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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. 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 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. 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 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 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 Milosevic, Catriona Thomson, Emma Illingworth, Christopher J. R. Smith-Palmer, Alison Nickbakhsh, Sema [0000-0001-9543-7536] Sreenu, Vattipally B [0000-0001-6673-4697] Orton, Richard [0000-0002-3389-4325] Thomson, Emma [0000-0003-1482-0889] Robertson, David L [0000-0001-6338-0221] Apollo - University of Cambridge Repository University of St Andrews. St Andrews Bioinformatics Unit University of St Andrews. Infection and Global Health Division University of St Andrews. Biomedical Sciences Research Complex University of St Andrews. School of Medicine
Publication Year :
2022
Publisher :
Springer Science and Business Media LLC, 2022.
Abstract
Funding: The CVR authors are supported by the Medical Research Council [MC_UU_12014/12 and MC_UU_12018/12]. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [Grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute. Whole 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. Publisher PDF
Details
ISSN :
20452322
Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....81533bb0876a603a8e1db4b882259ea8