Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
- Authors
- David M. Aanensen
- Chris Abell
- Khalil Abudahab
- Erwan Acheson
- Alexander Adams
- Helen Adams
- Safiah Afifi
- Dinesh Aggarwal
- Dinesh Aggarwal
- Shazaad S. Y. Ahmad
- Gabriela Ahmadi-Assalemi
- Louise Aigrain
- Mohammad T. Alam
- Adela Alcolea-Medina
- Alex Alderton
- Nabil-Fareed Alikhan
- Elias Allara
- Roberto Amato
- Monique Andersson
- Daniela De Angelis
- Daniela De Angelis
- Adrienn Angyal
- Elihu Aranday-Cortes
- Cristina V. Ariani
- Hibo Asad
- Patawee Asamaphan
- Amy Ash
- Fiona Ashcroft
- Laura Atkinson
- Stephen W. Attwood
- Cressida Auckland
- Ali R. Awan
- Alp Aydin
- David J. Baker
- Paul Baker
- Carlos E. Balcazar
- Jonathan Ball
- Jeff Barrett
- Edward Barton
- Matthew Bashton
- Andrew R. Bassett
- Rahul Batra
- Laura Baxter
- Nadua Bayzid
- Mathew A. Beale
- Charlotte Beaver
- Angela H. Beckett
- Luke Bedford
- Robert Beer
- Andrew Beggs
- Katherine L. Bellis
- Lisa Berry
- Louise Berry
- Sarah Berry
- Angus Best
- Gilberto Betancor
- Emma Betteridge
- Claire M. Bewshea
- David Bibby
- Kelly Bicknell
- Alec Birchley
- Paul Bird
- Chloe Bishop
- Rachel Blacow
- Victoria Blakey
- Beth Blane
- Frances Bolt
- James Bonfield
- Stephen Bonner
- David Bonsall
- Tim Boswell
- Andrew Bosworth
- Yann Bourgeois
- Olivia Boyd
- John BoYes
- Amanda Bradley
- Declan T. Bradley
- Daniel Bradshaw
- Vickie Braithwaite
- Cassie Breen
- Catherine Bresner
- Judith Breuer
- Hannah E. Bridgewater
- Craig Brierley
- Iraad F. Bronner
- Ellena Brooks
- Alice Broos
- Christopher Brown
- Christopher A. Brown
- Julianne R. Brown
- Nicholas M. Brown
- Paul E. Brown
- Rebecca Brown
- Giselda Bucca
- David Buck
- Matthew Bull
- Shirelle Burton-Fanning
- Sharon Campbell
- Alessandro M. Carabelli
- Holli Carden
- Matthew Carlile
- Stephen N. Carmichael
- Anna Casey
- Michelle Caspersz
- Matt Ceaser
- Alberto C. Cerda
- Vicki Chalker
- Meera Chand
- Michael H. S. Chapman
- Michael R. Chapman
- Joseph G. Chappell
- Themoula Charalampous
- Wendy Chatterton
- Afzal Chaudhry
- Yasmin Chaudhry
- Anoop J. Chauhan
- Jeffrey K. J. Cheng
- Carol M. Churcher
- Gemma Clark
- Roger Clark
- Rebecca Clarke
- Benjamin J. Cogger
- Francesc Coll
- Jennifer Collins
- David Connor
- Thomas R. Connor
- Chrystala Constantinidou
- Kate Cook
- Jason Coombes
- Sally Corden
- Claire Cormie
- Nick Cortes
- Marius Cotic
- Simon Cottrell
- Lindsay Coupland
- Angela Cowell
- Alison Cox
- Noel Craine
- Liam Crawford
- Michelle Cronin
- Derrick Crook
- Jon Crowcroft
- Nicola Cumley
- Martin D. Curran
- Tanya Curran
- Ana da Silva Filipe
- Gavin Dabrera
- Ashok Dadrah
- Aastha Dahal
- Darius Danaei
- John Danesh
- Alistair C. Darby
- Rose K. Davidson
- Alisha Davies
- Richard Davies
- Robert Davies
- Thomas Davis
- Mariateresa de Cesare
- Leonardo de Oliveira Martins
- Thushan I. de Silva
- Johnny Debebe
- Hannah Dent
- Samir Dervisevic
- Rebecca Dewar
- Maharshi Dhada
- Joana Dias
- Matthew J. Dorman
- Gordon Dougan
- Julie Douthwaite
- Fatima Downing
- Eleanor Drury
- Louis du Plessis
- Louis du Plessis
- Nichola Duckworth
- Jillian Durham
- Rory Dyer
- Richard Eccles
- Jonathan Edgeworth
- Sue Edwards
- Sahar Eldirdiri
- Nicholas Ellaby
- Sian Ellard
- Scott Elliott
- Gary Eltringham
- P. Emanuela
- Jessica Enright
- Leah Ensell
- Sarah Essex
- Cariad Evans
- Johnathan M. Evans
- David Eyre
- Derek J. Fairley
- Karlie Fallon
- Audrey Farbos
- Ben W. Farr
- Tania Fatseas
- Kathryn Faulkner
- Christopher Fearn
- Tom Feather
- Theresa Feltwell
- Melisa L. Fenton
- Mark Ferris
- Thomas Fieldman
- Laia Fina
- Chloe L. Fisher
- Flavia Flaviani
- Vicki M. Fleming
- Sally Forrest
- Luke Foulser
- Sarah Francois
- Christophe Fraser
- Anthony Freeling
- Timothy M. Freeman
- Lucy R. Frost
- Stewart Fuller
- William Fuller
- Katerina Galai
- Eileen Gallagher
- Michael D. Gallagher
- Marta Gallis
- Amy Gaskin
- Bree Gatica-Wilcox
- Lily Geidelberg
- Matthew Gemmell
- Iliana Georgana
- Ryan P. George
- Christine Georgiou
- Karen Gibbs
- Laura Gifford
- Lauren Gilbert
- Harmeet K. Gill
- Sophia T. Girgis
- Sharon Glaysher
- Rob Glew
- Michael Glover
- Tanya Golubchik
- Sonia Goncalves
- Robin Goodall
- Ian Goodfellow
- Ian G. Goodfellow
- Scott Goodwin
- Salman Goudarzi
- Marina Gourtovaia
- Clive Graham
- Lee Graham
- Dimitris Grammatopoulos
- Lucie Gransden
- Jane Greatorex
- Angie Green
- Luke R. Green
- Jane Greenaway
- Richard Gregory
- Danielle C. Groves
- Natalie Groves
- Martyn Guest
- Huw Gulliver
- Rory N. Gunson
- Ravi K. Gupta
- Bernardo Gutierrez
- Nazreen F. Hadjirin
- Sam T. Haldenby
- Antony D. Hale
- Grant Hall
- Fenella Halstead
- William L. Hamilton
- William L. Hamilton
- William L. Hamilton
- Dawn Hancock
- Sophie Hannan
- Tanzina Haque
- Katherine L. Harper
- Kathryn A. Harris
- Ewan M. Harrison
- Ian Harrison
- James W. Harrison
- Jennifer Hart
- John A. Hartley
- Hassan Hartman
- Mohammed O. Hassan-Ibrahim
- Judith Heaney
- Thomas Helmer
- Robert Henderson
- Andrew R. Hesketh
- David Heyburn
- Ellen E. Higginson
- Sarah Hilborne
- Verity Hill
- Ember Hilvers
- Julian A. Hiscox
- Steve Hoensch
- Wendy Hogsden
- Matthew T. G. Holden
- Jon Holgate
- Victoria Hollamby
- Alison Holmes
- Christopher Holmes
- Nadine Holmes
- Richard Hopes
- Aleksandra Hosaja
- Myra Hosmillo
- Myra Hosmillo
- Robin Howe
- Rob Howes
- Hannah C. Howson-Wells
- Jonathan Hubb
- Gareth J. Hughes
- Joseph Hughes
- Margaret Hughes
- Robert Hughes
- Martin Hunt
- Stephanie Hutchings
- Chris Illingworth
- Chris J. Illingworth
- Robert Impey
- Dianne Irish-Tavares
- Miren Iturriza-Gomara
- Rhys Izuagbe
- Chris Jackson
- David K. Jackson
- Kathryn A. Jackson
- Aminu Jahun
- Aminu S. Jahun
- Keith James
- Laura James
- Dorota Jamrozy
- Riaz Jannoo
- Aaron R. Jeffries
- Sarah Jeremiah
- Natasha G. Jesudason
- Michaela John
- Dean Johnson
- Kate Johnson
- Natasha Johnson
- Rob Johnson
- Ian Johnston
- Carl Jones
- Christopher R. Jones
- Daniel R. Jones
- Hannah Jones
- Katie Jones
- Rachel Jones
- Sophie Jones
- Sinead Jordan
- David Jorgensen
- Amelia Joseph
- Anita Justice
- Mahin Bagheri Kahkeshi
- Leanne Kane
- Angeliki Karamani
- Gemma L. Kay
- Sally Kay
- Jon-Paul Keatley
- Alexander J. Keeley
- Martin Keen
- Anita Kenyon
- Leanne M. Kermack
- Manjinder Khakh
- Stephen Kidd
- Christine Kitchen
- James Knapton
- Bridget A. Knight
- Cherian Koshy
- Moritz U. G. Kraemer
- Mark Kristiansen
- Fred Kuenzi
- Sara Kumziene-SummerhaYes
- Dominic Kwiatkowski
- Angie Lackenby
- Elen De Lacy
- Oliver Lambson
- Cordelia F. Langford
- Mara Lawniczak
- Thanh Le-Viet
- Juan Ledesma
- David Lee
- Jack C. D. Lee
- Danielle Leek
- Paul Lehner
- Stefanie V. Lensing
- Steven Leonard
- Clare Leong
- Ian Leslie
- Laura Letchford
- Nick Levene
- Lisa J. Levett
- Kevin Lewis
- Kathy K. Li
- Kathleen Liddell
- Jennifier Liddle
- Steven Liggett
- Benjamin B. Lindsey
- Michelle M. Lister
- Rich Livett
- Allyson Lloyd
- Stephanie Lo
- Nicholas J. Loman
- Matthew W. Loose
- Stavroula F. Louka
- Katie F. Loveson
- Hannah Lowe
- Helen L. Lowe
- Anita O. Lucaci
- Catherine Ludden
- Catherine Ludden
- Jessica Lynch
- Ronan A. Lyons
- Louissa R. Macfarlane-Smith
- Nicholas W. Machin
- George MacIntyre-Cockett
- Alasdair Maclean
- Lenette Mactavous
- Pinglawathee Madona
- Mailis Maes
- Adhyana I. K. Mahanama
- Tabitha W. Mahungu
- Daniel Mair
- Joshua Maksimovic
- Alex Makunin
- Cassandra S. Malone
- Nikos Manesis
- Robin Manley
- Carmen Manso
- Angela Marchbank
- Filippo Marchetti
- Ben Margolis
- Inigo Martincorena
- Jane A. H. Masoli
- Jenifer Mason
- Alison E. Mather
- Nicholas Matheson
- Nicholas J. Matheson
- Nick Mathieson
- Steve Matthews
- Patrick Maxwell
- Patrick H. Maxwell
- Megan Mayhew
- Tamyo Mbisa
- Clare McCann
- Shane McCarthy
- Kathryn McCluggage
- Patrick C. McClure
- Duncan McFarlane
- Samantha McGuigan
- Martin P. McHugh
- James P. McKenna
- Caoimhe McKerr
- Georgina M. McManus
- Claire McMurray
- Alan McNally
- Claire McNulty
- Emma J. Meader
- Lizzie Meadows
- Oliver Megram
- Mirko Menegazzo
- Ian Merrick
- Tammy V. Merrill
- Marina Metaxaki
- Shahjahan Miah
- Stephen L. Michell
- Michelle L. Michelsen
- John Mills
- Jeremy Mirza
- Emma Moles-Garcia
- Robin J. Moll
- Guy Mollett
- Zoltan Molnar
- Lynn Monaghan
- Siddharth Mookerjee
- Catherine Moore
- Christopher Moore
- Jonathan Moore
- Nathan Moore
- Mari Morgan
- Sally Morgan
- Sian Morgan
- Matilde Mori
- Samuel Moses
- Barbara Mozdzen
- Peter Muir
- Diane Mungovan
- Robert Munn
- Edna Murphy
- Richard Myers
- Fabricia F. Nascimento
- Gaia Nebbia
- Andy Neely
- Andrew Nelson
- Charlotte Nelson
- Rachel Nelson
- Sam Nicholls
- Jenna Nichols
- Seema Nickbakhsh
- Marc O. Niebel
- Katya Nikitina
- Kyriaki Nomikou
- Olisaeloka Nsonwu
- Rocio T. Martinez Nunez
- Karen Oliver
- Alexandra Orton
- Richard J. Orton
- Husam Osman
- Sascha Ott
- Sarah O’Brien
- Justin O’Grady
- Elaine O’Toole
- Áine O’Toole
- Nicole Pacchiarini
- Simon Packer
- Debra Padgett
- Andrew J. Page
- Sophie Palmer
- Steve Palmer
- Sarojini Pandey
- Naomi R. Park
- Matthew D. Parker
- Ajith Parlikad
- Surendra Parmar
- Paul J. Parsons
- David G. Partridge
- Amita Patel
- Minal Patel
- Vineet Patel
- Steve Paterson
- Hannah Paul
- Brendan AI. Payne
- Sharon J. Peacock
- Sharon J. Peacock
- Clare Pearson
- Benita Percival
- Malorie Perry
- Timothy Peto
- Malte Pinckert
- Malte L. Pinckert
- Steven Platt
- Amy Plimmer
- Radoslaw Poplawski
- Steve Poppitt
- Liam Prestwood
- Anna Price
- James Price
- Jacqui A. Prieto
- Christoph Puethe
- Monika Pusok
- Oliver G. Pybus
- Hannah M. Pymont
- Michael A. Quail
- Joshua Quick
- Natalie Quinnell
- Asako Radecki
- Jayna Raghwani
- Manon Ragonnet-Cronin
- Lucille Rainbow
- Diana Rajan
- Shavanthi Rajatileka
- Andrew Rambaut
- Mary Ramsay
- Paul A. Randell
- Jennifer Rankin
- Liz Ratcliffe
- Gabor Raub
- Veena Raviprakash
- Mohammad Raza
- Nicholas M. Redshaw
- Steve Rees
- Sara Rey
- Nicola Reynolds
- Alex Richter
- Tom Ridgman
- David L. Robertson
- Esther Robinson
- Trevor I. Robinson
- Samuel C. Robson
- Stefan Rooke
- Aileen Rowan
- Will Rowe
- Sunando Roy
- Steven Rudder
- Chris Ruis
- Steven Rushton
- Matthew Russell
- Kordo Saeed
- Tranprit Saluja
- Buddhini Samaraweera
- Christine M. Sambles
- Vijay Samtani
- Richard Samworth
- Fei Sang
- Aris Sato
- Garry P. Scarlett
- Ulf Schaefer
- Carol Scott
- Garren Scott
- Paul Searle
- Sharif Shaaban
- Divya Shah
- Rajiv N. Shah
- Giri Shankar
- Ashley Shaw
- Zara Sheldrake
- James G. Shepherd
- Linda Sheridan
- Nicola Sheriff
- Lesley Shirley
- Adrian W. Signell
- John Sillitoe
- Siona Silveira
- David A. Simpson
- Robert Sing
- Joshua B. Singer
- Venkat Sivaprakasam
- Igor Siveroni
- Tim J. Sloan
- Graciela Sluga
- Colin P. Smith
- Darren Smith
- Kim S. Smith
- Louise Smith
- Nikki Smith
- Wendy Smith
- Katherine L. Smollett
- Luke B. Snell
- Joel Southgate
- Karla Spellman
- Sushmita Sridhar
- Rachael Stanley
- Thomas D. Stanton
- Igor Starinskij
- Richard Stark
- Joanne Stockton
- Susanne Stonehouse
- Nathaniel Storey
- David J. Studholme
- Emma Swindells
- Amanda Symmonds
- Yusri Taha
- Julian Tang
- Ben E. W. Taylor
- Graham P. Taylor
- Peter Taylor
- Sarah Taylor
- Grace Taylor-Joyce
- Ben Temperton
- Kate E. Templeton
- The Cambridge Covid-19 testing Centre,
- The COVID-19 Genomics UK (COG-UK) Consortium,
- Thomas Thompson
- Emma C. Thomson
- Alicia Thornton
- Scott A. J. Thurston
- John A. Todd
- Jonathan Tolhurst
- Lily Tong
- Gerry Tonkin-Hill
- M. Estee Torok
- Jaime M. Tovar-Corona
- Amy Trebes
- Alexander J. Trotter
- Theocharis Tsoleridis
- Rachel M. Tucker
- Lance Turtle
- Katherine A. Twohig
- Jo Tynan
- Anthony P. Underwood
- University of Cambridge Asymptomatic COVID-19 Screening Programm,
- Meera Unnikrishnan
- Sally Valletta
- Edith E. Vamos
- Tetyana I. Vasylyeva
- Sreenu Vattipally
- Gabrielle Vernet
- Anna Vignoles
- Martin Vinnell
- Ian B. Vipond
- Erik M. Volz
- Ian Waddell
- Sarah Walsh
- Dennis Wang
- Michelle Wantoch
- Ben Warne
- Joanna Warwick-Dugdale
- Elizabeth Wastenge
- Emmeline Watkins
- Joanne Watkins
- Joanne Watts
- Sheila Waugh
- Gillian Weale
- Hermione J. Webster
- Michael P. Weekes
- Danni Weldon
- Adam P. Westhorpe
- Phil White
- Mark Whitehead
- Max Whiteley
- Andrew Whitwham
- Claudia Wierzbicki
- Charlotte A. Williams
- Chris Williams
- David Williams
- Lesley-Anne Williams
- Rachel J. Williams
- Rebecca Williams
- Thomas Williams
- Kathleen A. Williamson
- Jack Williman
- Iona Willingham
- Mark Wills
- Harry D. Wilson
- Karl Wilson
- Rebekah E. Wilson
- Eleri Wilson-Davies
- Jennifer Winster
- Emma Wise
- Eric Witele
- Chris Workman
- Trudy Workman
- Elizabeth Wright
- Elizabeth Wright
- Giles Wright
- Jo Wright
- Victoria Wright
- Tim Wyatt
- Matthew Wyles
- Sarah Wyllie
- Li Xu-McCrae
- Corin A. Yeats
- Wen Chyin Yew
- Greg Young
- Jamie Young
- Marina Escalera Zamudio
- Alex E. Zarebski
- Peijun Zhang
- Publication date
- 8 February 2022
- Publisher
- Nature Communications
- Doi
Abstract
AbstractUnderstanding 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.</jats:pSimilar works
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Last time updated on 06/06/2022