Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

da Silva Filipe, Ana, Shepherd, James G., Williams, Thomas, Hughes, Joseph, Aranday-Cortes, Elihu, Asamaphan, Patawee, Ashraf, Shirin, Balcazar, Carlos, Brunker, Kirstyn, Campbell, Alasdair, Carmichael, Stephen, Davis, Chris, Dewar, Rebecca, Gallagher, Michael D., Gunson, Rory, Hill, Verity, Ho, Antonia, Jackson, Ben, James, Edward, Jesudason, Natasha, Johnson, Natasha, McWilliam Leitch, E. Carol, Li, Kathy, MacLean, Alasdair, Mair, Daniel, McAllister, David A., McCrone, John T., McDonald, Sarah E., McHugh, Martin P., Morris, A. Keith, Nichols, Jenna, Niebel, Marc, Nomikou, Kyriaki, Orton, Richard J., O’Toole, Áine, Palmarini, Massimo, Parcell, Benjamin J., Parr, Yasmin A., Rambaut, Andrew, Rooke, Stefan, Shaaban, Sharif, Shah, Rajiv, Singer, Joshua B., Smollett, Katherine, Starinskij, Igor, Tong, Lily, Sreenu, Vattipally B., Wastnedge, Elizabeth, Holden, Matthew T. G., Robertson, David L., Templeton, Kate, Thomson, Emma C., Bashton, Matthew, Nelson, Andrew, Smith, Darren, Young, Greg and The COVID-19 Genomics UK (COG-UK) consortium, (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6 (1). pp. 112-122. ISSN 2058-5276

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Official URL: https://doi.org/10.1038/s41564-020-00838-z

Abstract

Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and epidemiological approach. Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to estimate that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Epidemiological analysis confirmed that early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). We identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. Community transmission occurred after 2 March, 3 weeks before control measures were introduced. Earlier travel restrictions or quarantine measures, both locally and internationally, would have reduced the number of COVID-19 cases in Scotland. The risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity.

Item Type: Article
Additional Information: Funding information: We thank all staff at the Scottish NHS virology laboratories who provided samples for sequencing, as well as the global researchers who shared genome data on GISAID (https://www.gisaid.org). We thank R. Kuo, T. Regan and A. Warr (The Roslin Institute, University of Edinburgh) for sequencing reagents, and S. Arkison for server maintenance. The study was funded by the Medical Research Council (MRC) core award (MC UU 1201412), a Wellcome Trust Collaborator Award (206298/Z/17/Z – for the ARTIC Network), and a Wellcome Trust Award (204802/Z/16/Z). COG-UK is supported by funding from the MRC part of UK Research and Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. The Cloud Infrastructure for Microbial Bioinformatics is funded by the MRC through grant MR/L015080/1. Matthew Bashton, Darren L. Smith, Gregory R. Young and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium.
Subjects: C700 Molecular Biology, Biophysics and Biochemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Elena Carlaw
Date Deposited: 21 Jun 2021 11:53
Last Modified: 23 Jun 2021 11:30
URI: http://nrl.northumbria.ac.uk/id/eprint/46498

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