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dc.contributor.authorVöhringer, Harald S
dc.contributor.authorSanderson, Theo
dc.contributor.authorSinnott, Matthew
dc.contributor.authorDe Maio, Nicola
dc.contributor.authorNguyen, Thuy
dc.contributor.authorGoater, Richard
dc.contributor.authorSchwach, Frank
dc.contributor.authorHarrison, Ian
dc.contributor.authorHellewell, Joel
dc.contributor.authorAriani, Cristina V
dc.contributor.authorGonçalves, Sonia
dc.contributor.authorJackson, David K
dc.contributor.authorJohnston, Ian
dc.contributor.authorJung, Alexander W
dc.contributor.authorSaint, Callum
dc.contributor.authorSillitoe, John
dc.contributor.authorSuciu, Maria
dc.contributor.authorGoldman, Nick
dc.contributor.authorPanovska-Griffiths, Jasmina
dc.contributor.authorWellcome Sanger Institute COVID-19 Surveillance Team
dc.contributor.authorCOVID-19 Genomics UK (COG-UK) Consortium*
dc.contributor.authorBirney, Ewan
dc.contributor.authorVolz, Erik
dc.contributor.authorFunk, Sebastian
dc.contributor.authorKwiatkowski, Dominic
dc.contributor.authorChand, Meera
dc.contributor.authorMartincorena, Inigo
dc.contributor.authorBarrett, Jeffrey C
dc.contributor.authorGerstung, Moritz
dc.date.accessioned2022-01-05T10:46:57Z
dc.date.available2022-01-05T10:46:57Z
dc.date.issued2021-12
dc.date.submitted2021-05-22
dc.identifier.issn0028-0836
dc.identifier.others41586-021-04069-y
dc.identifier.other4069
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/331988
dc.description.abstractThe 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.
dc.languageen
dc.publisherSpringer Science and Business Media LLC
dc.subjectArticle
dc.subject/631/181/2474
dc.subject/692/699/255/2514
dc.subject/692/308/174
dc.subject/631/326/596/4130
dc.subject/45
dc.subject/119
dc.subject/141
dc.subjectarticle
dc.titleGenomic reconstruction of the SARS-CoV-2 epidemic in England.
dc.typeArticle
dc.date.updated2022-01-05T10:46:53Z
prism.endingPage511
prism.issueIdentifier7889
prism.publicationNameNature
prism.startingPage506
prism.volume600
dc.identifier.doi10.17863/CAM.79436
dcterms.dateAccepted2021-09-29
rioxxterms.versionofrecord10.1038/s41586-021-04069-y
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidSinnott, Matthew [0000-0002-3054-7846]
dc.contributor.orcidGoater, Richard [0000-0001-9954-841X]
dc.contributor.orcidHarrison, Ian [0000-0003-4117-961X]
dc.contributor.orcidHellewell, Joel [0000-0003-2683-0849]
dc.contributor.orcidJackson, David K [0000-0002-8090-9462]
dc.contributor.orcidSaint, Callum [0000-0001-8720-9736]
dc.contributor.orcidGoldman, Nick [0000-0001-8486-2211]
dc.contributor.orcidPanovska-Griffiths, Jasmina [0000-0002-7720-1121]
dc.contributor.orcidBirney, Ewan [0000-0001-8314-8497]
dc.contributor.orcidVolz, Erik [0000-0001-6268-8937]
dc.contributor.orcidFunk, Sebastian [0000-0002-2842-3406]
dc.contributor.orcidKwiatkowski, Dominic [0000-0002-5023-0176]
dc.contributor.orcidMartincorena, Inigo [0000-0003-1122-4416]
dc.contributor.orcidBarrett, Jeffrey C [0000-0002-1152-370X]
dc.contributor.orcidGerstung, Moritz [0000-0001-6709-963X]
dc.identifier.eissn1476-4687
pubs.funder-project-idMRC (MC_PC_19027)
pubs.funder-project-idMedical Research Council (MC_PC_19027)
cam.issuedOnline2021-10-14


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