TY - JOUR
T1 - Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland
AU - The COVID-19 Genomics UK (COG-UK) Consortium
AU - da Silva Filipe, Ana
AU - Shepherd, James G.
AU - Williams, Thomas
AU - Hughes, Joseph
AU - Aranday-Cortes, Elihu
AU - Asamaphan, Patawee
AU - Ashraf, Shirin
AU - Balcazar, Carlos
AU - Brunker, Kirstyn
AU - Campbell, Alasdair
AU - Carmichael, Stephen
AU - Davis, Chris
AU - Dewar, Rebecca
AU - Gallagher, Michael D.
AU - Gunson, Rory
AU - Hill, Verity
AU - Ho, Antonia
AU - Jackson, Ben
AU - James, Edward
AU - Jesudason, Natasha
AU - Johnson, Natasha
AU - McWilliam Leitch, E. Carol
AU - Li, Kathy
AU - MacLean, Alasdair
AU - Mair, Daniel
AU - McAllister, David A.
AU - McCrone, John T.
AU - McDonald, Sarah E.
AU - McHugh, Martin P.
AU - Morris, A. Keith
AU - Nichols, Jenna
AU - Niebel, Marc
AU - Nomikou, Kyriaki
AU - Orton, Richard J.
AU - O’Toole, Áine
AU - Palmarini, Massimo
AU - Parcell, Benjamin J.
AU - Parr, Yasmin A.
AU - Rambaut, Andrew
AU - Rooke, Stefan
AU - Shaaban, Sharif
AU - Shah, Rajiv
AU - Singer, Joshua B.
AU - Smollett, Katherine
AU - Starinskij, Igor
AU - Tong, Lily
AU - Sreenu, Vattipally B.
AU - Wastnedge, Elizabeth
AU - Holden, Matthew T.G.
AU - Robertson, David L.
AU - Bashton, Matthew
AU - Nelson, Andrew
AU - Smith, Darren
AU - Young, Greg
N1 - 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.
PY - 2021/1/1
Y1 - 2021/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85097954045&partnerID=8YFLogxK
U2 - 10.1038/s41564-020-00838-z
DO - 10.1038/s41564-020-00838-z
M3 - Article
C2 - 33349681
AN - SCOPUS:85097954045
VL - 6
SP - 112
EP - 122
JO - Nature Microbiology
JF - Nature Microbiology
SN - 2058-5276
IS - 1
ER -