TY - JOUR
T1 - Genomic reconstruction of the SARS-CoV-2 epidemic in England
AU - Vöhringer, Harald S.
AU - Sanderson, Theo
AU - Sinnott, Matthew
AU - De Maio, Nicola
AU - Nguyen, 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 - The Wellcome Sanger Institute Covid-19 Surveillance Team
AU - The COVID-19 Genomics UK (COG-UK) Consortium
AU - Birney, Ewan
AU - Volz, Erik
AU - Funk, Sebastian
AU - Kwiatkowski, Dominic
AU - Chand, Meera
AU - Martincorena, Inigo
AU - Barrett, Jeffrey C.
AU - Gerstung, Moritz
AU - Davidson, Rosemary
N1 - Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature Limited.
PY - 2021/12/16
Y1 - 2021/12/16
N2 - 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.
AB - 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.
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
VL - 600
SP - 506
EP - 511
JO - Nature
JF - Nature
SN - 0028-0836
ER -