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, Tom; 

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.; 

Howes, Rob; 

McFarlane, Duncan; 

Dougan, Gordon; 

Pybus, Oliver G. ; 

Angelis, Daniela De; 

Maxwell, Patrick H.; 

Peacock, Sharon J.; 

Weekes, Michael P.; 

Illingworth, Christopher J.R. ; 

Harrison, Ewen M. ; 

Matheson, Nicholas J.; 

Goodfellow, Ian G.; 

Orton, Alexandra; 

Douthwaite, Julie; 

Rees, Steve; 

Brown, Christopher A.; 

Clark, Roger; 

Jones, Daniel R.; 

Kuenzi, Fred; 

Rankin, Jennifer; 

Waddell, Ian; 

Maxwell, Patrick H.; 

Matheson, Nicholas J.; 

Abell, Chris; 

Braithwaite, Vickie; 

Brierley, Craig; 

Crowcroft, Jon; 

Dahal, Aastha; 

Faulkner, Kathryn; 

Glover, Michael; 

Goodfellow, Ian G.; 

Greatorex, Jane; 

James, Laura; 

Lehner, Paul J.; 

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, Stephen P.; 

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 S.; 

Pinckert, Malte L.; 

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; 

Aggarwal, Dinesh ; 

Brooks, Ellena; 

Carabelli, Alessandro M. ; 

Churcher, Carol M.; 

Galai, Katerina; 

Girgis, Sophia T.; 

Gupta, Ravindra K. ; 

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, Claire; 

Platt, Steve; 

Pymont, Hannah M.; 

Ramsay, Mary E.; 

Robinson, Esther; 

Schaefer, Ulf; 

Thornton, Alicia; 

Twohig, Katherine A.; 

Vipond, Ian B.; 

Williams, David; 

Aigrain, Louise; 

Alderton, Alex; 

Amato, Roberto; 

Ariani, Cristina V.; 

Barrett, Jeffrey C.; 

Bassett, Andrew R.; 

Beale, Mathew A.; 

Beaver, Charlotte; 

Bellis, Katherine L.; 

Betteridge, Emma; 

Bonfield, James; 

Bronner, Iraad; 

Chapman, Michael H. S.; 

Danesh, John; 

Davies, Robert M.; 

Dorman, Matthew J.; 

Drury, Eleanor; 

Durham, Jillian; 

Farr, Ben W.; 

Foulser, Luke; 

Gonçalves, Sónia; 

Goodwin, Scott; 

Gourtovaia, Marina; 

Jackson, David K.; 

James, Keith; 

Jamrozy, Dorota; 

Johnston, Ian; 

Kane, Leanne; 

Kay, Sally; 

Keatley, Jon-Paul; 

Kwiatkowski, Dominic P.; 

Langford, Cordelia F.; 

Lawniczak, Mara; 

Lensing, Stefanie V.; 

Leonard, Steven; 

Letchford, Laura; 

Lewis, Kevin; 

Liddle, Jennifer; 

Livett, Rich; 

Lo, Stephanie; 

Makunin, Alexsei; 

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; 

Attwood, Stephen W.; 

Escalera-Zamudio, Marina ; 

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, Christopher J.R. ; 

Jackson, Chris; 

Aranday-Cortes, Elihu; 

Asamaphan, Patawee; 

Broos, Alice; 

Carmichael, Stephen; 

da Silva Filipe, Ana; 

Hughes, Joseph; 

Jesudason, Natasha; 

Johnson, Natasha; 

Li, Kathy K.; 

Mair, Daniel; 

Nichols, Jenna; 

Nickbakhsh, Sema ; 

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, Nicholas; 

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; 

Batra, Rahul; 

Charalampous, Themoula; 

Edgeworth, Jonathan D.; 

Nebbia, Gaia; 

Beckett, Angela H.; 

Robson, Samuel; 

Aanensen, David M.; 

Abu-Dahab, Khalil; 

Menegazzo, Mirko; 

Taylor, Ben; 

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 W.; 

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; 

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; 

Young, Gregory R.; 

Bolt, Frances; 

Cox, Alison; 

Holmes, Alison; 

Madona, Pinglawathee; 

Mookerjee, Siddharth; 

Price, James R.; 

Randell, Paul A.; 

Boyd, Olivia; 

Nascimento, Fabricia F.; 

Geidelberg, Lily; 

Johnson, Robert ; 

Jorgensen, David; 

Ragonnet-Cronin, Manon; 

Rowan, Aileen; 

Siveroni, Igor; 

Taylor, Graham P.; 

Volz, Erik M.; 

Smollett, Katherine; 

Loman, Nicholas J. ; 

McMurray, Claire L.; 

McNally, Alan; 

Nicholls, Samuel M.; 

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; 

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 A.I.; 

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 W. ; 

Eyre, David W. ; 

Justice, Anita; 

Peto, Timothy E.A.; 

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.; 

Shabaan, Sharif; 

Adams, Alexander; 

Asad, Hibo; 

Birchley, Alec; 

Bull, Matthew; 

Coombes, Jason; 

Corden, Sally; 

Cottrell, Simon; 

Craine, Noel; 

Cronin, Michelle; 

Davies, Alisha; 

De Lacy, Elen; 

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; 

Thompson, Thomas; 

Auckland, Cressida; 

Ellard, Sian; 

Jones, Christopher R.; 

Knight, Bridget A.; 

Masoli, Jane; 

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 F.; 

Dent, Hannah; 

Fearn, Christopher; 

Goudarzi, Salman; 

Loveson, Katie F.; 

Paul, Hannah; 

Evans, Cariad; 

Johnson, Kate; 

Partridge, David G.; 

Raza, Mohammad; 

Baker, Paul A.; 

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, Kate; 

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 Niamh ; 

Rambaut, Andrew ; 

Rooke, Stefan; 

Stanton, Thomas D.; 

Williams, Thomas; 

Williamson, Kathleen A.; 

Bewshea, Claire; 

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 C.W. ; 

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, Christopher; 

Sridhar, Sushmita; 

Young, Jamie

Source

Nature Communications