Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
08 02 2022
08 02 2022
Historique:
received:
19
05
2021
accepted:
17
12
2021
entrez:
9
2
2022
pubmed:
10
2
2022
medline:
19
2
2022
Statut:
epublish
Résumé
Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.
Identifiants
pubmed: 35136068
doi: 10.1038/s41467-021-27942-w
pii: 10.1038/s41467-021-27942-w
pmc: PMC8826310
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
751Subventions
Organisme : Medical Research Council
ID : MC_UU_12014/12
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_19026
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/N029399/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S00291X/1
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust (Wellcome)
ID : 222903/Z/21/Z
Organisme : Medical Research Council
ID : MR/P008801/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_00002/11
Pays : United Kingdom
Investigateurs
Alexandra Orton
(A)
Julie Douthwaite
(J)
Steve Rees
(S)
Christopher Brown
(C)
Roger Clark
(R)
Daniel R Jones
(DR)
Fred Kuenzi
(F)
Jennifer Rankin
(J)
Ian Waddell
(I)
Patrick Maxwell
(P)
Nicholas Matheson
(N)
Chris Abell
(C)
Vickie Braithwaite
(V)
Craig Brierley
(C)
Jon Crowcroft
(J)
Aastha Dahal
(A)
Kathryn Faulkner
(K)
Michael Glover
(M)
Ian Goodfellow
(I)
Jane Greatorex
(J)
Laura James
(L)
Paul Lehner
(P)
Ian Leslie
(I)
Kathleen Liddell
(K)
Ben Margolis
(B)
Sally Morgan
(S)
Linda Sheridan
(L)
Sally Valletta
(S)
Anna Vignoles
(A)
Martin Vinnell
(M)
Mark Wills
(M)
Sarah Hilborne
(S)
Sarah Berry
(S)
Mahin Bagheri Kahkeshi
(MB)
Dawn Hancock
(D)
Jennifer Winster
(J)
Jessica Enright
(J)
Richard Samworth
(R)
Vijay Samtani
(V)
Gabriela Ahmadi-Assalemi
(G)
Tom Feather
(T)
Robin Goodall
(R)
Steve Hoensch
(S)
Dean Johnson
(D)
Martin Hunt
(M)
Nick Mathieson
(N)
Katya Nikitina
(K)
Zara Sheldrake
(Z)
Martin Keen
(M)
Aris Sato
(A)
David Connor
(D)
Jonathan Tolhurst
(J)
Jack Williman
(J)
Victoria Hollamby
(V)
Sinead Jordan
(S)
Tania Fatseas
(T)
Peter Taylor
(P)
Christine Georgiou
(C)
Michelle Caspersz
(M)
Claire McNulty
(C)
Richard Davies
(R)
Rebecca Clarke
(R)
Darius Danaei
(D)
Rory Dyer
(R)
Rob Glew
(R)
Oliver Lambson
(O)
Karen Gibbs
(K)
Barbara Mozdzen
(B)
Gabor Raub
(G)
Asako Radecki
(A)
Phil White
(P)
Robert Hughes
(R)
Lucie Gransden
(L)
Matt Ceaser
(M)
Robert Sing
(R)
Karl Wilson
(K)
Ajith Parlikad
(A)
Maharshi Dhada
(M)
Tom Ridgman
(T)
Diane Mungovan
(D)
Steve Matthews
(S)
Paul Searle
(P)
John Mills
(J)
Andy Neely
(A)
Robert Henderson
(R)
Edna Murphy
(E)
Matthew Russell
(M)
Anthony Freeling
(A)
Steve Poppitt
(S)
Jo Tynan
(J)
James Knapton
(J)
Filippo Marchetti
(F)
Daniela De Angelis
(D)
Theresa Feltwell
(T)
Nazreen F Hadjirin
(NF)
William L Hamilton
(WL)
Aminu Jahun
(A)
Malte Pinckert
(M)
Ashley Shaw
(A)
Afzal Chaudhry
(A)
Nicholas M Brown
(NM)
Lenette Mactavous
(L)
Sophie Hannan
(S)
Aleksandra Hosaja
(A)
Clare Leong
(C)
Jo Wright
(J)
Natalie Quinnell
(N)
Chris Workman
(C)
Mark Ferris
(M)
Giles Wright
(G)
Elizabeth Wright
(E)
Dinesh Aggarwal
(D)
Ellena Brooks
(E)
Alessandro M Carabelli
(AM)
Carol M Churcher
(CM)
Katerina Galai
(K)
Sophia T Girgis
(ST)
Ravi K Gupta
(RK)
Catherine Ludden
(C)
Georgina M McManus
(GM)
Sophie Palmer
(S)
Sharon J Peacock
(SJ)
Kim S Smith
(KS)
Elias Allara
(E)
David Bibby
(D)
Chloe Bishop
(C)
Andrew Bosworth
(A)
Daniel Bradshaw
(D)
Vicki Chalker
(V)
Meera Chand
(M)
Gavin Dabrera
(G)
Nicholas Ellaby
(N)
Eileen Gallagher
(E)
Natalie Groves
(N)
Ian Harrison
(I)
Hassan Hartman
(H)
Richard Hopes
(R)
Jonathan Hubb
(J)
Stephanie Hutchings
(S)
Angie Lackenby
(A)
Juan Ledesma
(J)
David Lee
(D)
Nikos Manesis
(N)
Carmen Manso
(C)
Tamyo Mbisa
(T)
Shahjahan Miah
(S)
Peter Muir
(P)
Husam Osman
(H)
Vineet Patel
(V)
Clare Pearson
(C)
Steven Platt
(S)
Hannah M Pymont
(HM)
Mary Ramsay
(M)
Esther Robinson
(E)
Ulf Schaefer
(U)
Alicia Thornton
(A)
Katherine A Twohig
(KA)
Ian B Vipond
(IB)
David Williams
(D)
William L Hamilton
(WL)
Louise Aigrain
(L)
Alex Alderton
(A)
Roberto Amato
(R)
Cristina V Ariani
(CV)
Jeff Barrett
(J)
Andrew R Bassett
(AR)
Mathew A Beale
(MA)
Charlotte Beaver
(C)
Katherine L Bellis
(KL)
Emma Betteridge
(E)
James Bonfield
(J)
Iraad F Bronner
(IF)
Michael H S Chapman
(MHS)
John Danesh
(J)
Robert Davies
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Matthew J Dorman
(MJ)
Eleanor Drury
(E)
Jillian Durham
(J)
Ben W Farr
(BW)
Luke Foulser
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Scott Goodwin
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(DK)
Keith James
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Dorota Jamrozy
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Ian Johnston
(I)
Leanne Kane
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Sally Kay
(S)
Jon-Paul Keatley
(JP)
Dominic Kwiatkowski
(D)
Cordelia F Langford
(CF)
Mara Lawniczak
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Stefanie V Lensing
(SV)
Steven Leonard
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Jennifier Liddle
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Rich Livett
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Stephanie Lo
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Alex Makunin
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Inigo Martincorena
(I)
Shane McCarthy
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Samantha McGuigan
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Robin J Moll
(RJ)
Rachel Nelson
(R)
Karen Oliver
(K)
Steve Palmer
(S)
Naomi R Park
(NR)
Minal Patel
(M)
Liam Prestwood
(L)
Christoph Puethe
(C)
Michael A Quail
(MA)
Diana Rajan
(D)
Shavanthi Rajatileka
(S)
Nicholas M Redshaw
(NM)
Carol Scott
(C)
Lesley Shirley
(L)
John Sillitoe
(J)
Scott A J Thurston
(SAJ)
Gerry Tonkin-Hill
(G)
Jaime M Tovar-Corona
(JM)
Danni Weldon
(D)
Andrew Whitwham
(A)
Myra Hosmillo
(M)
Stephen W Attwood
(SW)
Louis du Plessis
(L)
Marina Escalera Zamudio
(ME)
Sarah Francois
(S)
Bernardo Gutierrez
(B)
Moritz U G Kraemer
(MUG)
Jayna Raghwani
(J)
Tetyana I Vasylyeva
(TI)
Alex E Zarebski
(AE)
Nabil-Fareed Alikhan
(NF)
Alp Aydin
(A)
David J Baker
(DJ)
Leonardo de Oliveira Martins
(L)
Gemma L Kay
(GL)
Thanh Le-Viet
(T)
Alison E Mather
(AE)
Lizzie Meadows
(L)
Justin O'Grady
(J)
Steven Rudder
(S)
Alexander J Trotter
(AJ)
Chris J Illingworth
(CJ)
Chris Jackson
(C)
Elihu Aranday-Cortes
(E)
Patawee Asamaphan
(P)
Alice Broos
(A)
Stephen N Carmichael
(SN)
Ana da Silva Filipe
(A)
Joseph Hughes
(J)
Natasha G Jesudason
(NG)
Natasha Johnson
(N)
Kathy K Li
(KK)
Daniel Mair
(D)
Jenna Nichols
(J)
Seema Nickbakhsh
(S)
Marc O Niebel
(MO)
Kyriaki Nomikou
(K)
Richard J Orton
(RJ)
David L Robertson
(DL)
Rajiv N Shah
(RN)
James G Shepherd
(JG)
Joshua B Singer
(JB)
Igor Starinskij
(I)
Emma C Thomson
(EC)
Lily Tong
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Sreenu Vattipally
(S)
Amy Ash
(A)
Cherian Koshy
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Nick Cortes
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Stephen Kidd
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Jessica Lynch
(J)
Nathan Moore
(N)
Matilde Mori
(M)
Emma Wise
(E)
Tanya Curran
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Derek J Fairley
(DJ)
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(JP)
Helen Adams
(H)
David Bonsall
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Christophe Fraser
(C)
Tanya Golubchik
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Benjamin J Cogger
(BJ)
Mohammed O Hassan-Ibrahim
(MO)
Cassandra S Malone
(CS)
Nicola Reynolds
(N)
Michelle Wantoch
(M)
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Joshua Maksimovic
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(TR)
William Fuller
(W)
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(H)
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(A)
Ian Merrick
(I)
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(R)
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(J)
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(T)
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(A)
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(LB)
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(T)
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(J)
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(G)
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(AH)
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(SC)
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(DM)
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(K)
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(M)
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(BEW)
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(AP)
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(CA)
Louise Berry
(L)
Tim Boswell
(T)
Gemma Clark
(G)
Vicki M Fleming
(VM)
Hannah C Howson-Wells
(HC)
Carl Jones
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Amelia Joseph
(A)
Manjinder Khakh
(M)
Michelle M Lister
(MM)
Wendy Smith
(W)
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Sharon Campbell
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Veena Raviprakash
(V)
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(N)
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(LA)
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(J)
Nadine Holmes
(N)
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(MW)
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(C)
Fei Sang
(F)
Victoria Wright
(V)
Francesc Coll
(F)
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(G)
Adrian W Signell
(AW)
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(HD)
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(T)
Sahar Eldirdiri
(S)
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(A)
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(ME)
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(J)
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(J)
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(JR)
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(KA)
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(JCD)
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(D)
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(F)
Adela Alcolea-Medina
(A)
Gabrielle Vernet
(G)
Rebecca Williams
(R)
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(MR)
Wendy Chatterton
(W)
Judith Heaney
(J)
Lisa J Levett
(LJ)
Monika Pusok
(M)
Li Xu-McCrae
(L)
Matthew Bashton
(M)
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(DL)
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(GR)
Frances Bolt
(F)
Alison Cox
(A)
Alison Holmes
(A)
Pinglawathee Madona
(P)
Siddharth Mookerjee
(S)
James Price
(J)
Paul A Randell
(PA)
Olivia Boyd
(O)
Fabricia F Nascimento
(FF)
Lily Geidelberg
(L)
Rob Johnson
(R)
David Jorgensen
(D)
Manon Ragonnet-Cronin
(M)
Aileen Rowan
(A)
Igor Siveroni
(I)
Graham P Taylor
(GP)
Erik M Volz
(EM)
Katherine L Smollett
(KL)
Nicholas J Loman
(NJ)
Claire McMurray
(C)
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(A)
Sam Nicholls
(S)
Radoslaw Poplawski
(R)
Joshua Quick
(J)
Will Rowe
(W)
Joanne Stockton
(J)
Rocio T Martinez Nunez
(RTM)
Cassie Breen
(C)
Angela Cowell
(A)
Jenifer Mason
(J)
Elaine O'Toole
(E)
Trevor I Robinson
(TI)
Joanne Watts
(J)
Graciela Sluga
(G)
Shazaad S Y Ahmad
(SSY)
Ryan P George
(RP)
Nicholas W Machin
(NW)
Fenella Halstead
(F)
Wendy Hogsden
(W)
Venkat Sivaprakasam
(V)
Holli Carden
(H)
Antony D Hale
(AD)
Katherine L Harper
(KL)
Louissa R Macfarlane-Smith
(LR)
Shirelle Burton-Fanning
(S)
Jennifer Collins
(J)
Gary Eltringham
(G)
Brendan Ai Payne
(BA)
Yusri Taha
(Y)
Sheila Waugh
(S)
Sarah O'Brien
(S)
Steven Rushton
(S)
Rachel Blacow
(R)
Amanda Bradley
(A)
Alasdair Maclean
(A)
Guy Mollett
(G)
Rebecca Dewar
(R)
Martin P McHugh
(MP)
Kate E Templeton
(KE)
Elizabeth Wastenge
(E)
Lindsay Coupland
(L)
Samir Dervisevic
(S)
Emma J Meader
(EJ)
Rachael Stanley
(R)
Louise Smith
(L)
Edward Barton
(E)
Clive Graham
(C)
Debra Padgett
(D)
Garren Scott
(G)
Jane Greenaway
(J)
Emma Swindells
(E)
Clare M McCann
(CM)
Andrew Nelson
(A)
Wen C Yew
(WC)
Monique Andersson
(M)
Derrick Crook
(D)
David Eyre
(D)
Anita Justice
(A)
Timothy Peto
(T)
Nichola Duckworth
(N)
Tim J Sloan
(TJ)
Sarah Walsh
(S)
Kelly Bicknell
(K)
Anoop J Chauhan
(AJ)
Scott Elliott
(S)
Sharon Glaysher
(S)
Robert Impey
(R)
Allyson Lloyd
(A)
Sarah Wyllie
(S)
Nick Levene
(N)
Lynn Monaghan
(L)
Declan T Bradley
(DT)
Tim Wyatt
(T)
Martin D Curran
(MD)
Surendra Parmar
(S)
Matthew T G Holden
(MTG)
Sharif Shaaban
(S)
Alexander Adams
(A)
Hibo Asad
(H)
Alec Birchley
(A)
Matthew Bull
(M)
Jason Coombes
(J)
Sally Corden
(S)
Simon Cottrell
(S)
Noel Craine
(N)
Michelle Cronin
(M)
Alisha Davies
(A)
Elen De Lacy
(E)
Fatima Downing
(F)
Sue Edwards
(S)
Johnathan M Evans
(JM)
Laia Fina
(L)
Amy Gaskin
(A)
Bree Gatica-Wilcox
(B)
Laura Gifford
(L)
Lauren Gilbert
(L)
Lee Graham
(L)
David Heyburn
(D)
Ember Hilvers
(E)
Robin Howe
(R)
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(H)
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(R)
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(S)
Sara Kumziene-SummerhaYes
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Caoimhe McKerr
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Catherine Moore
(C)
Mari Morgan
(M)
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(N)
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(A)
Sara Rey
(S)
Giri Shankar
(G)
Sarah Taylor
(S)
Joanne Watkins
(J)
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(C)
Anna Casey
(A)
Liz Ratcliffe
(L)
Erwan Acheson
(E)
Zoltan Molnar
(Z)
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(DA)
Thomas Thompson
(T)
Cressida Auckland
(C)
Sian Ellard
(S)
Christopher R Jones
(CR)
Bridget A Knight
(BA)
Jane A H Masoli
(JAH)
Tanzina Haque
(T)
Jennifer Hart
(J)
Dianne Irish-Tavares
(D)
Tabitha W Mahungu
(TW)
Eric Witele
(E)
Ashok Dadrah
(A)
Melisa L Fenton
(ML)
Tranprit Saluja
(T)
Amanda Symmonds
(A)
Yann Bourgeois
(Y)
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(GP)
Kate Cook
(K)
Hannah Dent
(H)
Christopher Fearn
(C)
Salman Goudarzi
(S)
Katie F Loveson
(KF)
Hannah Paul
(H)
Cariad Evans
(C)
Kate Johnson
(K)
David G Partridge
(DG)
Mohammad Raza
(M)
Paul Baker
(P)
Stephen Bonner
(S)
Sarah Essex
(S)
Steven Liggett
(S)
Ronan A Lyons
(RA)
Adhyana I K Mahanama
(AIK)
Kordo Saeed
(K)
Buddhini Samaraweera
(B)
Siona Silveira
(S)
Eleri Wilson-Davies
(E)
P Emanuela
(P)
Nadua Bayzid
(N)
Marius Cotic
(M)
Leah Ensell
(L)
John A Hartley
(JA)
Riaz Jannoo
(R)
Angeliki Karamani
(A)
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(M)
Helen L Lowe
(HL)
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(S)
Adam P Westhorpe
(AP)
Rachel J Williams
(RJ)
Charlotte A Williams
(CA)
Sarah Jeremiah
(S)
Jacqui A Prieto
(JA)
Lisa Berry
(L)
Dimitris Grammatopoulos
(D)
Katie Jones
(K)
Sarojini Pandey
(S)
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(A)
Alex Richter
(A)
Fiona Ashcroft
(F)
Angus Best
(A)
Liam Crawford
(L)
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(N)
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(M)
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(O)
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(J)
Emma Moles-Garcia
(E)
Benita Percival
(B)
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(G)
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(AR)
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(CP)
Rose K Davidson
(RK)
Carlos E Balcazar
(CE)
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(MD)
Áine O'Toole
(Á)
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(A)
Stefan Rooke
(S)
Thomas D Stanton
(TD)
Thomas Williams
(T)
Kathleen A Williamson
(KA)
Claire M Bewshea
(CM)
Audrey Farbos
(A)
James W Harrison
(JW)
Aaron R Jeffries
(AR)
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(R)
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(SL)
Michelle L Michelsen
(ML)
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(CM)
David J Studholme
(DJ)
Ben Temperton
(B)
Joanna Warwick-Dugdale
(J)
Alistair C Darby
(AC)
Richard Eccles
(R)
Matthew Gemmell
(M)
Richard Gregory
(R)
Sam T Haldenby
(ST)
Julian A Hiscox
(JA)
Margaret Hughes
(M)
Miren Iturriza-Gomara
(M)
Kathryn A Jackson
(KA)
Anita O Lucaci
(AO)
Charlotte Nelson
(C)
Steve Paterson
(S)
Lucille Rainbow
(L)
Lance Turtle
(L)
Edith E Vamos
(EE)
Hermione J Webster
(HJ)
Mark Whitehead
(M)
Claudia Wierzbicki
(C)
Adrienn Angyal
(A)
Rebecca Brown
(R)
Thushan I de Silva
(TI)
Timothy M Freeman
(TM)
Marta Gallis
(M)
Luke R Green
(LR)
Danielle C Groves
(DC)
Alexander J Keeley
(AJ)
Benjamin B Lindsey
(BB)
Stavroula F Louka
(SF)
Matthew D Parker
(MD)
Paul J Parsons
(PJ)
Nikki Smith
(N)
Rachel M Tucker
(RM)
Dennis Wang
(D)
Max Whiteley
(M)
Matthew Wyles
(M)
Peijun Zhang
(P)
Mohammad T Alam
(MT)
Laura Baxter
(L)
Hannah E Bridgewater
(HE)
Paul E Brown
(PE)
Jeffrey K J Cheng
(JKJ)
Chrystala Constantinidou
(C)
Lucy R Frost
(LR)
Sascha Ott
(S)
Richard Stark
(R)
Grace Taylor-Joyce
(G)
Meera Unnikrishnan
(M)
Alberto C Cerda
(AC)
Tammy V Merrill
(TV)
Rebekah E Wilson
(RE)
Jonathan Ball
(J)
Joseph G Chappell
(JG)
Patrick C McClure
(PC)
Theocharis Tsoleridis
(T)
David Buck
(D)
Mariateresa de Cesare
(M)
Angie Green
(A)
George MacIntyre-Cockett
(G)
John A Todd
(JA)
Amy Trebes
(A)
Rory N Gunson
(RN)
Claire Cormie
(C)
Joana Dias
(J)
Sally Forrest
(S)
Harmeet K Gill
(HK)
Ellen E Higginson
(EE)
Leanne M Kermack
(LM)
Mailis Maes
(M)
Chris Ruis
(C)
Sushmita Sridhar
(S)
Jamie Young
(J)
Informations de copyright
© 2022. The Author(s).
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