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

Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)

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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.

Item Type:Articles
Additional Information: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.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Shah, Dr Rajiv and Li, Dr Kathy and Aranday-Cortes, Dr Elihu and Robertson, Professor David and Singer, Dr Joshua and McAllister, Professor David and Asamaphan, Dr Patawee and Palmarini, Professor Massimo and Tong, Dr Lily and Mair, Mr Daniel and Davis, Dr Chris and Orton, Dr Richard and Jesudason, Dr Natasha and Da Silva Filipe, Dr Ana and Shepherd, Dr James and Gunson, Dr Rory and Hughes, Dr Joseph and McDonald, Dr Sarah and Rooke, Stefan and Carmichael, Dr Stephen and Nichols, Mrs Jenna and Vattipally, Dr Sreenu and Ho, Dr Antonia and Nomikou, Dr Kyriaki and Thomson, Professor Emma and Leitch, Dr Carol and Brunker, Dr Kirstyn and Parr, Ms Yasmin and Johnson, Miss Natasha and Smollett, Dr Katherine and MacLean, Dr Alasdair and Niebel, Mr Marc and Ashraf, Dr Shirin
Authors: Da Silva Filipe, A., Shepherd, J. G., Williams, T., Hughes, J., Aranday-Cortes, E., Asamaphan, P., Ashraf, S., Balcazar, C., Brunker, K., Campbell, A., Carmichael, S., Davis, C., Dewar, R., Gallagher, M. D., Gunson, R., Hill, V., Ho, A., Jackson, B., James, E., Jesudason, N., Johnson, N., Leitch, E. C. M., Li, K., MacLean, A., Mair, D., McAllister, D. A., McCrone, J. T., McDonald, S. E., McHugh, M. P., Morris, A. K., Nichols, J., Niebel, M., Nomikou, K., Orton, R. J., O'Toole, Á., Palmarini, M., Parcell, B. J., Parr, Y. A., Rambaut, A., Rooke, S., Shaaban, S., Shah, R., Singer, J. B., Smollett, K., Starinskij, I., Tong, L., Sreenu, V. B., Wastnedge, E., COVID-19 Genomics UK (COG-UK) Consortium, ., Holden, M. T.G., Robertson, D. L., Templeton, K., and Thomson, E. C.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > Institute of Health and Wellbeing > Public Health
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Nature Microbiology
Publisher:Nature Research
ISSN:2058-5276
ISSN (Online):2058-5276
Published Online:21 December 2020
Copyright Holders:Copyright © 2020 Springer Nature
First Published:First published in Nature Microbiology 6(1):112-122
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher

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