Genomic reconstruction of the SARS-CoV-2 epidemic in England

Vöhringer, Harald S., Sanderson, Theo, Sinnott, Matthew, De Maio, Nicola, Nguyen, Thuy, Goater, Richard, Schwach, Frank, Harrison, Ian, Hellewell, Joel, Ariani, Cristina V., Gonçalves, Sonia, Jackson, David K., Johnston, Ian, Jung, Alexander W., Saint, Callum, Sillitoe, John, Suciu, Maria, Goldman, Nick, Panovska-Griffiths, Jasmina, Birney, Ewan, Volz, Erik, Funk, Sebastian, Kwiatkowski, Dominic, Chand, Meera, Martincorena, Inigo, Barrett, Jeffrey C., Gerstung, Moritz, The Wellcome Sanger Institute Covid-19 Surveillance Team, , The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, McCann, Clare, Nelson, Andrew, Smith, Darren and Young, Greg (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature. ISSN 0028-0836 (In Press)

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Official URL: https://doi.org/10.1038/s41586-021-04069-y

Abstract

The evolution of the SARS-CoV-2 pandemic continuously produces new variants, which warrant timely epidemiological characterisation. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. Alpha grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed Alpha and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to have exceeded that of Alpha. Finally, B.1.617.2/Delta was repeatedly introduced to England and grew rapidly in the early summer of 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June.

Item Type: Article
Additional Information: Matthew Bashton, Andrew Nelson, Clare McCann, Greg Young and Darren Smith are members of the COVID-19 Genomics UK (COG-UK) consortium. Funding information: COG-UK HOCI funded by COG-UK consortium. Funding information: s COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. Additional sequence generation was funded by the Department of Health and Social Care. We would like to thank our colleagues at EMBL-EBI, the Wellcome Sanger Institute and from COG-UK for stimulating discussions and helpful comments on this manuscript. HSV, JPG and MG are supported by a grant from the Department of Health and Social Care. AWJ, EB and MG are beneficiaries from grant NNF17OC0027594 from the Novo Nordisk Foundation. EV is supported by Wellcome Trust grant 220885/Z/20/Z. TS is supported by grant 210918/Z/18/Z, and JH and SF by grant 210758/Z/18/Z from the Wellcome Trust. HSV, NDM, AWJ, NG, EB and MG are supported by EMBL. We would like to thank Elias Allara (Cambridge) and Georgia Whitton (Sanger) for providing outer postcodes to LTLA mappings, Rupert Beale for comments and John McCrone for setting up Thorney Beast analysis. We thank all the contributors who submitted genome sequences to GISAID. Acknowledgement tables for individual sequences are deposited at https://github.com/NicolaDM/phylogeographySARS-CoV-2.
Subjects: B100 Anatomy, Physiology and Pathology
C500 Microbiology
C700 Molecular Biology, Biophysics and Biochemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Elena Carlaw
Date Deposited: 19 Nov 2021 15:33
Last Modified: 19 Nov 2021 15:45
URI: http://nrl.northumbria.ac.uk/id/eprint/47798

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