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

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.