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

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.