Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Amino Acid Substitution
COVID-19
/ epidemiology
England
/ epidemiology
Epidemiological Monitoring
Genome, Viral
/ genetics
Genomics
Humans
Molecular Epidemiology
Mutation
Quarantine
/ statistics & numerical data
SARS-CoV-2
/ classification
Spatio-Temporal Analysis
Spike Glycoprotein, Coronavirus
/ genetics
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
12 2021
12 2021
Historique:
received:
22
05
2021
accepted:
29
09
2021
pubmed:
15
10
2021
medline:
12
1
2022
entrez:
14
10
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 34649268
doi: 10.1038/s41586-021-04069-y
pii: 10.1038/s41586-021-04069-y
pmc: PMC8674138
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
506-511Subventions
Organisme : Medical Research Council
ID : MC_PC_19012
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_12014/12
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_19026
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 210758/Z/18/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_19027
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 204911/Z/16/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 220885/Z/20/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 210818/Z/18/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Investigateurs
Irina Abnizova
(I)
Louise Aigrain
(L)
Alex Alderton
(A)
Mozam Ali
(M)
Laura Allen
(L)
Roberto Amato
(R)
Ralph Anderson
(R)
Cristina Ariani
(C)
Siobhan Austin-Guest
(S)
Sendu Bala
(S)
Jeffrey Barrett
(J)
Andrew Bassett
(A)
Kristina Battleday
(K)
James Beal
(J)
Mathew Beale
(M)
Charlotte Beaver
(C)
Sam Bellany
(S)
Tristram Bellerby
(T)
Katie Bellis
(K)
Duncan Berger
(D)
Matt Berriman
(M)
Emma Betteridge
(E)
Paul Bevan
(P)
Simon Binley
(S)
Jason Bishop
(J)
Kirsty Blackburn
(K)
James Bonfield
(J)
Nick Boughton
(N)
Sam Bowker
(S)
Timothy Brendler-Spaeth
(T)
Iraad Bronner
(I)
Tanya Brooklyn
(T)
Sarah Kay Buddenborg
(SK)
Robert Bush
(R)
Catarina Caetano
(C)
Alex Cagan
(A)
Nicola Carter
(N)
Joanna Cartwright
(J)
Tiago Carvalho Monteiro
(TC)
Liz Chapman
(L)
Tracey-Jane Chillingworth
(TJ)
Peter Clapham
(P)
Richard Clark
(R)
Adrian Clarke
(A)
Catriona Clarke
(C)
Daryl Cole
(D)
Elizabeth Cook
(E)
Maria Coppola
(M)
Linda Cornell
(L)
Clare Cornwell
(C)
Craig Corton
(C)
Abby Crackett
(A)
Alison Cranage
(A)
Harriet Craven
(H)
Sarah Craw
(S)
Mark Crawford
(M)
Tim Cutts
(T)
Monika Dabrowska
(M)
Matt Davies
(M)
Robert Davies
(R)
Joseph Dawson
(J)
Callum Day
(C)
Aiden Densem
(A)
Thomas Dibling
(T)
Cat Dockree
(C)
David Dodd
(D)
Sunil Dogga
(S)
Matthew Dorman
(M)
Gordon Dougan
(G)
Martin Dougherty
(M)
Alexander Dove
(A)
Lucy Drummond
(L)
Eleanor Drury
(E)
Monika Dudek
(M)
Jillian Durham
(J)
Laura Durrant
(L)
Elizabeth Easthope
(E)
Sabine Eckert
(S)
Pete Ellis
(P)
Ben Farr
(B)
Michael Fenton
(M)
Marcella Ferrero
(M)
Neil Flack
(N)
Howerd Fordham
(H)
Grace Forsythe
(G)
Luke Foulser
(L)
Matt Francis
(M)
Audrey Fraser
(A)
Adam Freeman
(A)
Anastasia Galvin
(A)
Maria Garcia-Casado
(M)
Alex Gedny
(A)
Sophia Girgis
(S)
James Glover
(J)
Sonia Goncalves
(S)
Scott Goodwin
(S)
Oliver Gould
(O)
Marina Gourtovaia
(M)
Andy Gray
(A)
Emma Gray
(E)
Coline Griffiths
(C)
Yong Gu
(Y)
Florence Guerin
(F)
Will Hamilton
(W)
Hannah Hanks
(H)
Ewan Harrison
(E)
Alexandria Harrott
(A)
Edward Harry
(E)
Julia Harvison
(J)
Paul Heath
(P)
Anastasia Hernandez-Koutoucheva
(A)
Rhiannon Hobbs
(R)
Dave Holland
(D)
Sarah Holmes
(S)
Gary Hornett
(G)
Nicholas Hough
(N)
Liz Huckle
(L)
Lena Hughes-Hallet
(L)
Adam Hunter
(A)
Stephen Inglis
(S)
Sameena Iqbal
(S)
Adam Jackson
(A)
David Jackson
(D)
Keith James
(K)
Dorota Jamrozy
(D)
Carlos Jimenez Verdejo
(CJ)
Matthew Jones
(M)
Kalyan Kallepally
(K)
Leanne Kane
(L)
Keely Kay
(K)
Sally Kay
(S)
Jon Keatley
(J)
Alan Keith
(A)
Alison King
(A)
Lucy Kitchin
(L)
Matt Kleanthous
(M)
Martina Klimekova
(M)
Petra Korlevic
(P)
Ksenia Krasheninnkova
(K)
Greg Lane
(G)
Cordelia Langford
(C)
Adam Laverack
(A)
Katharine Law
(K)
Mara Lawniczak
(M)
Stefanie Lensing
(S)
Steven Leonard
(S)
Laura Letchford
(L)
Kevin Lewis
(K)
Amanah Lewis-Wade
(A)
Jennifer Liddle
(J)
Quan Lin
(Q)
Sarah Lindsay
(S)
Sally Linsdell
(S)
Rich Livett
(R)
Stephanie Lo
(S)
Rhona Long
(R)
Jamie Lovell
(J)
Jon Lovell
(J)
Catherine Ludden
(C)
James Mack
(J)
Mark Maddison
(M)
Aleksei Makunin
(A)
Irfan Mamun
(I)
Jenny Mansfield
(J)
Neil Marriott
(N)
Matt Martin
(M)
Matthew Mayho
(M)
Shane McCarthy
(S)
Jo McClintock
(J)
Samantha McGuigan
(S)
Sandra McHugh
(S)
Liz McMinn
(L)
Carl Meadows
(C)
Emily Mobley
(E)
Robin Moll
(R)
Maria Morra
(M)
Leanne Morrow
(L)
Kathryn Murie
(K)
Sian Nash
(S)
Claire Nathwani
(C)
Plamena Naydenova
(P)
Alexandra Neaverson
(A)
Rachel Nelson
(R)
Ed Nerou
(E)
Jon Nicholson
(J)
Tabea Nimz
(T)
Guillaume G Noell
(GG)
Sarah O'Meara
(S)
Valeriu Ohan
(V)
Karen Oliver
(K)
Charles Olney
(C)
Doug Ormond
(D)
Agnes Oszlanczi
(A)
Steve Palmer
(S)
Yoke Fei Pang
(YF)
Barbora Pardubska
(B)
Naomi Park
(N)
Aaron Parmar
(A)
Gaurang Patel
(G)
Minal Patel
(M)
Maggie Payne
(M)
Sharon Peacock
(S)
Arabella Petersen
(A)
Deborah Plowman
(D)
Tom Preston
(T)
Liam Prestwood
(L)
Christoph Puethe
(C)
Michael Quail
(M)
Diana Rajan
(D)
Shavanthi Rajatileka
(S)
Richard Rance
(R)
Suzannah Rawlings
(S)
Nicholas Redshaw
(N)
Joe Reynolds
(J)
Mark Reynolds
(M)
Simon Rice
(S)
Matt Richardson
(M)
Connor Roberts
(C)
Katrina Robinson
(K)
Melanie Robinson
(M)
David Robinson
(D)
Hazel Rogers
(H)
Eduardo Martin Rojo
(EM)
Daljit Roopra
(D)
Mark Rose
(M)
Luke Rudd
(L)
Ramin Sadri
(R)
Nicholas Salmon
(N)
David Saul
(D)
Frank Schwach
(F)
Carol Scott
(C)
Phil Seekings
(P)
Lesley Shirley
(L)
Alison Simms
(A)
Matthew Sinnott
(M)
Shanthi Sivadasan
(S)
Bart Siwek
(B)
Dale Sizer
(D)
Kenneth Skeldon
(K)
Jason Skelton
(J)
Joanna Slater-Tunstill
(J)
Lisa Sloper
(L)
Nathalie Smerdon
(N)
Chris Smith
(C)
Christen Smith
(C)
James Smith
(J)
Katie Smith
(K)
Michelle Smith
(M)
Sean Smith
(S)
Tina Smith
(T)
Leighton Sneade
(L)
Carmen Diaz Soria
(CD)
Catarina Sousa
(C)
Emily Souster
(E)
Andrew Sparkes
(A)
Michael Spencer-Chapman
(M)
Janet Squares
(J)
Robert Stanley
(R)
Claire Steed
(C)
Tim Stickland
(T)
Ian Still
(I)
Michael R Stratton
(MR)
Michelle Strickland
(M)
Allen Swann
(A)
Agnieszka Swiatkowska
(A)
Neil Sycamore
(N)
Emma Swift
(E)
Edward Symons
(E)
Suzanne Szluha
(S)
Emma Taluy
(E)
Nunu Tao
(N)
Katy Taylor
(K)
Sam Taylor
(S)
Stacey Thompson
(S)
Mark Thompson
(M)
Mark Thomson
(M)
Nicholas Thomson
(N)
Scott Thurston
(S)
Gerry Tonkin-Hill
(G)
Dee Toombs
(D)
Benjamin Topping
(B)
Jaime Tovar-Corona
(J)
Daniel Ungureanu
(D)
James Uphill
(J)
Jana Urbanova
(J)
Philip Jansen Van Vuuren
(PJ)
Valerie Vancollie
(V)
Paul Voak
(P)
Danielle Walker
(D)
Matthew Walker
(M)
Matt Waller
(M)
Gary Ward
(G)
Charlie Weatherhogg
(C)
Niki Webb
(N)
Danni Weldon
(D)
Alan Wells
(A)
Eloise Wells
(E)
Luke Westwood
(L)
Theo Whipp
(T)
Thomas Whiteley
(T)
Georgia Whitton
(G)
Andrew Whitwham
(A)
Sara Widaa
(S)
Mia Williams
(M)
Mark Wilson
(M)
Sean Wright
(S)
Samuel C Robson
(SC)
Thomas R Connor
(TR)
Nicholas J Loman
(NJ)
Tanya Golubchik
(T)
Rocio T Martinez Nunez
(RT)
David Bonsall
(D)
Andrew Rambaut
(A)
Luke B Snell
(LB)
Catherine Ludden
(C)
Sally Corden
(S)
Eleni Nastouli
(E)
Gaia Nebbia
(G)
Katrina Lythgoe
(K)
M Estee Torok
(ME)
Ian G Goodfellow
(IG)
Jacqui A Prieto
(JA)
Kordo Saeed
(K)
Catherine Houlihan
(C)
Dan Frampton
(D)
William L Hamilton
(WL)
Adam A Witney
(AA)
Giselda Bucca
(G)
Cassie F Pope
(CF)
Catherine Moore
(C)
Emma C Thomson
(EC)
Ewan M Harrison
(EM)
Colin P Smith
(CP)
Fiona Rogan
(F)
Shaun M Beckwith
(SM)
Abigail Murray
(A)
Dawn Singleton
(D)
Kirstine Eastick
(K)
Liz A Sheridan
(LA)
Paul Randell
(P)
Leigh M Jackson
(LM)
Sónia Gonçalves
(S)
Derek J Fairley
(DJ)
Matthew W Loose
(MW)
Joanne Watkins
(J)
Samuel Moses
(S)
Sam Nicholls
(S)
Matthew Bull
(M)
Darren L Smith
(DL)
David M Aanensen
(DM)
Dinesh Aggarwal
(D)
James G Shepherd
(JG)
Martin D Curran
(MD)
Surendra Parmar
(S)
Matthew D Parker
(MD)
Catryn Williams
(C)
Sharon Glaysher
(S)
Anthony P Underwood
(AP)
Matthew Bashton
(M)
Nicole Pacchiarini
(N)
Katie F Loveson
(KF)
Matthew Byott
(M)
Alessandro M Carabelli
(AM)
Kate E Templeton
(KE)
Thushan I de Silva
(TI)
Dennis Wang
(D)
Cordelia F Langford
(CF)
Rory N Gunson
(RN)
Simon Cottrell
(S)
Justin O'Grady
(J)
Dominic Kwiatkowski
(D)
Patrick J Lillie
(PJ)
Nicholas Cortes
(N)
Nathan Moore
(N)
Claire Thomas
(C)
Phillipa J Burns
(PJ)
Tabitha W Mahungu
(TW)
Steven Liggett
(S)
Angela H Beckett
(AH)
Matthew T G Holden
(MTG)
Lisa J Levett
(LJ)
Husam Osman
(H)
Mohammed O Hassan-Ibrahim
(MO)
David A Simpson
(DA)
Meera Chand
(M)
Ravi K Gupta
(RK)
Alistair C Darby
(AC)
Steve Paterson
(S)
Oliver G Pybus
(OG)
Erik Volz
(E)
Daniela de Angelis
(D)
David L Robertson
(DL)
Andrew J Page
(AJ)
Andrew R Bassett
(AR)
Nick Wong
(N)
Yusri Taha
(Y)
Michelle J Erkiert
(MJ)
Michael H Spencer Chapman
(MH)
Rebecca Dewar
(R)
Martin P McHugh
(MP)
Siddharth Mookerjee
(S)
Stephen Aplin
(S)
Matthew Harvey
(M)
Thea Sass
(T)
Helen Umpleby
(H)
Helen Wheeler
(H)
James P McKenna
(JP)
Ben Warne
(B)
Joshua F Taylor
(JF)
Yasmin Chaudhry
(Y)
Rhys Izuagbe
(R)
Aminu S Jahun
(AS)
Gregory R Young
(GR)
Claire McMurray
(C)
Clare M McCann
(CM)
Andrew Nelson
(A)
Scott Elliott
(S)
Hannah Lowe
(H)
Anna Price
(A)
Matthew R Crown
(MR)
Sara Rey
(S)
Sunando Roy
(S)
Ben Temperton
(B)
Sharif Shaaban
(S)
Andrew R Hesketh
(AR)
Kenneth G Laing
(KG)
Irene M Monahan
(IM)
Judith Heaney
(J)
Emanuela Pelosi
(E)
Siona Silviera
(S)
Eleri Wilson-Davies
(E)
Helen Fryer
(H)
Helen Adams
(H)
Louis du Plessis
(L)
Rob Johnson
(R)
William T Harvey
(WT)
Joseph Hughes
(J)
Richard J Orton
(RJ)
Lewis G Spurgin
(LG)
Yann Bourgeois
(Y)
Chris Ruis
(C)
Áine O'Toole
(Á)
Theo Sanderson
(T)
Christophe Fraser
(C)
Jonathan Edgeworth
(J)
Judith Breuer
(J)
Stephen L Michell
(SL)
John A Todd
(JA)
Michaela John
(M)
David Buck
(D)
Kavitha Gajee
(K)
Gemma L Kay
(GL)
Sharon J Peacock
(SJ)
David Heyburn
(D)
Katie Kitchman
(K)
Alan McNally
(A)
David T Pritchard
(DT)
Samir Dervisevic
(S)
Peter Muir
(P)
Esther Robinson
(E)
Barry B Vipond
(BB)
Newara A Ramadan
(NA)
Christopher Jeanes
(C)
Jana Catalan
(J)
Neil Jones
(N)
Ana da Silva Filipe
(A)
Chris Williams
(C)
Marc Fuchs
(M)
Julia Miskelly
(J)
Aaron R Jeffries
(AR)
Naomi R Park
(NR)
Amy Ash
(A)
Cherian Koshy
(C)
Magdalena Barrow
(M)
Sarah L Buchan
(SL)
Anna Mantzouratou
(A)
Gemma Clark
(G)
Christopher W Holmes
(CW)
Sharon Campbell
(S)
Thomas Davis
(T)
Ngee Keong Tan
(NK)
Julianne R Brown
(JR)
Kathryn A Harris
(KA)
Stephen P Kidd
(SP)
Paul R Grant
(PR)
Li Xu-McCrae
(L)
Alison Cox
(A)
Pinglawathee Madona
(P)
Marcus Pond
(M)
Paul A Randell
(PA)
Karen T Withell
(KT)
Cheryl Williams
(C)
Clive Graham
(C)
Rebecca Denton-Smith
(R)
Emma Swindells
(E)
Robyn Turnbull
(R)
Tim J Sloan
(TJ)
Andrew Bosworth
(A)
Stephanie Hutchings
(S)
Hannah M Pymont
(HM)
Anna Casey
(A)
Liz Ratcliffe
(L)
Christopher R Jones
(CR)
Bridget A Knight
(BA)
Tanzina Haque
(T)
Jennifer Hart
(J)
Dianne Irish-Tavares
(D)
Eric Witele
(E)
Craig Mower
(C)
Louisa K Watson
(LK)
Jennifer Collins
(J)
Gary Eltringham
(G)
Dorian Crudgington
(D)
Ben Macklin
(B)
Miren Iturriza-Gomara
(M)
Anita O Lucaci
(AO)
Patrick C McClure
(PC)
Matthew Carlile
(M)
Nadine Holmes
(N)
Christopher Moore
(C)
Nathaniel Storey
(N)
Stefan Rooke
(S)
Gonzalo Yebra
(G)
Noel Craine
(N)
Malorie Perry
(M)
Nabil-Fareed Alikhan
(NF)
Stephen Bridgett
(S)
Kate F Cook
(KF)
Christopher Fearn
(C)
Salman Goudarzi
(S)
Ronan A Lyons
(RA)
Thomas Williams
(T)
Sam T Haldenby
(ST)
Robert M Davies
(RM)
Rahul Batra
(R)
Beth Blane
(B)
Moira J Spyer
(MJ)
Perminder Smith
(P)
Mehmet Yavus
(M)
Rachel J Williams
(RJ)
Adhyana I K Mahanama
(AIK)
Buddhini Samaraweera
(B)
Sophia T Girgis
(ST)
Samantha E Hansford
(SE)
Angie Green
(A)
Katherine L Bellis
(KL)
Matthew J Dorman
(MJ)
Joshua Quick
(J)
Radoslaw Poplawski
(R)
Nicola Reynolds
(N)
Andrew Mack
(A)
Arthur Morriss
(A)
Thomas Whalley
(T)
Bindi Patel
(B)
Iliana Georgana
(I)
Myra Hosmillo
(M)
Malte L Pinckert
(ML)
Joanne Stockton
(J)
John H Henderson
(JH)
Amy Hollis
(A)
William Stanley
(W)
Wen C Yew
(WC)
Richard Myers
(R)
Alicia Thornton
(A)
Alexander Adams
(A)
Tara Annett
(T)
Hibo Asad
(H)
Alec Birchley
(A)
Jason Coombes
(J)
Johnathan M Evans
(JM)
Laia Fina
(L)
Bree Gatica-Wilcox
(B)
Lauren Gilbert
(L)
Lee Graham
(L)
Jessica Hey
(J)
Ember Hilvers
(E)
Sophie Jones
(S)
Hannah Jones
(H)
Sara Kumziene-Summerhayes
(S)
Caoimhe McKerr
(C)
Jessica Powell
(J)
Georgia Pugh
(G)
Sarah Taylor
(S)
Alexander J Trotter
(AJ)
Charlotte A Williams
(CA)
Leanne M Kermack
(LM)
Benjamin H Foulkes
(BH)
Marta Gallis
(M)
Hailey R Hornsby
(HR)
Stavroula F Louka
(SF)
Manoj Pohare
(M)
Paige Wolverson
(P)
Peijun Zhang
(P)
George MacIntyre-Cockett
(G)
Amy Trebes
(A)
Robin J Moll
(RJ)
Lynne Ferguson
(L)
Emily J Goldstein
(EJ)
Alasdair Maclean
(A)
Rachael Tomb
(R)
Igor Starinskij
(I)
Laura Thomson
(L)
Joel Southgate
(J)
Moritz U G Kraemer
(MUG)
Jayna Raghwani
(J)
Alex E Zarebski
(AE)
Olivia Boyd
(O)
Lily Geidelberg
(L)
Chris J Illingworth
(CJ)
Chris Jackson
(C)
David Pascall
(D)
Sreenu Vattipally
(S)
Timothy M Freeman
(TM)
Sharon N Hsu
(SN)
Benjamin B Lindsey
(BB)
Jaime M Tovar-Corona
(JM)
MacGregor Cox
(M)
Khalil Abudahab
(K)
Mirko Menegazzo
(M)
Ben E W Taylor
(BEW)
Corin A Yeats
(CA)
Afrida Mukaddas
(A)
Derek W Wright
(DW)
Leonardo de Oliveira Martins
(L)
Rachel Colquhoun
(R)
Verity Hill
(V)
Ben Jackson
(B)
J T McCrone
(JT)
Nathan Medd
(N)
Emily Scher
(E)
Jon-Paul Keatley
(JP)
Tanya Curran
(T)
Sian Morgan
(S)
Patrick Maxwell
(P)
Ken Smith
(K)
Sahar Eldirdiri
(S)
Anita Kenyon
(A)
Alison H Holmes
(AH)
James R Price
(JR)
Tim Wyatt
(T)
Alison E Mather
(AE)
Timofey Skvortsov
(T)
John A Hartley
(JA)
Martyn Guest
(M)
Christine Kitchen
(C)
Ian Merrick
(I)
Robert Munn
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Commentaires et corrections
Type : ErratumIn
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