Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission-Reference-Cited by-同舟云学术

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Published:2022-02-08 Issue:1 Volume:13 Page:
ISSN:2041-1723
Container-title:Nature Communications
language:en
Short-container-title:Nat Commun

Author:

Aggarwal Dinesh^ORCID,Warne Ben^ORCID,Jahun Aminu S.^ORCID,Hamilton William L.^ORCID,Fieldman Thomas,du Plessis Louis^ORCID,Hill Verity^ORCID,Blane Beth^ORCID,Watkins Emmeline,Wright Elizabeth^ORCID,Hall Grant^ORCID,Ludden Catherine,Myers Richard,Hosmillo Myra,Chaudhry Yasmin^ORCID,Pinckert Malte L.^ORCID,Georgana Iliana,Izuagbe Rhys^ORCID,Leek Danielle,Nsonwu Olisaeloka^ORCID,Hughes Gareth J.^ORCID,Packer Simon^ORCID,Page Andrew J.^ORCID,Metaxaki Marina^ORCID,Fuller Stewart,Weale Gillian^ORCID,Holgate Jon,Brown Christopher A.^ORCID,Orton Alexandra,Douthwaite Julie,Rees Steve,Brown Christopher,Clark Roger,Jones Daniel R.,Kuenzi Fred,Rankin Jennifer,Waddell Ian,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^ORCID,Aggarwal Dinesh^ORCID,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.^ORCID,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.^ORCID,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^ORCID,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.^ORCID,Angelis Daniela De,Maxwell Patrick H.,Peacock Sharon J.^ORCID,Weekes Michael P.^ORCID,Illingworth Chris,Harrison Ewan M.^ORCID,Matheson Nicholas J.^ORCID,Goodfellow Ian G.^ORCID, , ,

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.

Funder

Wellcome Trust

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary

Link

https://www.nature.com/articles/s41467-021-27942-w.pdf

Reference52 articles.

1. Zhou, F. et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet 395, 1054–1062 (2020).

2. Yang, J. et al. Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a systematic review and meta-analysis. Int J. Infect. Dis. 94, 91–95 (2020).

3. Amoolya Vusirikala, H. W. et al. Gayatri Amirthalingam. Seroprevalence of SARS-CoV-2 Antibodies in University Students: cross-sectional study, December 2020, England. (2021).