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

Graham W. Taylor | Scott M Elliott | Jaime M. Tovar-Corona | Andrew R. Bassett | Anthony N. S. Freeling | Gemma L. Kay | A. Neely | J. Danesh | J. O’Grady | N. Loman | C. Constantinidou | J. Quick | J. Todd | Katerina Galai | J. Bonfield | R. Samworth | C. Langford | O. Pybus | C. Workman | C. Fraser | I. Martincorena | G. Dougan | C. Churcher | T. Feltwell | S. Ellard | R. Lyons | D. Bonsall | B. Gutiérrez | L. du Plessis | O. Boyd | L. Geidelberg | D. Jorgensen | I. Siveroni | E. Volz | L. Rainbow | L. Baxter | Steven Leonard | A. Parlikad | A. Rambaut | Lesley M Shirley | A. Vignoles | A. Davies | M. Weekes | Kevin Lewis | S. Ott | T. Peto | D. Crook | M. de Cesare | D. Buck | D. Aanensen | Louise Aigrain | R. Gregory | M. Wills | Sunando Roy | J. Hughes | S. Vattipally | C. Illingworth | M. Bashton | Martin Hunt | D. Angelis | A. Awan | R. Orton | M. Lawniczak | J. Raghwani | M. Loose | M. Kristiansen | J. Hartley | S. Glaysher | M. Iturriza-Gómara | S. Mookerjee | F. Bolt | M. Dhada | Eleanor Drury | R. Amato | A. Jeffries | S. Michell | S. Peacock | M. Holden | C. Ariani | W. Hamilton | A. Trebes | T. Golubchik | N. Brown | D. Eyre | E. Aranday-Cortes | A. da Silva Filipe | C. Holmes | T. Mbisa | E. Thomson | D. Studholme | S. Corden | S. Paterson | S. Haldenby | J. Hiscox | J. Ledesma | A. Lackenby | S. Waugh | V. Hill | C. Ruis | M. Parker | D. Partridge | C. Evans | T. Freeman | T. D. de Silva | A. Angyal | Rebecca Brown | Luke R. Green | Danielle C. Groves | Katie Johnson | A. Keeley | B. Lindsey | M. Raza | Rachel M. Tucker | Dennis Wang | M. Wyles | B. Temperton | S. Rooke | N. Alikhan | S. Nicholls | M. Michelsen | K. Twohig | B. Warne | G. Tonkin-Hill | C. Sambles | A. Lucaci | G. Bucca | A. Hesketh | Colin P. Smith | Ulf Schaefer | S. Rajatileka | A. Alderton | Rachel Nelson | C. Beaver | N. Matheson | H. Hartman | A. Best | Y. Chaudhry | I. Goodfellow | T. Robinson | L. de Oliveira Martins | A. Mather | K. Harris | S. Wyllie | C. Auckland | Clive Graham | J. Edgeworth | L. Bedford | Veena Raviprakash | L. Letchford | M. John | C. Wierzbicki | R. Munn | D. Rajan | L. Turtle | G. Hughes | A. Underwood | A. Chauhan | J. Enright | A. Green | N. Holmes | A. Page | P. Emanuela | J. Prieto | R. Davidson | G. Eltringham | B. Knight | E. Allara | A. McNally | Paul E. Brown | R. Batra | W. Smith | L. Berry | J. Mason | P. Baker | David Williams | K. Templeton | Emma Betteridge | N. Redshaw | Scott Goodwin | S. Thurston | Stefanie V. Lensing | I. Johnston | Steve Rees | R. Glew | Andrew Whitwham | M. Gemmell | F. Coll | A. Richter | R. Stark | Leanne Kane | C. Yeats | J. Coombes | I. Harrison | W. Rowe | J. Nichols | T. Charalampous | G. Kay | Alp Aydin | E. Harrison | M. Dorman | Julianne R. Brown | M. Beale | Ben Margolis | Khalil AbuDahab | Ben Taylor | S. Hilborne | F. F. Nascimento | B. Percival | T. Mahungu | K. Williamson | Andrew Nelson | K. Jackson | G. Dabrera | S. Cottrell | C. Moore | R. Gunson | V. Sivaprakasam | S. Parmar | S. Sridhar | B. Blane | T. Haque | Y. Taha | A. Thornton | I. Georgana | A. Bosworth | I. Bronner | R. Howe | T. Curran | T. Tsoleridis | J. Douthwaite | S. Essex | A. Hale | C. Kitchen | K. Saeed | Shazaad Ahmad | T. Vasylyeva | Tim Wyatt | S. Gonçalves | J. Warwick-Dugdale | I. Vipond | N. Cortes | Hannah E. Bridgewater | J. Durham | M. McHugh | C. Ludden | Michael D. Gallagher | L. Macfarlane-Smith | D. Aggarwal | J. Masoli | A. Marchbank | S. Forrest | Emmeline R. Watkins | Claire L. McNulty | Malorie Perry | M. Ragonnet-Cronin | Charlotte Nelson | P. Randell | B. Cogger | W. Yew | N. Storey | M. Maes | D. Jamrozy | L. Ensell | A. Karamani | L. Williams | M. Hosmillo | L. Berry | T. Boswell | Patawee Asamaphan | A. Broos | K. Smollett | C. Manso | D. Bibby | E. Barton | M. Torok | Joanne Watts | A. Rowan | G. Macintyre-Cockett | N. Hadjirin | E. Meader | D. Bradley | Robert Beer | D. Robertson | K. Nomikou | J. Greatorex | A. Cox | B. Payne | A. Maclean | J. Heaney | J. Shepherd | Rajiv Shah | N. Jesudason | Kathy K Li | N. Johnson | Daniel Mair | S. Carmichael | Hannah Dent | M. Zamudio | S. Dervisevic | N. Craine | Elizabeth Wright | N. Moore | J. Lynch | M. Mori | A. Justice | S. Miah | M. Unnikrishnan | E. Higginson | S. Attwood | T. Connor | Sarah François | R. Myers | N. Ellaby | S. Platt | N. Groves | E. Gallagher | M. Chand | Rebecca Williams | G. Vernet | C. McMurray | M. Morgan | G. Nebbia | S. Bonner | Stephanie H. Lo | P. Bird | R. Dewar | A. Price | S. Robson | J. Singer | E. Wilson-Davies | C. McKerr | Sharif Shaaban | K. Bicknell | S. Louka | N. Matheson | D. Fairley | C. Williams | Tranprit Saluja | L. Levett | G. Clark | K. Liddell | L. Sheridan | A. Westhorpe | L. Snell | Sarojini Pandey | Rachel Jones | R. George | B. Samaraweera | A. Mahanama | G. Betancor | Sian Morgan | Thomas Helmer | M. Pinckert | M. Ramsay | J. Ball | C. Bresner | G. Wright | A. Carabelli | Igor Starinskij | L. James | O. Nsonwu | S. Hannan | C. Brown | T. Williams | M. Niebel | A. Farbos | L. Fina | S. Moses | R. Blacow | Michael A. Quail | S. Rey | T. Sloan | S. Burton-Fanning | J. Breuer | A. Jahun | M. Alam | Jennifer E Collins | Christopher Moore | J. Chappell | M. Carlile | Fei Sang | I. Willingham | Amelia Joseph | M. Khakh | V. Fleming | M. Lister | H. Howson-Wells | Clare Leong | A. Orton | Rob Howes | L. Turtle | C. Cormie | M. Andersson | A. Trotter | D. Grammatopoulos | A. Holmes | J. Price | Thanh Le-Viet | Steven J. Rudder | Rachael Stanley | Lizzie Meadows | L. Coupland | G. Hall | Safiah Afifi | Kathryn Mccluggage | Joshua Maksimovic | Karla Spellman | Joel Southgate | R. Eccles | F. Halstead | Chloe Fisher | N. Duckworth | Sarah Walsh | J. Watkins | Alec Birchley | Bree Gatica-Wilcox | L. Gilbert | Sara Kumžiene-Summerhayes | Nicole Pacchiarini | Alexander Adams | Amy Gaskin | Laura Gifford | Johnny Debebe | Steven Liggett | G. Scarlett | K. Loveson | A. Beckett | William Fuller | T. 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Kenyon | Thomas Davis | Hannah Lowe | Susanne Stonehouse | J. Boyes | D. Shah | Laura Atkinson | A. Alcolea-Medina | W. Chatterton | Monika Pusok | Li Xu-McCrae | G. Young | Radoslaw Poplawski | Cathy Breen | A. Cowell | Graciela Sluga | Wendy Hogsden | P. Asamaphan | Seema Nickbakhsh | A. Bradley | G. Mollett | Elizabeth Wastenge | Louise Smith | D. Padgett | Garren Scott | E. Swindells | J. Greenaway | C. McCann | R. Impey | Nick Levene | Lynn Monaghan | C. Pearson | R. Hopes | Hannah M. Pymont | David Lee | Nikos Manesis | Vineet Patel | Chris J Williams | David Heyburn | Ember Hilvers | Fatima Downing | John Evans | Sophie Jones | Sue Edwards | Liz Ratcliffe | T. Thompson | Erwan Acheson | Dianne Irish-Tavares | J. Hart | Eric Witele | M. Fenton | Ashok Dadrah | Amanda Symmonds | C. Fearn | Siona Silveira | N. Bayzid | Riaz Jannoo | Sarah Jeremiah | K. Jones | F. Ashcroft | Nicola J. Cumley | Harmeet K. Gill | Jamie Young | L. Kermack | Sophie Palmer | E. Brooks | Georgina M. McManus | Carlos E. Balcazar | R. Manley | Edith E. Vamos | M. Whiteley | M. Gallis | Jeffrey K J Cheng | Lucy R Frost | Grace Taylor-Joyce | A. Cerda | Tamara Merrill | P. McClure | Luke Foulser | M. Gourtovaia | J. Keatley | Samantha McGuigan | Steven O. Palmer | Liam J. Prestwood | Christoph Puethe | C. Scott | Danni Weldon | Jennifier Liddle | Keith James | J. Barrett | Lenette Mactavous | Peijun Zhang | Gabriela Ahmadi-Assalemi | Karen Gibbs | J. McKenna | Allyson Lloyd | Christopher R. Jones | Ben W. Farr | Robin J. Moll | David A. Simpson | M. Glover | Andrew Beggs | C. McNulty | R. Henderson | C. Koshy | Martyn F Guest | Kim S. Smith | P. Maxwell | Rhys Izuagbe | Jack C. D. Lee | Darren L. Smith | N. Machin | S. O’Brien | S. Rushton | E. Robinson | Peter Muir | Vicki Chalker | H. Jones | Matthew Bull | David J. Baker | Y. Bourgeois | Kate F. Cook | Helen L. Lowe | Joana Dias | Margaret Hughes | Nikki Smith | C. Abell | Marina Metaxaki | S. Fuller | G. Weale | C. Brierley | Mahin Bagheri Kahkeshi | Darius Danaei | R. Dyer | Oliver Lambson | Naomi R. Park | S. Morgan | R. Clark | Emma Wise | D. Bradshaw | A. Patel | D. Groves | Dominic P. Kwiatkowski | Victoria Hollamby | Mark Whitehead | R. Sing | P. Madona | Ian Leslie | Joanne Stockton | R. M. Nunez | J. Moore | Stephen Kidd | JamesW. Harrison | Rebekah E. Wilson | P. Parsons | T. Feather | T. Ridgman | Á. O’Toole | E. O’Toole | Katherine L. Bellis | David K. Jackson | Elen De Lacy | Marius Cotic | R. Gupta | M. H. S. Chapman | R. Davies | Shane A. McCarthy | Lily Tong | Lee H. Graham | Julian W Tang | S. Hutchings | Z. Molnár | Rachel J. Williams | Jon Holgate | Christopher A. Brown | Alexandra Julie Steve Christopher Roger Daniel R. Fred Jenni Orton Douthwaite Rees Brown Clark Jones | Daniel R. Jones | Fred Kuenzi | J. Rankin | I. Waddell | Patrick Nicholas Chris Vickie Craig Jon Aastha Kathryn Mic Maxwell Matheson Abell Braithwaite Brierl | Jon Crowcroft | Aastha Dahal | Kathryn P. A. Faulkner | Sally Valletta | Martin Vinnell | Sarah F. Berry | D. Hancock | J. Winster | Robin Goodall | Steve Hoensch | N. Mathieson | K. Nikitina | Zara Sheldrake | Martin G. Keen | Aris Sato | Jonathan Tolhurst | J. Williman | Sinead Jordan | Tania Fatseas | Peter Taylor | Christine Georgiou | Michelle Caspersz | Richard Davies | Rebecca Clarke | Barbara Mozdzen | Gabor Raub | Asako Radecki | Phil White | R. Hughes | Lucie Gransden | Matt Ceaser | Karl Wilson | Diane Mungovan | Steve Matthews | Paule Searle | J. Mills | E. Murphy | Matthew Russell | Steve Poppitt | John Tynan | F. Marchetti | Aleksandra Hosaja | Jordon Wright | Natalie Quinnell | Dinesh Ellena Alessandro M. Carol M. Katerina Sophia T. R Aggarwal Brooks Carabelli Churcher Galai G | D. McFarlane | E. Lacy | Steven Rudder | C. Nelson | Jack C D Lee | H. Bridgewater | D. Mcfarlane | S. Jordan | Harmeet Gill | David L. Robertson | Guy Mollett | Rachel M Blacow | Katherine Smollett | Ana da Silva Filipe | A. Joseph | J. Collins | Ian Harrison | Nazreen F. Hadjirin | Scott A. J. Thurston | Stephen Carmichael | S. Nickbakhsh | Karen Oliver | Mailis Maes | J. Hughes | Dorota Jamrozy | Afzal Chaudhry | J. Tynan | David Connor | Francesc Coll | John Boyes | Stefan Rooke | Christopher A. Brown | Richard Davies

[1]  William L. Hamilton,et al.  Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission , 2021, Nature communications.

[2]  S. Bhatt,et al.  Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza , 2021, medRxiv.

[3]  N. Loman,et al.  CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance , 2021, Genome Biology.

[4]  N. Loman,et al.  CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance , 2021, Genome biology.

[5]  A. Neely,et al.  Feasibility and efficacy of mass testing for SARS-CoV-2 in a UK university using swab pooling and PCR , 2021 .

[6]  D. O’Connor,et al.  Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in Intercollegiate Athletics Not Fully Mitigated With Daily Antigen Testing , 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[7]  S. Michie,et al.  Adherence to the test, trace, and isolate system in the UK: results from 37 nationally representative surveys , 2021, BMJ.

[8]  Graham W. Taylor,et al.  Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Nature.

[9]  K. V. Parag,et al.  Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK , 2020, medRxiv.

[10]  T. Vaughan,et al.  The origin and early spread of SARS-CoV-2 in Europe , 2020, Proceedings of the National Academy of Sciences.

[11]  J. Bloom,et al.  Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020 , 2020, medRxiv.

[12]  Christopher J. R. Illingworth,et al.  A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events , 2020, medRxiv.

[13]  T. Vaughan,et al.  Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data , 2020, medRxiv.

[14]  R. Walensky,et al.  Covid-19: re-opening universities is high risk , 2020, BMJ.

[15]  J. Quick nCoV-2019 sequencing protocol v3 (LoCost) , 2020 .

[16]  Colin Simpson,et al.  Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand , 2020, Nature Communications.

[17]  Edward C. Holmes,et al.  A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology , 2020, Nature Microbiology.

[18]  R. Hayes,et al.  A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings , 2020, Journal of Clinical Microbiology.

[19]  William L. Hamilton,et al.  Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study , 2020, The Lancet Infectious Diseases.

[20]  S. Robson,et al.  An integrated national scale SARS-CoV-2 genomic surveillance network , 2020, The Lancet Microbe.

[21]  J. Hur,et al.  Public Health Emergency and Crisis Management: Case Study of SARS-CoV-2 Outbreak , 2020, International journal of environmental research and public health.

[22]  Mark B. Schultz,et al.  Tracking the COVID-19 pandemic in Australia using genomics , 2020, Nature Communications.

[23]  William L. Hamilton,et al.  Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission , 2020, medRxiv.

[24]  P. Sahu Closure of Universities Due to Coronavirus Disease 2019 (COVID-19): Impact on Education and Mental Health of Students and Academic Staff , 2020, Cureus.

[25]  Ruiyun Li,et al.  Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2) , 2020, Science.

[26]  Rui Ji,et al.  Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a systematic review and meta-analysis , 2020, International Journal of Infectious Diseases.

[27]  J. Xiang,et al.  Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study , 2020, The Lancet.

[28]  V. Corman,et al.  Severe Acute Respiratory Syndrome Coronavirus 2 Outbreak Related to a Nightclub, Germany, 2020 , 2020, Emerging infectious diseases.

[29]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[30]  Sebastián Duchêne,et al.  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis , 2018, bioRxiv.

[31]  M. Suchard,et al.  Posterior summarisation in Bayesian phylogenetics using Tracer , 2022 .

[32]  Daniel L. Ayres,et al.  Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 , 2018, Virus evolution.

[33]  M. Delgado-Rodríguez,et al.  Systematic review and meta-analysis. , 2017, Medicina intensiva.

[34]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[35]  Dennis Andersson,et al.  A retrospective cohort study , 2018 .

[36]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[37]  Yuelong Shu,et al.  GISAID: Global initiative on sharing all influenza data – from vision to reality , 2017, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[38]  Guy Cochrane,et al.  European Nucleotide Archive in 2016 , 2016, Nucleic Acids Res..

[39]  Khalil Abudahab,et al.  Microreact: visualizing and sharing data for genomic epidemiology and phylogeography , 2016, Microbial genomics.

[40]  Andy Smith,et al.  CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community , 2016, bioRxiv.

[41]  Andrew Rambaut,et al.  Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) , 2016, Virus evolution.

[42]  Minh Anh Nguyen,et al.  Ultrafast Approximation for Phylogenetic Bootstrap , 2013, Molecular biology and evolution.

[43]  S. Bonhoeffer,et al.  Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV) , 2012, Proceedings of the National Academy of Sciences.

[44]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[45]  M. Plummer,et al.  CODA: convergence diagnosis and output analysis for MCMC , 2006 .

[46]  S. Tavaré Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .