Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.
COVID-19
SARS-CoV-2
epidemiology
evolution
founder effect
spike
Journal
Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066
Informations de publication
Date de publication:
07 01 2021
07 01 2021
Historique:
received:
21
08
2020
revised:
14
10
2020
accepted:
11
11
2020
pubmed:
5
12
2020
medline:
16
1
2021
entrez:
4
12
2020
Statut:
ppublish
Résumé
Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant.
Identifiants
pubmed: 33275900
pii: S0092-8674(20)31537-3
doi: 10.1016/j.cell.2020.11.020
pmc: PMC7674007
pii:
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Aspartic Acid
30KYC7MIAI
Glycine
TE7660XO1C
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
64-75.e11Subventions
Organisme : Medical Research Council
ID : MC_PC_19012
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_19026
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/L015080/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S035362/1
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 : Medical Research Council
ID : MR/S00291X/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/M009157/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/M006212/1
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Department of Health
ID : RP-PG-0514-20018
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/M501621/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/J014370/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_12014/3
Pays : United Kingdom
Investigateurs
Cherian Koshy
(C)
Emma Wise
(E)
Nick Cortes
(N)
Jessica Lynch
(J)
Stephen Kidd
(S)
Matilde Mori
(M)
Derek J Fairley
(DJ)
Tanya Curran
(T)
James P McKenna
(JP)
Helen Adams
(H)
Christophe Fraser
(C)
Tanya Golubchik
(T)
David Bonsall
(D)
Catrin Moore
(C)
Sarah L Caddy
(SL)
Fahad A Khokhar
(FA)
Michelle Wantoch
(M)
Nicola Reynolds
(N)
Ben Warne
(B)
Joshua Maksimovic
(J)
Karla Spellman
(K)
Kathryn McCluggage
(K)
Michaela John
(M)
Robert Beer
(R)
Safiah Afifi
(S)
Sian Morgan
(S)
Angela Marchbank
(A)
Anna Price
(A)
Christine Kitchen
(C)
Huw Gulliver
(H)
Ian Merrick
(I)
Joel Southgate
(J)
Martyn Guest
(M)
Robert Munn
(R)
Trudy Workman
(T)
Thomas R Connor
(TR)
William Fuller
(W)
Catherine Bresner
(C)
Luke B Snell
(LB)
Themoula Charalampous
(T)
Gaia Nebbia
(G)
Rahul Batra
(R)
Jonathan Edgeworth
(J)
Samuel C Robson
(SC)
Angela Beckett
(A)
Katie F Loveson
(KF)
David M Aanensen
(DM)
Anthony P Underwood
(AP)
Corin A Yeats
(CA)
Khalil Abudahab
(K)
Ben E W Taylor
(BEW)
Mirko Menegazzo
(M)
Gemma Clark
(G)
Wendy Smith
(W)
Manjinder Khakh
(M)
Vicki M Fleming
(VM)
Michelle M Lister
(MM)
Hannah C Howson-Wells
(HC)
Louise Berry
(L)
Tim Boswell
(T)
Amelia Joseph
(A)
Iona Willingham
(I)
Paul Bird
(P)
Thomas Helmer
(T)
Karlie Fallon
(K)
Christopher Holmes
(C)
Julian Tang
(J)
Veena Raviprakash
(V)
Sharon Campbell
(S)
Nicola Sheriff
(N)
Matthew W Loose
(MW)
Nadine Holmes
(N)
Christopher Moore
(C)
Matthew Carlile
(M)
Victoria Wright
(V)
Fei Sang
(F)
Johnny Debebe
(J)
Francesc Coll
(F)
Adrian W Signell
(AW)
Gilberto Betancor
(G)
Harry D Wilson
(HD)
Theresa Feltwell
(T)
Charlotte J Houldcroft
(CJ)
Sahar Eldirdiri
(S)
Anita Kenyon
(A)
Thomas Davis
(T)
Oliver Pybus
(O)
Louis du Plessis
(L)
Alex Zarebski
(A)
Jayna Raghwani
(J)
Moritz Kraemer
(M)
Sarah Francois
(S)
Stephen Attwood
(S)
Tetyana Vasylyeva
(T)
M Estee Torok
(ME)
William L Hamilton
(WL)
Ian G Goodfellow
(IG)
Grant Hall
(G)
Aminu S Jahun
(AS)
Yasmin Chaudhry
(Y)
Myra Hosmillo
(M)
Malte L Pinckert
(ML)
Iliana Georgana
(I)
Anna Yakovleva
(A)
Luke W Meredith
(LW)
Samuel Moses
(S)
Hannah Lowe
(H)
Felicity Ryan
(F)
Chloe L Fisher
(CL)
Ali R Awan
(AR)
John Boyes
(J)
Judith Breuer
(J)
Kathryn Ann Harris
(KA)
Julianne Rose Brown
(JR)
Divya Shah
(D)
Laura Atkinson
(L)
Jack C D Lee
(JCD)
Adela Alcolea-Medina
(A)
Nathan Moore
(N)
Nicholas Cortes
(N)
Rebecca Williams
(R)
Michael R Chapman
(MR)
Lisa J Levett
(LJ)
Judith Heaney
(J)
Darren L Smith
(DL)
Matthew Bashton
(M)
Gregory R Young
(GR)
John Allan
(J)
Joshua Loh
(J)
Paul A Randell
(PA)
Alison Cox
(A)
Pinglawathee Madona
(P)
Alison Holmes
(A)
Frances Bolt
(F)
James Price
(J)
Siddharth Mookerjee
(S)
Aileen Rowan
(A)
Graham P Taylor
(GP)
Manon Ragonnet-Cronin
(M)
Fabricia F Nascimento
(FF)
David Jorgensen
(D)
Igor Siveroni
(I)
Rob Johnson
(R)
Olivia Boyd
(O)
Lily Geidelberg
(L)
Erik M Volz
(EM)
Kirstyn Brunker
(K)
Katherine L Smollett
(KL)
Nicholas J Loman
(NJ)
Joshua Quick
(J)
Claire McMurray
(C)
Joanne Stockton
(J)
Sam Nicholls
(S)
Will Rowe
(W)
Radoslaw Poplawski
(R)
Rocio T Martinez-Nunez
(RT)
Jenifer Mason
(J)
Trevor I Robinson
(TI)
Elaine O'Toole
(E)
Joanne Watts
(J)
Cassie Breen
(C)
Angela Cowell
(A)
Catherine Ludden
(C)
Graciela Sluga
(G)
Nicholas W Machin
(NW)
Shazaad S Y Ahmad
(SSY)
Ryan P George
(RP)
Fenella Halstead
(F)
Venkat Sivaprakasam
(V)
Emma C Thomson
(EC)
James G Shepherd
(JG)
Patawee Asamaphan
(P)
Marc O Niebel
(MO)
Kathy K Li
(KK)
Rajiv N Shah
(RN)
Natasha G Jesudason
(NG)
Yasmin A Parr
(YA)
Lily Tong
(L)
Alice Broos
(A)
Daniel Mair
(D)
Jenna Nichols
(J)
Stephen N Carmichael
(SN)
Kyriaki Nomikou
(K)
Elihu Aranday-Cortes
(E)
Natasha Johnson
(N)
Igor Starinskij
(I)
Ana da Silva Filipe
(A)
David L Robertson
(DL)
Richard J Orton
(RJ)
Joseph Hughes
(J)
Sreenu Vattipally
(S)
Joshua B Singer
(JB)
Antony D Hale
(AD)
Louissa R Macfarlane-Smith
(LR)
Katherine L Harper
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Yusri Taha
(Y)
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Shirelle Burton-Fanning
(S)
Sheila Waugh
(S)
Jennifer Collins
(J)
Gary Eltringham
(G)
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Rachael Stanley
(R)
Reenesh Prakash
(R)
Claire Stuart
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Ngozi Elumogo
(N)
Dheeraj K Sethi
(DK)
Emma J Meader
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Edward Barton
(E)
Debra Padgett
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Garren Scott
(G)
Emma Swindells
(E)
Jane Greenaway
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Andrew Nelson
(A)
Wen C Yew
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Paola C Resende Silva
(PC)
Monique Andersson
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Robert Shaw
(R)
Timothy Peto
(T)
Anita Justice
(A)
David Eyre
(D)
Derrick Crooke
(D)
Sarah Hoosdally
(S)
Tim J Sloan
(TJ)
Nichola Duckworth
(N)
Sarah Walsh
(S)
Anoop J Chauhan
(AJ)
Sharon Glaysher
(S)
Kelly Bicknell
(K)
Sarah Wyllie
(S)
Ethan Butcher
(E)
Scott Elliott
(S)
Allyson Lloyd
(A)
Robert Impey
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Nick Levene
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Lynn Monaghan
(L)
Declan T Bradley
(DT)
Elias Allara
(E)
Clare Pearson
(C)
Peter Muir
(P)
Ian B Vipond
(IB)
Richard Hopes
(R)
Hannah M Pymont
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Stephanie Hutchings
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Martin D Curran
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Surendra Parmar
(S)
Angie Lackenby
(A)
Tamyo Mbisa
(T)
Steven Platt
(S)
Shahjahan Miah
(S)
David Bibby
(D)
Carmen Manso
(C)
Jonathan Hubb
(J)
Meera Chand
(M)
Gavin Dabrera
(G)
Mary Ramsay
(M)
Daniel Bradshaw
(D)
Alicia Thornton
(A)
Richard Myers
(R)
Ulf Schaefer
(U)
Natalie Groves
(N)
Eileen Gallagher
(E)
David Lee
(D)
David Williams
(D)
Nicholas Ellaby
(N)
Ian Harrison
(I)
Hassan Hartman
(H)
Nikos Manesis
(N)
Vineet Patel
(V)
Chloe Bishop
(C)
Vicki Chalker
(V)
Husam Osman
(H)
Andrew Bosworth
(A)
Esther Robinson
(E)
Matthew T G Holden
(MTG)
Sharif Shaaban
(S)
Alec Birchley
(A)
Alexander Adams
(A)
Alisha Davies
(A)
Amy Gaskin
(A)
Amy Plimmer
(A)
Bree Gatica-Wilcox
(B)
Caoimhe McKerr
(C)
Catherine Moore
(C)
Chris Williams
(C)
David Heyburn
(D)
Elen De Lacy
(E)
Ember Hilvers
(E)
Fatima Downing
(F)
Giri Shankar
(G)
Hannah Jones
(H)
Hibo Asad
(H)
Jason Coombes
(J)
Joanne Watkins
(J)
Johnathan M Evans
(JM)
Laia Fina
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Laura Gifford
(L)
Lauren Gilbert
(L)
Lee Graham
(L)
Malorie Perry
(M)
Mari Morgan
(M)
Matthew Bull
(M)
Michelle Cronin
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Nicole Pacchiarini
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Noel Craine
(N)
Rachel Jones
(R)
Robin Howe
(R)
Sally Corden
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Sara Rey
(S)
Sara Kumziene-Summerhayes
(S)
Sarah Taylor
(S)
Simon Cottrell
(S)
Sophie Jones
(S)
Sue Edwards
(S)
Justin O'Grady
(J)
Andrew J Page
(AJ)
John Wain
(J)
Mark A Webber
(MA)
Alison E Mather
(AE)
David J Baker
(DJ)
Steven Rudder
(S)
Muhammad Yasir
(M)
Nicholas M Thomson
(NM)
Alp Aydin
(A)
Ana P Tedim
(AP)
Gemma L Kay
(GL)
Alexander J Trotter
(AJ)
Rachel A J Gilroy
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Nabil-Fareed Alikhan
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Thanh Le-Viet
(T)
Lizzie Meadows
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Anastasia Kolyva
(A)
Maria Diaz
(M)
Andrew Bell
(A)
Ana Victoria Gutierrez
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Ian G Charles
(IG)
Evelien M Adriaenssens
(EM)
Robert A Kingsley
(RA)
Anna Casey
(A)
David A Simpson
(DA)
Zoltan Molnar
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Thomas Thompson
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Erwan Acheson
(E)
Jane A H Masoli
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Bridget A Knight
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Andrew Hattersley
(A)
Sian Ellard
(S)
Cressida Auckland
(C)
Tabitha W Mahungu
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Dianne Irish-Tavares
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Tanzina Haque
(T)
Yann Bourgeois
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Garry P Scarlett
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David G Partridge
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Mohammad Raza
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Cariad Evans
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Kate Johnson
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Steven Liggett
(S)
Paul Baker
(P)
Sarah Essex
(S)
Ronan A Lyons
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Laura G Caller
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Sergi Castellano
(S)
Rachel J Williams
(RJ)
Mark Kristiansen
(M)
Sunando Roy
(S)
Charlotte A Williams
(CA)
Patricia L Dyal
(PL)
Helena J Tutill
(HJ)
Yasmin N Panchbhaya
(YN)
Leysa M Forrest
(LM)
Paola Niola
(P)
Jacqueline Findlay
(J)
Tony T Brooks
(TT)
Artemis Gavriil
(A)
Lamia Mestek-Boukhibar
(L)
Sam Weeks
(S)
Sarojini Pandey
(S)
Lisa Berry
(L)
Katie Jones
(K)
Alex Richter
(A)
Andrew Beggs
(A)
Colin P Smith
(CP)
Giselda Bucca
(G)
Andrew R Hesketh
(AR)
Ewan M Harrison
(EM)
Sharon J Peacock
(SJ)
Sophie Palmer
(S)
Carol M Churcher
(CM)
Katherine L Bellis
(KL)
Sophia T Girgis
(ST)
Plamena Naydenova
(P)
Beth Blane
(B)
Sushmita Sridhar
(S)
Chris Ruis
(C)
Sally Forrest
(S)
Claire Cormie
(C)
Harmeet K Gill
(HK)
Joana Dias
(J)
Ellen E Higginson
(EE)
Mailis Maes
(M)
Jamie Young
(J)
Leanne M Kermack
(LM)
Nazreen F Hadjirin
(NF)
Dinesh Aggarwal
(D)
Luke Griffith
(L)
Tracey Swingler
(T)
Rose K Davidson
(RK)
Andrew Rambaut
(A)
Thomas Williams
(T)
Carlos E Balcazar
(CE)
Michael D Gallagher
(MD)
Áine O'Toole
(Á)
Stefan Rooke
(S)
Ben Jackson
(B)
Rachel Colquhoun
(R)
Jordan Ashworth
(J)
Verity Hill
(V)
J T McCrone
(JT)
Emily Scher
(E)
Xiaoyu Yu
(X)
Kathleen A Williamson
(KA)
Thomas D Stanton
(TD)
Stephen L Michell
(SL)
Claire M Bewshea
(CM)
Ben Temperton
(B)
Michelle L Michelsen
(ML)
Joanna Warwick-Dugdale
(J)
Robin Manley
(R)
Audrey Farbos
(A)
James W Harrison
(JW)
Christine M Sambles
(CM)
David J Studholme
(DJ)
Aaron R Jeffries
(AR)
Alistair C Darby
(AC)
Julian A Hiscox
(JA)
Steve Paterson
(S)
Miren Iturriza-Gomara
(M)
Kathryn A Jackson
(KA)
Anita O Lucaci
(AO)
Edith E Vamos
(EE)
Margaret Hughes
(M)
Lucille Rainbow
(L)
Richard Eccles
(R)
Charlotte Nelson
(C)
Mark Whitehead
(M)
Lance Turtle
(L)
Sam T Haldenby
(ST)
Richard Gregory
(R)
Matthew Gemmell
(M)
Dominic Kwiatkowski
(D)
Thushan I de Silva
(TI)
Nikki Smith
(N)
Adrienn Angyal
(A)
Benjamin B Lindsey
(BB)
Danielle C Groves
(DC)
Luke R Green
(LR)
Dennis Wang
(D)
Timothy M Freeman
(TM)
Matthew D Parker
(MD)
Alexander J Keeley
(AJ)
Paul J Parsons
(PJ)
Rachel M Tucker
(RM)
Rebecca Brown
(R)
Matthew Wyles
(M)
Chrystala Constantinidou
(C)
Meera Unnikrishnan
(M)
Sascha Ott
(S)
Jeffrey K J Cheng
(JKJ)
Hannah E Bridgewater
(HE)
Lucy R Frost
(LR)
Grace Taylor-Joyce
(G)
Richard Stark
(R)
Laura Baxter
(L)
Mohammad T Alam
(MT)
Paul E Brown
(PE)
Patrick C McClure
(PC)
Joseph G Chappell
(JG)
Theocharis Tsoleridis
(T)
Jonathan Ball
(J)
Dimitris Grammatopoulos
(D)
David Buck
(D)
John A Todd
(JA)
Angie Green
(A)
Amy Trebes
(A)
George MacIntyre-Cockett
(G)
Mariateresa de Cesare
(M)
Cordelia Langford
(C)
Alex Alderton
(A)
Roberto Amato
(R)
Sonia Goncalves
(S)
David K Jackson
(DK)
Ian Johnston
(I)
John Sillitoe
(J)
Steve Palmer
(S)
Mara Lawniczak
(M)
Matt Berriman
(M)
John Danesh
(J)
Rich Livett
(R)
Lesley Shirley
(L)
Ben Farr
(B)
Mike Quail
(M)
Scott Thurston
(S)
Naomi Park
(N)
Emma Betteridge
(E)
Danni Weldon
(D)
Scott Goodwin
(S)
Rachel Nelson
(R)
Charlotte Beaver
(C)
Laura Letchford
(L)
David A Jackson
(DA)
Luke Foulser
(L)
Liz McMinn
(L)
Liam Prestwood
(L)
Sally Kay
(S)
Leanne Kane
(L)
Matthew J Dorman
(MJ)
Inigo Martincorena
(I)
Christoph Puethe
(C)
Jon-Paul Keatley
(JP)
Gerry Tonkin-Hill
(G)
Christen Smith
(C)
Dorota Jamrozy
(D)
Mathew A Beale
(MA)
Minal Patel
(M)
Cristina Ariani
(C)
Michael Spencer-Chapman
(M)
Eleanor Drury
(E)
Stephanie Lo
(S)
Shavanthi Rajatileka
(S)
Carol Scott
(C)
Keith James
(K)
Sarah K Buddenborg
(SK)
Duncan J Berger
(DJ)
Gaurang Patel
(G)
Maria V Garcia-Casado
(MV)
Thomas Dibling
(T)
Samantha McGuigan
(S)
Hazel A Rogers
(HA)
Adam D Hunter
(AD)
Emily Souster
(E)
Alexandra S Neaverson
(AS)
Informations de copyright
Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Interests The authors declare no competing interests.
Références
EBioMedicine. 2020 Dec;62:103112
pubmed: 33186810
Virus Evol. 2018 Jun 08;4(1):vey016
pubmed: 29942656
J Mol Evol. 1985;22(2):160-74
pubmed: 3934395
Syst Biol. 2018 Sep 1;67(5):901-904
pubmed: 29718447
Wellcome Open Res. 2020 Apr 9;5:67
pubmed: 32685698
PLoS Comput Biol. 2019 Apr 8;15(4):e1006650
pubmed: 30958812
Nat Commun. 2020 Nov 2;11(1):5518
pubmed: 33139704
J Virol. 2015 Feb;89(4):1954-64
pubmed: 25428871
Nature. 2020 Aug;584(7820):257-261
pubmed: 32512579
PLoS Comput Biol. 2018 Nov 13;14(11):e1006546
pubmed: 30422979
Proc Natl Acad Sci U S A. 2020 Sep 22;117(38):23652-23662
pubmed: 32868447
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Virus Evol. 2020 Aug 19;6(2):veaa061
pubmed: 33235813
Nat Commun. 2020 May 27;11(1):2688
pubmed: 32461612
Science. 2005 Sep 16;309(5742):1864-8
pubmed: 16166518
Science. 2020 Jul 24;369(6502):413-422
pubmed: 32532802
Cell. 2020 Aug 20;182(4):794-795
pubmed: 32697970
Microb Genom. 2016 Sep 20;2(9):e000086
pubmed: 28785418
Lancet Microbe. 2020 Jul;1(3):e99-e100
pubmed: 32835336
Cell. 2020 Aug 20;182(4):812-827.e19
pubmed: 32697968
Bioinformatics. 2019 Feb 1;35(3):526-528
pubmed: 30016406
Nature. 2020 May;581(7809):465-469
pubmed: 32235945
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5871-6
pubmed: 19321428
Nat Commun. 2020 Nov 25;11(1):5986
pubmed: 33239633
Viruses. 2020 Jul 24;12(8):
pubmed: 32722343
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
JAMA. 2020 May 12;323(18):1775-1776
pubmed: 32203977
Nat Med. 2020 Aug;26(8):1205-1211
pubmed: 32546824
Syst Biol. 2018 Jul 1;67(4):719-728
pubmed: 29432602
J Gen Virol. 2014 Mar;95(Pt 3):614-626
pubmed: 24362959
Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15214-9
pubmed: 25288733
Nature. 2020 Oct 26;:
pubmed: 33106671
Bioinformatics. 2004 Jan 22;20(2):289-90
pubmed: 14734327
Nat Rev Genet. 2009 Aug;10(8):540-50
pubmed: 19564871
N Engl J Med. 2020 Mar 5;382(10):970-971
pubmed: 32003551
Science. 2020 Dec 18;370(6523):1464-1468
pubmed: 33184236
Nucleic Acids Res. 1996 Jan 1;24(1):6-12
pubmed: 8594602
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Nature. 2020 Mar;579(7798):265-269
pubmed: 32015508