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, Elizabeth Wastnedge, Matthew T G Holden, David L Robertson, Kate Templeton

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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
Issue number1
Publication statusPublished - 21 Dec 2020


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