Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Abstract

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16–20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement.

Metadata

Item Type:	Article
Authors/Creators:	Aggarwal, D Page, AJ Schaefer, U Savva, GM Myers, R Volz, E Ellaby, N Platt, S Groves, N Gallagher, E Tumelty, NM Le Viet, T Hughes, GJ Chen, C Turner, C Logan, S Harrison, A Koshy, C Ash, A Wise, E Moore, N Mori, M Cortes, N Lynch, J Kidd, S Fairley, DJ Curran, T McKenna, JP Adams, H Fraser, C Golubchik, T Bonsall, D Hassan-Ibrahim, MO Malone, CS Cogger, BJ Wantoch, M Reynolds, N Warne, B Maksimovic, J Spellman, K McCluggage, K John, M Beer, R Afifi, S Morgan, S Marchbank, A Price, A Kitchen, C Gulliver, H Merrick, I Southgate, J Guest, M Munn, R Workman, T Connor, TR Fuller, W Bresner, C Snell, LB Patel, A Charalampous, T Nebbia, G Batra, R Edgeworth, J Robson, SC Beckett, AH Aanensen, DM Underwood, AP Yeats, CA Abudahab, K Taylor, BEW Menegazzo, M Clark, G Smith, W Khakh, M Fleming, VM Lister, MM Howson-Wells, HC Berry, L Boswell, T Joseph, A Willingham, I Jones, C Holmes, C Bird, P Helmer, T Fallon, K Tang, J Raviprakash, V Campbell, S Sheriff, N Blakey, V Williams, L-A Loose, MW Holmes, N Moore, C Carlile, M Wright, V Sang, F Debebe, J Coll, F Signell, AW Betancor, G Wilson, HD Eldirdiri, S Kenyon, A Davis, T Pybus, OG du Plessis, L Zarebski, AE Raghwani, J Kraemer, MUG Francois, S Attwood, SW Vasylyeva, TI Zamudio, ME Gutierrez, B Torok, ME Hamilton, WL Goodfellow, IG Hall, G Jahun, AS Chaudhry, Y Hosmillo, M Pinckert, ML Georgana, I Moses, S Lowe, H Bedford, L Moore, J Stonehouse, S Fisher, CL Awan, AR BoYes, J Breuer, J Harris, KA Brown, JR Shah, D Atkinson, L Lee, JCD Storey, N Flaviani, F Alcolea-Medina, A Williams, R Vernet, G Chapman, MR Levett, LJ Heaney, J Chatterton, W Pusok, M Xu-McCrae, L Smith, DL Bashton, M Young, GR Holmes, A Randell, PA Cox, A Madona, P Bolt, F Price, J Mookerjee, S Ragonnet-Cronin, M Nascimento, FF Jorgensen, D Siveroni, I Johnson, R Boyd, O Geidelberg, L Volz, EM Rowan, A Taylor, GP Smollett, KL Loman, NJ Quick, J McMurray, C Stockton, J Nicholls, S Rowe, W Poplawski, R McNally, A Nunez, RTM Mason, J Robinson, TI O’Toole, E Watts, J Breen, C Cowell, A Sluga, G Machin, NW Ahmad, SSY George, RP Halstead, F Sivaprakasam, V Hogsden, W Illingworth, CJ Jackson, C Thomson, EC Shepherd, JG Asamaphan, P Niebel, MO Li, KK Shah, RN Jesudason, NG Tong, L Broos, A Mair, D Nichols, J Carmichael, SN Nomikou, K Aranday-Cortes, E Johnson, N Starinskij, I da Silva Filipe, A Robertson, DL Orton, RJ Hughes, J Vattipally, S Singer, JB Nickbakhsh, S Hale, AD Macfarlane-Smith, LR Harper, KL Carden, H Taha, Y Payne, BAI Burton-Fanning, S Waugh, S Collins, J Eltringham, G Rushton, S O’Brien, S Bradley, A Maclean, A Mollett, G Blacow, R Templeton, KE McHugh, MP Dewar, R Wastenge, E Dervisevic, S Stanley, R Meader, EJ Coupland, L Smith, L Graham, C Barton, E Padgett, D Scott, G Swindells, E Greenaway, J Nelson, A McCann, CM Yew, WC Andersson, M Peto, T Justice, A Eyre, D Crook, D Sloan, TJ Duckworth, N Walsh, S Chauhan, AJ Glaysher, S Bicknell, K Wyllie, S Elliott, S Lloyd, A Impey, R Levene, N Monaghan, L Bradley, DT Wyatt, T Allara, E Pearson, C Osman, H Bosworth, A Robinson, E Muir, P Vipond, IB Hopes, R Pymont, HM Hutchings, S Curran, MD Parmar, S Lackenby, A Mbisa, T Miah, S Bibby, D Manso, C Hubb, J Dabrera, G Ramsay, M Bradshaw, D Thornton, A Gallagher, E Lee, D Williams, D Harrison, I Hartman, H Manesis, N Patel, V Bishop, C Chalker, V Ledesma, J Twohig, KA Holden, MTG Shaaban, S Birchley, A Adams, A Davies, A Gaskin, A Plimmer, A Gatica-Wilcox, B McKerr, C Moore, C Williams, C Heyburn, D De Lacy, E Hilvers, E Downing, F Shankar, G Jones, H Asad, H Coombes, J Watkins, J Evans, JM Fina, L Gifford, L Gilbert, L Graham, L Perry, M Morgan, M Bull, M Cronin, M Pacchiarini, N Craine, N Jones, R Howe, R Corden, S Rey, S Kumziene-SummerhaYes, S Taylor, S Cottrell, S Jones, S Edwards, S O’Grady, J Mather, AE Baker, DJ Rudder, S Aydin, A Kay, GL Trotter, AJ Alikhan, N-F de Oliveira Martins, L Le-Viet, T Meadows, L Casey, A Ratcliffe, L Simpson, DA Molnar, Z Thompson, T Acheson, E Masoli, JAH Knight, BA Ellard, S Auckland, C Jones, CR Mahungu, TW Irish-Tavares, D Haque, T Hart, J Witele, E Fenton, ML Dadrah, A Symmonds, A Saluja, T Bourgeois, Y Scarlett, GP Loveson, KF Goudarzi, S Fearn, C Cook, K Dent, H Paul, H Partridge, DG https://orcid.org/0000-0002-0417-2016 Raza, M Evans, C Johnson, K Liggett, S Baker, P Bonner, S Essex, S Lyons, RA Saeed, K Mahanama, AIK Samaraweera, B Silveira, S Pelosi, E Wilson-Davies, E Williams, RJ Kristiansen, M Roy, S Williams, CA Cotic, M Bayzid, N Westhorpe, AP Hartley, JA Jannoo, R Lowe, HL Karamani, A Ensell, L Prieto, JA Jeremiah, S Grammatopoulos, D Pandey, S Berry, L Jones, K Richter, A Beggs, A Best, A Percival, B Mirza, J Megram, O Mayhew, M Crawford, L Ashcroft, F Moles-Garcia, E Cumley, N Smith, CP Bucca, G Hesketh, AR Blane, B Girgis, ST Leek, D Sridhar, S Forrest, S Cormie, C Gill, HK Dias, J Higginson, EE Maes, M Young, J Kermack, LM Gupta, RK Ludden, C Peacock, SJ Palmer, S Churcher, CM Hadjirin, NF Carabelli, AM Brooks, E Smith, KS Galai, K McManus, GM Ruis, C Davidson, RK Rambaut, A Williams, T Balcazar, CE Gallagher, MD O’Toole, Á Rooke, S Hill, V Williamson, KA Stanton, TD Michell, SL Bewshea, CM Temperton, B Michelsen, ML Warwick-Dugdale, J Manley, R Farbos, A Harrison, JW Sambles, CM Studholme, DJ Jeffries, AR Darby, AC Hiscox, JA Paterson, S Iturriza-Gomara, M Jackson, KA Lucaci, AO Vamos, EE Hughes, M Rainbow, L Eccles, R Nelson, C Whitehead, M Turtle, L Haldenby, ST Gregory, R Gemmell, M Wierzbicki, C Webster, HJ de Silva, TI Smith, N Angyal, A Lindsey, BB Groves, DC Green, LR Wang, D Freeman, TM Parker, MD Keeley, AJ Parsons, PJ Tucker, RM Brown, R Wyles, M Whiteley, M Zhang, P Gallis, M Louka, SF Constantinidou, C Unnikrishnan, M Ott, S Cheng, JKJ Bridgewater, HE Frost, LR Taylor-Joyce, G Stark, R Baxter, L Alam, MT Brown, PE Aggarwal, D Cerda, AC Merrill, TV Wilson, RE McClure, PC Chappell, JG Tsoleridis, T Ball, J Buck, D Todd, JA Green, A Trebes, A MacIntyre-Cockett, G de Cesare, M Alderton, A Amato, R Ariani, CV Beale, MA Beaver, C Bellis, KL Betteridge, E Bonfield, J Danesh, J Dorman, MJ Drury, E Farr, BW Foulser, L Goncalves, S Goodwin, S Gourtovaia, M Harrison, EM Jackson, DK Jamrozy, D Johnston, I Kane, L Kay, S Keatley, J-P Kwiatkowski, D Langford, CF Lawniczak, M Letchford, L Livett, R Lo, S Martincorena, I McGuigan, S Nelson, R Palmer, S Park, NR Patel, M Prestwood, L Puethe, C Quail, MA Rajatileka, S Scott, C Shirley, L Sillitoe, J Chapman, MHS Thurston, SAJ Tonkin-Hill, G Weldon, D Rajan, D Bronner, IF Aigrain, L Redshaw, NM Lensing, SV Davies, R Whitwham, A Liddle, J Lewis, K Tovar-Corona, JM Leonard, S Durham, J Bassett, AR McCarthy, S Moll, RJ James, K Oliver, K Makunin, A Barrett, J Gunson, RN Peacock, SJ Chand, M Harrison, EM
Copyright, Publisher and Additional Information:	© 2022 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Dates:	Accepted: 18 January 2022 Published (online): 23 February 2022 Published: 23 February 2022
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Sheffield Teaching Hospitals
Depositing User:	Symplectic Sheffield
Date Deposited:	28 Feb 2022 13:58
Last Modified:	28 Feb 2022 13:58
Status:	Published
Publisher:	Springer Nature
Refereed:	Yes
Identification Number:	10.1038/s41467-022-28371-z
Related URLs:	PubMed URL
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:184181

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Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

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