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

Research output: Contribution to journalArticle


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.


  • Ana da Silva Filipe
  • James G Shepherd
  • Thomas Williams
  • Joseph Hughes
  • Elihu Aranday-Cortes
  • Patawee Asamaphan
  • Shirin Ashraf
  • Carlos Enrique Balcazar Lopez
  • Kirstyn Brunker
  • Alasdair Campbell
  • Stephen Carmichael
  • Chris Davis
  • Rebecca Dewar
  • Michael D Gallagher
  • Rory Gunson
  • Verity Hill
  • Antonia Ho
  • Ben Jackson
  • Edward James
  • Natasha Jesudason
  • Natasha 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
  • COVID-19 Genomics UK (COG-UK) Consortium
External organisations
  • Ninewells Hospital and Medical School
  • University of Edinburgh
  • University of Glasgow
  • Glasgow Royal Infirmary
  • Royal Infirmary of Edinburgh
  • Borders General Hospital
  • University of St Andrews
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Infectious Medicine


  • Adult, Aged, COVID-19/epidemiology, Europe/epidemiology, Genome, Viral, High-Throughput Nucleotide Sequencing, Humans, Male, Middle Aged, Molecular Epidemiology, Phylogeny, SARS-CoV-2/genetics, Spain/epidemiology, Travel/statistics & numerical data
Original languageEnglish
Pages (from-to)112-122
Number of pages11
JournalNature Microbiology
Issue number1
Publication statusPublished - 2021 Jan
Publication categoryResearch
Externally publishedYes

Bibliographic note

These authors jointly supervised this work: Matthew T. G. Holden, David L. Robertson, Kate Templeton, Emma C. Thomson.