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

Dinesh Aggarwal; Andrew J. Page; Ulf Schaefer; George M. Savva; Richard Myers; Erik Volz; Nicholas Ellaby; Steven Platt; Natalie Groves; Eileen Gallagher; Niamh M. Tumelty; Thanh Le Viet; Gareth J. Hughes; Cong Chen; Charlie Turner; Sophie Logan; Abbie Harrison; The COVID-19 Genomics UK (COG-UK) Consortium; Sharon J. Peacock; Meera Chand; Ewan M. Harrison; Darren L. Smith; Matthew Bashton; Gregory R. Young; Andrew Nelson; Clare M. McCann; Wen C. Yew

doi:10.1038/s41467-022-28371-z

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

Dinesh Aggarwal^*, Andrew J. Page, Ulf Schaefer, George M. Savva, Richard Myers, Erik Volz, Nicholas Ellaby, Steven Platt, Natalie Groves, Eileen Gallagher, Niamh M. Tumelty, Thanh Le Viet, Gareth J. Hughes, Cong Chen, Charlie Turner, Sophie Logan, Abbie Harrison, The COVID-19 Genomics UK (COG-UK) Consortium, Sharon J. Peacock, Meera ChandEwan M. Harrison^*, Darren L. Smith, Matthew Bashton, Gregory R. Young, Andrew Nelson, Clare M. McCann, Wen C. Yew

^*Corresponding author for this work

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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.

Original language	English
Article number	1012
Pages (from-to)	1-13
Number of pages	13
Journal	Nature Communications
Volume	13
Issue number	1
Early online date	23 Feb 2022
DOIs	https://doi.org/10.1038/s41467-022-28371-z
Publication status	Published - 1 Dec 2022

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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Aggarwal, D., Page, A. J., Schaefer, U., Savva, G. M., Myers, R., Volz, E., Ellaby, N., Platt, S., Groves, N., Gallagher, E., Tumelty, N. M., Le Viet, T., Hughes, G. J., Chen, C., Turner, C., Logan, S., Harrison, A., The COVID-19 Genomics UK (COG-UK) Consortium, Peacock, S. J., ... Yew, W. C. (2022). Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13(1), 1-13. Article 1012. https://doi.org/10.1038/s41467-022-28371-z

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title = "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.",

author = "Dinesh Aggarwal and Page, \{Andrew J.\} and Ulf Schaefer and Savva, \{George M.\} and Richard Myers and Erik Volz and Nicholas Ellaby and Steven Platt and Natalie Groves and Eileen Gallagher and Tumelty, \{Niamh M.\} and \{Le Viet\}, Thanh and Hughes, \{Gareth J.\} and Cong Chen and Charlie Turner and Sophie Logan and Abbie Harrison and \{The COVID-19 Genomics UK (COG-UK) Consortium\} and Peacock, \{Sharon J.\} and Meera Chand and Harrison, \{Ewan M.\} and Smith, \{Darren L.\} and Matthew Bashton and Young, \{Gregory R.\} and Andrew Nelson and McCann, \{Clare M.\} and Yew, \{Wen C.\}",

note = "Funding information: We thank members of the COVID-19 Genomics Consortium UK and Test and Trace contact tracers for their contributions to generating the data used in this study. We thank the Sanger Covid Team for assisting with Samples and Logistics. We thank Sarah Mitchell from the Department of Plant Sciences, University of Cambridge, for direction on statistical analysis. D.A. is a Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant no. 222903/Z/21/Z). E.M.H. is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. A.J.P., T.L.V. and G.M.S. gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/ R012504/1 and its constituent project BBS/E/F/000PR10352, also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). The COVID-19 Genomics UK (COG-UK) Consortium is supported by funding from the Medical Research Council (MRC) part of UK Research \& Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. For the purpose of open access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.",

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doi = "10.1038/s41467-022-28371-z",

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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, The COVID-19 Genomics UK (COG-UK) Consortium, Peacock, SJ, Chand, M, Harrison, EM, Smith, DL , Bashton, M, Young, GR, Nelson, A , McCann, CM & Yew, WC 2022, 'Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission', Nature Communications, vol. 13, no. 1, 1012, pp. 1-13. https://doi.org/10.1038/s41467-022-28371-z

TY - JOUR

T1 - Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

AU - Aggarwal, Dinesh

AU - Page, Andrew J.

AU - Schaefer, Ulf

AU - Savva, George M.

AU - Myers, Richard

AU - Volz, Erik

AU - Ellaby, Nicholas

AU - Platt, Steven

AU - Groves, Natalie

AU - Gallagher, Eileen

AU - Tumelty, Niamh M.

AU - Le Viet, Thanh

AU - Hughes, Gareth J.

AU - Chen, Cong

AU - Turner, Charlie

AU - Logan, Sophie

AU - Harrison, Abbie

AU - The COVID-19 Genomics UK (COG-UK) Consortium

AU - Peacock, Sharon J.

AU - Chand, Meera

AU - Harrison, Ewan M.

AU - Smith, Darren L.

AU - Bashton, Matthew

AU - Young, Gregory R.

AU - Nelson, Andrew

AU - McCann, Clare M.

AU - Yew, Wen C.

N1 - Funding information: We thank members of the COVID-19 Genomics Consortium UK and Test and Trace contact tracers for their contributions to generating the data used in this study. We thank the Sanger Covid Team for assisting with Samples and Logistics. We thank Sarah Mitchell from the Department of Plant Sciences, University of Cambridge, for direction on statistical analysis. D.A. is a Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant no. 222903/Z/21/Z). E.M.H. is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. A.J.P., T.L.V. and G.M.S. gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/ R012504/1 and its constituent project BBS/E/F/000PR10352, also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). The COVID-19 Genomics UK (COG-UK) Consortium is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. For the purpose of open access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.

PY - 2022/12/1

Y1 - 2022/12/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85125215535

U2 - 10.1038/s41467-022-28371-z

DO - 10.1038/s41467-022-28371-z

M3 - Article

SN - 2041-1723

VL - 13

SP - 1

EP - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 1012

ER -

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

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