally 43, Funding acquisition, leadership & supervision, project administration, samples & logistics and sequencing & analysis Johnston Ian 47 Bonsall David 44, Funding acquisition, leadership & supervision, sequencing & analysis, software & analysis tools and visualization Smith Colin P. 48 Awan Ali R. 49, Funding acquisition, samples & logistics, sequencing & analysis, software & analysis tools and visualization Bucca Giselda 48, Leadership & supervision, metadata curation, project administration, samples & logistics and sequencing & analysis Estee Torok M. 3 50 51, Leadership & supervision, metadata curation, project administration, samples & logistics and visualization Saeed Kordo 52 53 Prieto Jacqui A. 52 54, Leadership & supervision, metadata curation, project administration, sequencing & analysis and software & analysis tools Jackson David K. 47, Metadata curation, project administration, samples & logistics, sequencing & analysis and software & analysis tools Hamilton William L. 50 51, Metadata curation, project administration, samples & logistics, sequencing & analysis and visualization Snell Luke B. 55, Funding acquisition, leadership & supervision, metadata curation and samples & logistics Moore Catherine 43, Funding acquisition, leadership & supervision, project administration and samples & logistics Harrison Ewan M. 46 47, Leadership & supervision, metadata curation, project administration and samples & logistics Goncalves Sonia 47, Leadership & supervision, metadata curation, samples & logistics and sequencing & analysis Fairley Derek J. 56 57 Loose Matthew W. 58 Watkins Joanne 43, Leadership & supervision, metadata curation, samples & logistics and software & analysis tools Livett Rich 47, Leadership & supervision, metadata curation, samples & logistics and visualization Moses Samuel 59 60, Leadership & supervision, metadata curation, sequencing & analysis and software & analysis tools Amato Roberto 47 Nicholls Sam 41 Bull Matthew 43, Leadership & supervision, project administration, samples & logistics and sequencing & analysis Smith Darren L. 61 62 63, Leadership & supervision, sequencing & analysis, software & analysis tools and visualization Barrett Jeff 47 Aanensen David M. 64, Metadata curation, project administration, samples & logistics and sequencing & analysis Curran Martin D. 65 Parmar Surendra 65 Aggarwal Dinesh 46 47 66 Shepherd James G. 67, Metadata curation, project administration, sequencing & analysis and software & analysis tools Parker Matthew D. 68, Metadata curation, samples & logistics, sequencing & analysis and visualization Glaysher Sharon 69, Metadata curation, sequencing & analysis, software & analysis tools and visualization Bashton Matthew 61 62 Underwood Anthony P. 64 Pacchiarini Nicole 43 Loveson Katie F. 70, Project administration, sequencing & analysis, software & analysis tools and visualization Carabelli Alessandro M. 46, Funding acquisition, leadership & supervision and metadata curatio Templeton Kate E. 71 72, Funding acquisition, leadership & supervision and project administration Langford Cordelia F. 47 Sillitoe John 47 de Silva Thushan I. 68 Wang Dennis 68, Funding acquisition, leadership & supervision and sequencing & analysis Kwiatkowski Dominic 47 73 Rambaut Andrew 72 O’Grady Justin 74 75 Cottrell Simon 43, Leadership & supervision, metadata curation and sequencing & analysis Holden Matthew TG 76 Thomson Emma C. 67, Leadership & supervision, project administration and samples & logistics Osman Husam 66 77 Andersson Monique 78 Chauhan Anoop J. 69 Hassan-Ibrahim Mohammed O. 79, Leadership & supervision, project administration and sequencing & analysis Lawniczak Mara 47, Leadership & supervision, samples & logistics and sequencing & analysis Alderton Alex 47 Chand Meera 66 Constantinidou Chrystala 80 Unnikrishnan Meera 80 Darby Alistair C. 81 Hiscox Julian A. 81 Paterson Steve 81, Leadership & supervision, sequencing & analysis and software & analysis tools Martincorena Inigo 47 Robertson David L. 67 Volz Erik M. 82 Page Andrew J. 74 Pybus Oliver G. 83, Leadership & supervision, sequencing & analysis and visualization Bassett Andrew R. 47, Metadata curation, project administration and samples & logistics Ariani Cristina V. 47 Spencer Chapman Michael H. 46 47 Li Kathy K. 67 Shah Rajiv N. 67 Jesudason Natasha G. 67 Taha Yusri 84, Metadata curation, project administration and sequencing & analysis McHugh Martin P. 71 Dewar Rebecca 71, Metadata curation, samples & logistics and sequencing & analysis Jahun Aminu S. 85 McMurray Claire 41 Pandey Sarojini 86 McKenna James P. 56 Nelson Andrew 62 63 Young Gregory R. 61 62 McCann Clare M. 62 63 Elliott Scott 69, Metadata curation, samples & logistics and visualization Lowe Hannah 59, Metadata curation, sequencing & analysis and software & analysis tools Temperton Ben 87 Roy Sunando 88 Price Anna 42 Rey Sara 43 Wyles Matthew 68, Metadata curation, sequencing & analysis and visualization Rooke Stefan 72 Shaaban Sharif 76, Project administration, samples & logistics and sequencing & analysis de Cesare Mariateresa 89, Project administration, samples & logistics and software & analysis tools Letchford Laura 47, Project administration, samples & logistics and visualization Silveira Siona 52 Pelosi Emanuela 52 Wilson-Davies Eleri 52, Samples & logistics, sequencing & analysis and software & analysis tools Hosmillo Myra 85, Sequencing & analysis, software & analysis tools and visualization O’Toole Áine 72 Hesketh Andrew R. 48 Stark Richard 80 du Plessis Louis 83 Ruis Chris 46 Adams Helen 90 Bourgeois Yann 91, Funding acquisition and leadership & supervision Michell Stephen L. 87 Grammatopoulos Dimitris 86 92 Edgeworth Jonathan 93 Breuer Judith 88 94 Todd John A. 89 Fraser Christophe 44, Funding acquisition and project administration Buck David 89 John Michaela 95, Leadership & supervision and metadata curation Kay Gemma L. 74, Leadership & supervision and project administration Palmer Steve 47 Peacock Sharon J. 46 66 Heyburn David 43, Leadership & supervision and samples & logistics Weldon Danni 47 Robinson Esther 66 77 McNally Alan 41 96 Muir Peter 66 Vipond Ian B. 66 Boyes John 97 Sivaprakasam Venkat 98 Salluja Tranprit 99 Dervisevic Samir 100 Meader Emma J. 100, Leadership & supervision and sequencing & analysis Park Naomi R. 47 Oliver Karen 47 Jeffries Aaron R. 87 Ott Sascha 80 da Silva Filipe Ana 67 Simpson David A. 57 Williams Chris 43, Leadership & supervision and visualization Masoli Jane AH 87 101, Metadata curation and software & analysis tools Davies Robert 47, Project administration and sequencing & analysis Hadjirin Nazreen F. 46 Quick Joshua 41, Project administration and software & analysis tools Poplawski Radoslaw 41, Samples & logistics and software & analysis tools Starinskij Igor 67, Software & analysis tools and visualization Keatley Jon-Paul 47 Singer Joshua B. 67 de Oliveira Martins Leonardo 74 Yeats Corin A. 64 Abudahab Khalil 64 Taylor Ben EW 64 Menegazzo Mirko 64, Software & analysis tools Bonfield James 47 Puethe Christoph 47 Whitwham Andrew 47 Liddle Jennifier 47 Rowe Will 41 Siveroni Igor 82 Le-Viet Thanh 74 Gaskin Amy 43, Visualization Johnson Rob 82
Publication date
2021/4/8
Journal
Nature
Volume
592
Issue
7853
Pages
277-282
Publisher
Nature Publishing Group UK
Description
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69 …
Total citations
202020212022202320247456334203106
Scholar articles
SA Kemp, DA Collier, RP Datir, IATM Ferreira, S Gayed… - Nature, 2021
SA Kemp, DA Collier, R Datir, IATM Ferreira, S Gayed… - MedRxiv, 2020
SA Kemp, DA Collier, RP Datir, I Ferreira, S Gayed… - Sharrocks K, Blane E, Modis Y, Leigh KE, Briggs JAG …, 2021
S Kemp, DA Collier, R Datir, IA Ferreira, S Gayed… - BioRxiv, 2020
SA Kemp, DA Collier, RP Datir, IATM Ferreira, S Gayed… - NATURE, 2022