TY - JOUR
T1 - Genomic reconstruction of the SARS-CoV-2 epidemic in England
AU - The Wellcome Sanger Institute Covid-19 Surveillance Team
AU - The COVID-19 Genomics UK (COG-UK) Consortium
AU - Vöhringer, Harald S.
AU - Sanderson, Theo
AU - Sinnott, Matthew
AU - De Maio, Nicola
AU - Nguyen, Vu Thu Thuy
AU - Goater, Richard
AU - Schwach, Frank
AU - Harrison, Ian
AU - Hellewell, Joel
AU - Ariani, Cristina V.
AU - Gonçalves, Sonia
AU - Jackson, David K.
AU - Johnston, Ian
AU - Jung, Alexander W.
AU - Saint, Callum
AU - Sillitoe, John
AU - Suciu, Maria
AU - Goldman, Nick
AU - Panovska-Griffiths, Jasmina
AU - Birney, Ewan
AU - Volz, Erik
AU - Funk, Sebastian
AU - Kwiatkowski, Dominic P.
AU - Chand, Meera
AU - Martincorena, Inigo
AU - Barrett, Jeffrey C.
AU - Gerstung, Moritz
AU - Bashton, Matthew
AU - Nelson, Andrew
AU - McCann, Clare
AU - Smith, Darren
AU - Young, Greg
N1 - 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.
PY - 2021/12/16
Y1 - 2021/12/16
N2 - The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data 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 subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant 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 the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
AB - The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data 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 subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant 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 the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
KW - Amino Acid Substitution
KW - COVID-19/epidemiology
KW - England/epidemiology
KW - Epidemiological Monitoring
KW - Genome, Viral/genetics
KW - Genomics
KW - Humans
KW - Molecular Epidemiology
KW - Mutation
KW - Quarantine/statistics & numerical data
KW - SARS-CoV-2/classification
KW - Spatio-Temporal Analysis
KW - Spike Glycoprotein, Coronavirus/genetics
UR - http://www.scopus.com/inward/record.url?scp=85117501846&partnerID=8YFLogxK
U2 - 10.1038/s41586-021-04069-y
DO - 10.1038/s41586-021-04069-y
M3 - Article
C2 - 34649268
AN - SCOPUS:85117501846
SN - 0028-0836
VL - 600
SP - 506
EP - 511
JO - Nature
JF - Nature
IS - 7889
ER -
