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

Ana da Silva Filipe, James G. Shepherd, Thomas Williams, Joseph Hughes, Elihu Aranday-Cortes, Patawee Asamaphan, Shirin Ashraf, Carlos Balcazar, Kirstyn Brunker, Alasdair Campbell, Stephen Carmichael, Chris Davis, Rebecca Dewar, Michael D. Gallagher, Rory Gunson, Verity Hill, Antonia Ho, Ben Jackson, Edward James, Natasha JesudasonNatasha Johnson, E. Carol McWilliam Leitch, Kathy Li, Alasdair MacLean, Daniel Mair, David A. McAllister, John T. McCrone, Sarah E. McDonald, Martin P. McHugh, A. Keith Morris, Jenna Nichols, Marc Niebel, Kyriaki Nomikou, Richard J. Orton, Áine O’Toole, Massimo Palmarini, Benjamin J. Parcell, Yasmin A. Parr, Andrew Rambaut, Stefan Rooke, Sharif Shaaban, Rajiv Shah, Joshua B. Singer, Katherine Smollett, Igor Starinskij, Lily Tong, Vattipally B. Sreenu, Elizabeth Wastnedge, , Matthew T. G. Holden, David L. Robertson, Kate Templeton, Emma C. Thomson

    Research output: Contribution to journalArticlepeer-review

    6 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)112-122
    Number of pages11
    JournalNature Microbiology
    Volume6
    Issue number1
    Early online date21 Dec 2020
    DOIs
    Publication statusPublished - Jan 2021

    Keywords

    • SARS-CoV-2
    • Viral epidemiology

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