Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning
Authors: Nickbakhsh Sema , Hughes Joseph , Christofidis Nicolaos , Griffiths Emily , Shaaban Sharif , Enright Jessica , Smollett Katherine , Nomikou Kyriaki , Palmalux Natasha , Tong Lily , Carmichael Stephen , Sreenu Vattipally B. , Orton Richard , Goldstein Emily J. , Tomb Rachael M. ,   The COVID-19 Genomics UK (COG-UK) Consortium, Robson Samuel C. , Connor Thomas R. , Loman Nicholas J. , Golubchik Tanya , Nunez Rocio T. Martinez , Bonsall David , Rambaut Andrew , Snell Luke B. , Livett Rich , Ludden Catherine , Corden Sally , Nastouli Eleni , Nebbia Gaia , Johnston Ian , Lythgoe Katrina , Torok M. Estee , Goodfellow Ian G. , Prieto Jacqui A. , Saeed Kordo , Jackson David K. , Houlihan Catherine , Frampton Dan , Hamilton William L. , Witney Adam A. , Bucca Giselda , Pope Cassie F. , Moore Catherine , Thomson Emma C. , Harrison Ewan M. , Smith Colin P. , Rogan Fiona , Beckwith Shaun M. , Murray Abigail , Singleton Dawn , Eastick Kirstine , Sheridan Liz A. , Randell Paul , Jackson Leigh M. , Ariani Cristina V. , Gonçalves Sónia , Fairley Derek J. , Loose Matthew W. , Watkins Joanne , Moses Samuel , Nicholls Sam , Bull Matthew , Amato Roberto , Smith Darren L. , Aanensen David M. , Barrett Jeffrey C. , Aggarwal Dinesh , Shepherd James G. , Curran Martin D. , Parmar Surendra , Parker Matthew D. , Williams Catryn , Glaysher Sharon , Underwood Anthony P. , Bashton Matthew , Pacchiarini Nicole , Loveson Katie F. , Byott Matthew , Carabelli Alessandro M. , Templeton Kate E. , de Silva Thushan I. , Wang Dennis , Langford Cordelia F. , Sillitoe John , Gunson Rory N. , Cottrell Simon , O’Grady Justin , Kwiatkowski Dominic , Lillie Patrick J. , Cortes Nicholas , Moore Nathan , Thomas Claire , Burns Phillipa J. , Mahungu Tabitha W. , Liggett Steven , Beckett Angela H. , Holden Matthew T. G. , Levett Lisa J. , Osman Husam , Hassan-Ibrahim Mohammed O. , Simpson David A. , Chand Mrera , Gupta Ravi K. , Darby Alistair C. , Paterson Steve , Pybus Oliver G. , Volz Erik M. , de Angelis Daniela , Robertson David L. , Page Andrew J. , Martincorena Inigo , Aigrain Louise , Bassett Andrew R. , Wong Nick , Taha Yusri , Erkiert Michelle J. , Chapman Michael H. Spencer , Dewar Rebecca , McHugh Martin P. , Mookerjee Siddharth , Aplin Stephen , Harvey Matthew , Sass Thea , Umpleby Helen , Wheeler Helen , McKenna James P. , Warne Ben , Taylor Joshua F. , Chaudhry Yasmin , Izuagbe Rhys , Jahun Aminu S. , Young Gregory R. , McMurray Claire , McCann Clare M. , Nelson Andrew , Elliott Scott , Lowe Hannah , Price Anna , Crown Matthew R. , Rey Sara , Roy Sunando , Temperton Ben , Shaaban Sharif , Hesketh Andrew R. , Laing Kenneth G. , Monahan Irene M. , Heaney Judith , Pelosi Emanuela , Silviera Siona , Wilson-Davies Eleri , Fryer Helen , Adams Helen , du Plessis Louis , Johnson Rob , Harvey William T. , Hughes Joseph , Orton Richard J. , Spurgin Lewis G. , Bourgeois Yann , Ruis Chris , O’Toole Áine , Gourtovaia Marina , Sanderson Theo , Fraser Christophe , Edgeworth Jonathan , Breuer Judith , Michell Stephen L. , Todd John A. , John Michaela , Buck David , Gajee Kavitha , Kay Gemma L. , Peacock Sharon J. , Heyburn David , Kitchman Katie , McNally Alan , Pritchard David T. , Dervisevic Samir , Muir Peter , Robinson Esther , Vipond Barry B. , Ramadan Newara A. , Jeanes Christopher , Weldon Danni , Catalan Jana , Jones Neil , da Silva Filipe Ana , Williams Chris , Fuchs Marc , Miskelly Julia , Jeffries Aaron R. , Oliver Karen , Park Naomi R. , Ash Amy , Koshy Cherian , Barrow Magdalena , Buchan Sarah L. , Mantzouratou Anna , Clark Gemma , Holmes Christopher W. , Campbell Sharon , Davis Thomas , Tan Ngee Keong , Brown Julianne R. , Harris Kathryn A. , Kidd Stephen P. , Grant Paul R. , Xu-McCrae Li , Cox Alison , Madona Pinglawathee , Pond Marcus , Randell Paul A. , Withell Karen T. , Williams Cheryl , Graham Clive , Denton-Smith Rebecca , Swindells Emma , Turnbull Robyn , Sloan Tim J. , Bosworth Andrew , Hutchings Stephanie , Pymont Hannah M. , Casey Anna , Ratcliffe Liz , Jones Christopher R. , Knight Bridget A. , Haque Tanzina , Hart Jennifer , Irish-Tavares Dianne , Witele Eric , Mower Craig , Watson Louisa K. , Collins Jennifer , Eltringham Gary , Crudgington Dorian , Macklin Ben , Iturriza-Gomara Miren , Lucaci Anita O. , McClure Patrick C. , Carlile Matthew , Holmes Nadine , Moore Christopher , Storey Nathaniel , Rooke Stefan , Yebra Gonzalo , Craine Noel , Perry Malorie , Alikhan Nabil-Fareed , Bridgett Stephen , Cook Kate F. , Fearn Christopher , Goudarzi Salman , Lyons Ronan A. , Williams Thomas , Haldenby Sam T. , Durham Jillian , Leonard Steven , Davies Robert M. , Batra Rahul , Blane Beth , Spyer Moira J. , Smith Perminder , Yavus Mehmet , Williams Rachel J. , Mahanama Adhyana I. K. , Samaraweera Buddhini , Girgis Sophia T. , Hansford Samantha E. , Green Angie , Beaver Charlotte , Bellis Katherine L. , Dorman Matthew J. , Kay Sally , Prestwood Liam , Rajatileka Shavanthi , Quick Joshua , Poplawski Radoslaw , Reynolds Nicola , Mack Andrew , Morriss Arthur , Whalley Thomas , Patel Bindi , Georgana Iliana , Hosmillo Myra , Pinckert Malte L. , Stockton Joanne , Henderson John H. , Hollis Amy , Stanley William , Yew Wen C. , Myers Richard , Thornton Alicia , Adams Alexander , Annett Tara , Asad Hibo , Birchley Alec , Coombes Jason , Evans Johnathan M. , Fina Laia , Gatica-Wilcox Bree , Gilbert Lauren , Graham Lee , Hey Jessica , Hilvers Ember , Jones Sophie , Jones Hannah , Kumziene-Summerhayes Sara , McKerr Caoimhe , Powell Jessica , Pugh Georgia , Taylor Sarah , Trotter Alexander J. , Williams Charlotte A. , Kermack Leanne M. , Foulkes Benjamin H. , Gallis Marta , Hornsby Hailey R. , Louka Stavroula F. , Pohare Manoj , Wolverson Paige , Zhang Peijun , MacIntyre-Cockett George , Trebes Amy , Moll Robin J. , Ferguson Lynne , Goldstein Emily J. , Maclean Alasdair , Tomb Rachael , Starinskij Igor , Thomson Laura , Southgate Joel , Kraemer Moritz U. G. , Raghwani Jayna , Zarebski Alex E. , Boyd Olivia , Geidelberg Lily , Illingworth Chris J. , Jackson Chris , Pascall David , Vattipally Sreenu , Freeman Timothy M. , Hsu Sharon N. , Lindsey Benjamin B. , James Keith , Lewis Kevin , Tonkin-Hill Gerry , Tovar-Corona Jaime M. , Cox MacGregor , Abudahab Khalil , Menegazzo Mirko , Taylor Ben E. W. , Yeats Corin A. , Mukaddas Afrida , Wright Derek W. , de Oliveira Martins Leonardo , Colquhoun Rachel , Hill Verity , Jackson Ben , McCrone J. T. , Medd Nathan , Scher Emily , Keatley Jon-Paul , Curran Tanya , Morgan Sian , Maxwell Patrick , Smith Ken , Eldirdiri Sahar , Kenyon Anita , Holmes Alison H. , Price James R. , Wyatt Tim , Mather Alison E. , SkvortsovHartley Timofey John A. , Guest Martyn , Kitchen Christine , Merrick Ian , Munn Robert , Bertolusso Beatrice , Lynch Jessica , Vernet Gabrielle , Kirk Stuart , Wastnedge Elizabeth , Stanley Rachael , Idle Giles , Bradley Declan T. , Poyner Jennifer , Mori Matilde , Jones Owen , Wright Victoria , Brooks Ellena , Churcher Carol M. , Fragakis Mireille , Galai Katerina , Jermy Andrew , Judges Sarah , McManus Georgina M. , Smith Kim S. , Westwick Elaine , Attwood Stephen W. , Bolt Frances , Davies Alisha , De Lacy Elen , Downing Fatima , Edwards Sue , Meadows Lizzie , Jeremiah Sarah , Smith Nikki , Foulser Luke , Charalampous Themoula , Patel Amita , Berry Louise , Boswell Tim , Fleming Vicki M. , Howson-Wells Hannah C. , Joseph Amelia , Khakh Manjinder , Lister Michelle M. , Bird Paul W. , Fallon Karlie , Helmer Thomas , McMurray Claire L. , Odedra Mina , Shaw Jessica , Tang Julian W. , Willford Nicholas J. , Blakey Victoria , Raviprakash Veena , Sheriff Nicola , Williams Lesley-Anne , Feltwell Theresa , Bedford Luke , Cargill James S. , Hughes Warwick , Moore Jonathan , Stonehouse Susanne , Atkinson Laura , Lee Jack C. D. , Shah Divya , Alcolea-Medina Adela , Ohemeng-Kumi Natasha , Ramble John , Sehmi Jasveen , Williams Rebecca , Chatterton Wendy , Pusok Monika , Everson William , Castigador Anibolina , Macnaughton Emily , El Bouzidi Kate , Lampejo Temi , Sudhanva Malur , Breen Cassie , Sluga Graciela , Ahmad Shazaad S. Y. , George Ryan P. , Machin Nicholas W. , Binns Debbie , James Victoria , Blacow Rachel , Coupland Lindsay , Smith Louise , Barton Edward , Padgett Debra , Scott Garren , Cross Aidan , Mirfenderesky Mariyam , Greenaway Jane , Cole Kevin , Clarke Phillip , Duckworth Nichola , Walsh Sarah , Bicknell Kelly , Impey Robert , Wyllie Sarah , Hopes Richard , Bishop Chloe , Chalker Vicki , Harrison Ian , Gifford Laura , Molnar Zoltan , Auckland Cressida , Evans Cariad , Johnson Kate , Partridge David G. , Raza Mohammad , Baker Paul , Bonner Stephen , Essex Sarah , Murray Leanne J. , Lawton Andrew I. , Burton-Fanning Shirelle , Payne Brendan A. I. , Waugh Sheila , Gomes Andrea N. , Kimuli Maimuna , Murray Darren R. , Ashfield Paula , Dobie Donald , Ashford Fiona , Best Angus , Crawford Liam , Cumley Nicola , Mayhew Megan , Megram Oliver , Mirza Jeremy , Moles-Garcia Emma , Percival Benita , Driscoll Megan , Ensell Leah , Lowe Helen L. , Maftei Laurentiu , Mondani Matteo , Chaloner Nicola J. , Cogger Benjamin J. , Easton Lisa J. , Huckson Hannah , Lewis Jonathan , Lowdon Sarah , Malone Cassandra S. , Munemo Florence , Mutingwende Manasa , Nicodemi Roberto , Podplomyk Olga , Somassa Thomas , Beggs Andrew , Richter Alex , Cormie Claire , Dias Joana , Forrest Sally , Higginson Ellen E. , Maes Mailis , Young Jamie , Davidson Rose K. , Jackson Kathryn A. , Turtle Lance , Keeley Alexander J. , Ball Jonathan , Byaruhanga Timothy , Chappell Joseph G. , Dey Jayasree , Hill Jack D. , Park Emily J. , Fanaie Arezou , Hilson Rachel A. , Yaze Geraldine , Lo Stephanie , Afifi Safiah , Beer Robert , Maksimovic Joshua , McCluggage Kathryn , Spellman Karla , Bresner Catherine , Fuller William , Marchbank Angela , Workman Trudy , Shelest Ekaterina , Debebe Johnny , Sang Fei , Zamudio Marina Escalera , Francois Sarah , Gutierrez Bernardo , Vasylyeva Tetyana I. , Flaviani Flavia , Ragonnet-Cronin Manon , Smollett Katherine L. , Broos Alice , Mair Daniel , Nichols Jenna , Nomikou Kyriaki , Tong Lily , Tsatsani Ioulia , O’Brien Sarah , Rushton Steven , Sanderson Roy , Perkins Jon , Cotton Seb , Gallagher Abbie , Allara Elias , Pearson Clare , Bibby David , Dabrera Gavin , Ellaby Nicholas , Gallagher Eileen , Hubb Jonathan , Lackenby Angie , Lee David , Manesis Nikos , Mbisa Tamyo , Platt Steven , Twohig Katherine A. , Morgan Mari , Aydin Alp , Baker David J. , Foster-Nyarko Ebenezer , Prosolek Sophie J. , Rudder Steven , Baxter Chris , Carvalho SÃ­lvia F. , Lavin Deborah , Mariappan Arun , Radulescu Clara , Singh Aditi , Tang Miao , Morcrette Helen , Bayzid Nadua , Cotic Marius , Balcazar Carlos E. , Gallagher Michael D. , Maloney Daniel , Stanton Thomas D. , Williamson Kathleen A. , Manley Robin , Michelsen Michelle L. , Sambles Christine M. , Studholme David J. , Warwick-Dugdale Joanna , Eccles Richard , Gemmell Matthew , Gregory Richard , Hughes Margaret , Nelson Charlotte , Rainbow Lucille , Vamos Edith E. , Webster Hermione J. , Whitehead Mark , Wierzbicki Claudia , Angyal Adrienn , Green Luke R. , Whiteley Max , Betteridge Emma , Bronner Iraad F. , Farr Ben W. , Goodwin Scott , Lensing Stefanie V. , McCarthy Shane A. , Quail Michael A. , Rajan Diana , Redshaw Nicholas M. , Scott Carol , Shirley Lesley , Thurston Scott A. J. , Rowe Will , Gaskin Amy , Le-Viet Thanh , Bonfield James , Liddle Jennifier , Whitwham Andrew , Templeton Kate , Gunson Rory N. , da Silva Filipe Ana , Milosevic Catriona , Thomson Emma , Robertson David L. , Holden Matthew T. G. , Illingworth Christopher J. R. , Smith-Palmer Alison 
Published: July 2022

AbstractWhole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings.