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The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.

Titel:	Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Autor/in / Beteiligte Person:	Vöhringer, HS ; Sanderson, T ; Sinnott, M ; De Maio, N ; Nguyen, T ; Goater, R ; Schwach, F ; Harrison, I ; Hellewell, J ; Ariani, CV ; Gonçalves, S ; Jackson, DK ; Johnston, I ; Jung, AW ; Saint, C ; Sillitoe, J ; Suciu, M ; Goldman, N ; Panovska-Griffiths, J ; Birney, E ; Volz, E ; Funk, S ; Kwiatkowski, D ; Chand, M ; Martincorena, I ; Barrett, JC ; Gerstung, M
Link:	Zum Volltext
Zeitschrift:	Nature, Jg. 600 (2021-12-01), Heft 7889, S. 506-511
Veröffentlichung:	Basingstoke : Nature Publishing Group ; <i>Original Publication</i>: London, Macmillan Journals ltd., 2021
Medientyp:	academicJournal
ISSN:	1476-4687 (electronic)
DOI:	10.1038/s41586-021-04069-y
Schlagwort:	Amino Acid Substitution COVID-19 transmission England epidemiology Epidemiological Monitoring Humans Molecular Epidemiology Mutation Quarantine statistics & numerical data SARS-CoV-2 classification Spatio-Temporal Analysis Spike Glycoprotein, Coronavirus genetics COVID-19 epidemiology COVID-19 virology Genome, Viral genetics Genomics SARS-CoV-2 genetics
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Corporate Authors: Wellcome Sanger Institute COVID-19 Surveillance Team ; COVID-19 Genomics UK (COG-UK) Consortium* Publication Type: Journal Article; Research Support, Non-U.S. Gov't Language: English [Nature] 2021 Dec; Vol. 600 (7889), pp. 506-511. <i>Date of Electronic Publication: </i>2021 Oct 14. MeSH Terms: Genomics* ; COVID-19 / epidemiology ; COVID-19 / virology ; Genome, Viral / genetics ; SARS-CoV-2 / genetics ; Amino Acid Substitution ; COVID-19 / transmission ; England / epidemiology ; Epidemiological Monitoring ; Humans ; Molecular Epidemiology ; Mutation ; Quarantine / statistics & numerical data ; SARS-CoV-2 / classification ; Spatio-Temporal Analysis ; Spike Glycoprotein, Coronavirus / genetics Comments: Erratum in: Nature. 2022 Jun;606(7915):E18. (PMID: 35701578) References: Rambaut, A. 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Grant Information: MC_PC_19012 United Kingdom MRC_ Medical Research Council; MC_UU_12014/12 United Kingdom MRC_ Medical Research Council; MC_PC_19026 United Kingdom MRC_ Medical Research Council; 21777 United Kingdom CRUK_ Cancer Research UK; 210758/Z/18/Z United Kingdom WT_ Wellcome Trust; MC_PC_19027 United Kingdom MRC_ Medical Research Council; 204911/Z/16/Z United Kingdom WT_ Wellcome Trust; 220885/Z/20/Z United Kingdom WT_ Wellcome Trust; United Kingdom WT_ Wellcome Trust; 210818/Z/18/Z United Kingdom WT_ Wellcome Trust; MR/R015600/1 United Kingdom MRC_ Medical Research Council Contributed Indexing: Investigator: I Abnizova; L Aigrain; A Alderton; M Ali; L Allen; R Amato; R Anderson; C Ariani; S Austin-Guest; S Bala; J Barrett; A Bassett; K Battleday; J Beal; M Beale; C Beaver; S Bellany; T Bellerby; K Bellis; D Berger; M Berriman; E Betteridge; P Bevan; S Binley; J Bishop; K Blackburn; J Bonfield; N Boughton; S Bowker; T Brendler-Spaeth; I Bronner; T Brooklyn; SK Buddenborg; R Bush; C Caetano; A Cagan; N Carter; J Cartwright; TC Monteiro; L Chapman; TJ Chillingworth; P Clapham; R Clark; A Clarke; C Clarke; D Cole; E Cook; M Coppola; L Cornell; C Cornwell; C Corton; A Crackett; A Cranage; H Craven; S Craw; M Crawford; T Cutts; M Dabrowska; M Davies; R Davies; J Dawson; C Day; A Densem; T Dibling; C Dockree; D Dodd; S Dogga; M Dorman; G Dougan; M Dougherty; A Dove; L Drummond; E Drury; M Dudek; J Durham; L Durrant; E Easthope; S Eckert; P Ellis; B Farr; M Fenton; M Ferrero; N Flack; H Fordham; G Forsythe; L Foulser; M Francis; A Fraser; A Freeman; A Galvin; M Garcia-Casado; A Gedny; S Girgis; J Glover; S Goncalves; S Goodwin; O Gould; M Gourtovaia; A Gray; E Gray; C Griffiths; Y Gu; F Guerin; W Hamilton; H Hanks; E Harrison; A Harrott; E Harry; J Harvison; P Heath; A Hernandez-Koutoucheva; R Hobbs; D Holland; S Holmes; G Hornett; N Hough; L Huckle; L Hughes-Hallet; A Hunter; S Inglis; S Iqbal; A Jackson; D Jackson; K James; D Jamrozy; CJ Verdejo; M Jones; K Kallepally; L Kane; K Kay; S Kay; J Keatley; A Keith; A King; L Kitchin; M Kleanthous; M Klimekova; P Korlevic; K Krasheninnkova; G Lane; C Langford; A Laverack; K Law; M Lawniczak; S Lensing; S Leonard; L Letchford; K Lewis; A Lewis-Wade; J Liddle; Q Lin; S Lindsay; S Linsdell; R Livett; S Lo; R Long; J Lovell; J Lovell; C Ludden; J Mack; M Maddison; A Makunin; I Mamun; J Mansfield; N Marriott; M Martin; M Mayho; S McCarthy; J McClintock; S McGuigan; S McHugh; L McMinn; C Meadows; E Mobley; R Moll; M Morra; L Morrow; K Murie; S Nash; C Nathwani; P Naydenova; A Neaverson; R Nelson; E Nerou; J Nicholson; T Nimz; GG Noell; S O'Meara; V Ohan; K Oliver; C Olney; D Ormond; A Oszlanczi; S Palmer; YF Pang; B Pardubska; N Park; A Parmar; G Patel; M Patel; M Payne; S Peacock; A Petersen; D Plowman; T Preston; L Prestwood; C Puethe; M Quail; D Rajan; S Rajatileka; R Rance; S Rawlings; N Redshaw; J Reynolds; M Reynolds; S Rice; M Richardson; C Roberts; K Robinson; M Robinson; D Robinson; H Rogers; EM Rojo; D Roopra; 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JP McKenna; B Warne; JF Taylor; Y Chaudhry; R Izuagbe; AS Jahun; GR Young; C McMurray; CM McCann; A Nelson; S Elliott; H Lowe; A Price; MR Crown; S Rey; S Roy; B Temperton; S Shaaban; AR Hesketh; KG Laing; IM Monahan; J Heaney; E Pelosi; S Silviera; E Wilson-Davies; H Fryer; H Adams; L du Plessis; R Johnson; WT Harvey; J Hughes; RJ Orton; LG Spurgin; Y Bourgeois; C Ruis; Á O'Toole; T Sanderson; C Fraser; J Edgeworth; J Breuer; SL Michell; JA Todd; M John; D Buck; K Gajee; GL Kay; SJ Peacock; D Heyburn; K Kitchman; A McNally; DT Pritchard; S Dervisevic; P Muir; E Robinson; BB Vipond; NA Ramadan; C Jeanes; J Catalan; N Jones; A da Silva Filipe; C Williams; M Fuchs; J Miskelly; AR Jeffries; NR Park; A Ash; C Koshy; M Barrow; SL Buchan; A Mantzouratou; G Clark; CW Holmes; S Campbell; T Davis; NK Tan; JR Brown; KA Harris; SP Kidd; PR Grant; L Xu-McCrae; A Cox; P Madona; M Pond; PA Randell; KT Withell; C Williams; C Graham; R Denton-Smith; E Swindells; R Turnbull; TJ Sloan; A Bosworth; S Hutchings; HM Pymont; A Casey; L Ratcliffe; CR Jones; BA Knight; T Haque; J Hart; D Irish-Tavares; E Witele; C Mower; LK Watson; J Collins; G Eltringham; D Crudgington; B Macklin; M Iturriza-Gomara; AO Lucaci; PC McClure; M Carlile; N Holmes; C Moore; N Storey; S Rooke; G Yebra; N Craine; M Perry; NF Alikhan; S Bridgett; KF Cook; C Fearn; S Goudarzi; RA Lyons; T Williams; ST Haldenby; RM Davies; R Batra; B Blane; MJ Spyer; P Smith; M Yavus; RJ Williams; AIK Mahanama; B Samaraweera; ST Girgis; SE Hansford; A Green; KL Bellis; MJ Dorman; J Quick; R Poplawski; N Reynolds; A Mack; A Morriss; T Whalley; B Patel; I Georgana; M Hosmillo; ML Pinckert; J Stockton; JH Henderson; A Hollis; W Stanley; WC Yew; R Myers; A Thornton; A Adams; T Annett; H Asad; A Birchley; J Coombes; JM Evans; L Fina; B Gatica-Wilcox; L Gilbert; L Graham; J Hey; E Hilvers; S Jones; H Jones; S Kumziene-Summerhayes; C McKerr; J Powell; G Pugh; S Taylor; AJ Trotter; CA Williams; LM Kermack; BH Foulkes; M Gallis; HR Hornsby; SF Louka; M Pohare; P Wolverson; P Zhang; G MacIntyre-Cockett; A Trebes; RJ Moll; L Ferguson; EJ Goldstein; A Maclean; R Tomb; I Starinskij; L Thomson; J Southgate; MUG Kraemer; J Raghwani; AE Zarebski; O Boyd; L Geidelberg; CJ Illingworth; C Jackson; D Pascall; S Vattipally; TM Freeman; SN Hsu; BB Lindsey; JM Tovar-Corona; M Cox; K Abudahab; M Menegazzo; BEW Taylor; CA Yeats; A Mukaddas; DW Wright; L de Oliveira Martins; R Colquhoun; V Hill; B Jackson; JT McCrone; N Medd; E Scher; JP Keatley; T Curran; S Morgan; P Maxwell; K Smith; S Eldirdiri; A Kenyon; AH Holmes; JR Price; T Wyatt; AE Mather; T Skvortsov; JA Hartley; M Guest; C Kitchen; I Merrick; R Munn; B Bertolusso; J Lynch; G Vernet; S Kirk; E Wastnedge; R Stanley; G Idle; DT Bradley; J Poyner; M Mori; O Jones; V Wright; E Brooks; CM Churcher; M Fragakis; K Galai; A Jermy; S Judges; GM McManus; KS Smith; E Westwick; SW Attwood; F Bolt; A Davies; E De Lacy; F Downing; S Edwards; L Meadows; S Jeremiah; N Smith; T Charalampous; A Patel; L Berry; T Boswell; VM Fleming; HC Howson-Wells; A Joseph; M Khakh; MM Lister; PW Bird; K Fallon; T Helmer; CL McMurray; M Odedra; J Shaw; JW Tang; NJ Willford; V Blakey; V Raviprakash; N Sheriff; LA Williams; T Feltwell; L Bedford; JS Cargill; W Hughes; J Moore; S Stonehouse; L Atkinson; JCD Lee; D Shah; A Alcolea; N Ohemeng-Kumi; J Ramble; J Sehmi; R Williams; W Chatterton; M Pusok; W Everson; A Castigador; E Macnaughton; K El Bouzidi; T Lampejo; M Sudhanva; C Breen; G Sluga; SSY Ahmad; RP George; NW Machin; D Binns; V James; R Blacow; L Coupland; L Smith; E Barton; D Padgett; G Scott; A Cross; M Mirfenderesky; J Greenaway; K Cole; P Clarke; N Duckworth; S Walsh; K Bicknell; R Impey; S Wyllie; R Hopes; C Bishop; V Chalker; L Gifford; Z Molnar; C Auckland; C Evans; K Johnson; DG Partridge; M Raza; P Baker; S Bonner; S Essex; LJ Murray; AI Lawton; S Burton-Fanning; BAI Payne; S Waugh; AN Gomes; M Kimuli; DR Murray; P Ashfield; D Dobie; F Ashford; A Best; L Crawford; N Cumley; M Mayhew; O Megram; J Mirza; E Moles-Garcia; B Percival; L Ensell; HL Lowe; L Maftei; M Mondani; NJ Chaloner; BJ Cogger; LJ Easton; H Huckson; J Lewis; S Lowdon; CS Malone; F Munemo; M Mutingwende; R Nicodemi; O Podplomyk; T Somassa; A Beggs; A Richter; C Cormie; J Dias; S Forrest; EE Higginson; M Maes; J Young; RK Davidson; KA Jackson; L Turtle; AJ Keeley; J Ball; T Byaruhanga; JG Chappell; J Dey; JD Hill; EJ Park; A Fanaie; RA Hilson; G Yaze; S Afifi; R Beer; J Maksimovic; KM Masters; K Spellman; C Bresner; W Fuller; A Marchbank; T Workman; E Shelest; J Debebe; F Sang; ME Zamudio; S Francois; B Gutierrez; TI Vasylyeva; F Flaviani; M Ragonnet-Cronin; KL Smollett; A Broos; D Mair; J Nichols; K Nomikou; L Tong; I Tsatsani; S O'Brien; S Rushton; R Sanderson; J Perkins; S Cotton; A Gallagher; E Allara; C Pearson; D Bibby; G Dabrera; N Ellaby; E Gallagher; J Hubb; A Lackenby; D Lee; N Manesis; T Mbisa; S Platt; KA Twohig; M Morgan; A Aydin; DJ Baker; E Foster-Nyarko; SJ Prosolek; S Rudder; C Baxter; SF Carvalho; D Lavin; A Mariappan; C Radulescu; A Singh; M Tang; H Morcrette; N Bayzid; M Cotic; CE Balcazar; MD Gallagher; D Maloney; TD Stanton; KA Williamson; R Manley; ML Michelsen; CM Sambles; DJ Studholme; J Warwick-Dugdale; R Eccles; M Gemmell; R Gregory; M Hughes; C Nelson; L Rainbow; EE Vamos; HJ Webster; M Whitehead; C Wierzbicki; A Angyal; LR Green; M Whiteley; IF Bronner; BW Farr; SV Lensing; SA McCarthy; MA Quail; NM Redshaw; SAJ Thurston; W Rowe; A Gaskin; T Le-Viet; J Liddle Substance Nomenclature: 0 (Spike Glycoprotein, Coronavirus) SCR Organism: SARS-CoV-2 variants Entry Date(s): Date Created: 20211014 Date Completed: 20220111 Latest Revision: 20240214 Update Code: 20240214 PubMed Central ID: PMC8674138

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Genomic reconstruction of the SARS-CoV-2 epidemic in England.