Cited by 1,611SARS-CoV-2 and COVID-19 ResearchCOVID-19 epidemiological studiesSARS-CoV-2 detection and testing

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Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

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The COVID-19 Genomics UK (COG-UK) consortium, Volz, Erik, Mishra, Swapnil, Chand, Meera, Barrett, Jeffrey C., Johnson, Robert, Geidelberg, Lily, Hinsley, Wes R., Laydon, Daniel J., Dabrera, Gavin, O’Toole, Áine, Amato, Robert, Ragonnet-Cronin, Manon, Harrison, Ian, Jackson, Ben, Ariani, Cristina V., Boyd, Olivia, Loman, Nicholas J., McCrone, John T., Gonçalves, Sónia, Jorgensen, David, Myers, Richard, Hill, Verity, Jackson, David K., Gaythorpe, Katy, Groves, Natalie, Sillitoe, John, Kwiatkowski, Dominic P., Flaxman, Seth, Ratmann, Oliver, Bhatt, Samir, Hopkins, Susan, Gandy, Axel, Rambaut, Andrew, Ferguson, Neil M.·2021·Nature

DOI 10.1038/s41586-021-03470-x

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Abstract

The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England 1, was first identified in the UK in late summer to early autumn 2020 2. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.

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Authors: The COVID-19 Genomics UK (COG-UK) consortium, Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O’Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S., Jorgensen, D., Myers, R., Hill, V., Jackson, D. K., Gaythorpe, K., Groves, N., Sillitoe, J., Kwiatkowski, D. P., Flaxman, S., Ratmann, O., Bhatt, S., Hopkins, S., Gandy, A., Rambaut, A., & Ferguson, N. M.
Affiliations: Imperial College London (GB)
Public Health England (GB)
Wellcome Sanger Institute (GB)
University of Edinburgh (GB)
University of Copenhagen (DK)
Corresponding author: Volz, Erik
Ferguson, Neil M.
ORCID: Volz, Erik
Mishra, Swapnil
Chand, Meera
Barrett, Jeffrey C.
Geidelberg, Lily
Hinsley, Wes R.
Laydon, Daniel J.
Dabrera, Gavin
Harrison, Ian
Jackson, Ben
Ariani, Cristina V.
Boyd, Olivia
Loman, Nicholas J.
McCrone, John T.
Gonçalves, Sónia
Jorgensen, David
Myers, Richard
Hill, Verity
Jackson, David K.
Gaythorpe, Katy
Groves, Natalie
Kwiatkowski, Dominic P.
Flaxman, Seth
Ratmann, Oliver
Bhatt, Samir
Hopkins, Susan
Gandy, Axel
Rambaut, Andrew
Ferguson, Neil M.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2021-03-25
Volume: 593
Issue: 7858
Pages: 266-269
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-021-03470-x
OpenAlex: W3136588845
Cited by: 1,611
References: 32
Citations by year: 2026: 38 · 2025: 86 · 2024: 116 · 2023: 216 · 2022: 464 · 2021: 685
FWCI: 116.92
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature (publishedVersion)
medRxiv (acceptedVersion, cc-by)
PubMed (publishedVersion)
Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
UEA Digital Repository (University of East Anglia) (submittedVersion)
RePEc: Research Papers in Economics (submittedVersion)
ePrints Soton (University of Southampton) (submittedVersion)
UCL Discovery (University College London) (submittedVersion)
Figshare (submittedVersion)
Research Portal (King's College London) (submittedVersion, other-oa)
Northumbria Research Link (Northumbria University) (submittedVersion)
University of Birmingham Research Portal (University of Birmingham) (submittedVersion, other-oa)
Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
Spiral (Imperial College London) (submittedVersion, cc-by)
Spiral (Imperial College London) (submittedVersion)
Apollo (University of Cambridge) (submittedVersion)
Apollo
Funders: Bill and Melinda Gates Foundation (OPP 1175094, 206194, OPP1197730, MR/R015600/1, OPP1084362)
Wellcome Trust (MR/R015600/1, 204911/Z/16/Z, Z/17/Z, 206298/Z/17/Z, RDA02, 206298, 206194)
UK Research and Innovation (MR/V038109/1, MR/R015600/1, MC_PC_19027)
National Institute for Health Research Health Protection Research Unit
Cancer Research UK (23923)
National Institute for Health and Care Research (PR-OD-1017–20002, MR/R015600/1, RDA02, NIHR301445, OPP1175094, ACF-2018-04-014)
Academy of Medical Sciences (AMS-CSF4-Torok, SBF004\1080)
Imperial College London (MR/R015600/1)
European Commission (725422, MR/R015600/1, 101003653, COVID-19, 206298/Z/17/Z)
Rural Development Administration
Novo Nordisk (NNF20OC0059309)
Novo Nordisk Fonden (NNF20OC0059309)
Medical Research Council (MR/R015600/1, MR/M006212/1, MC_PC_19026, MR/V038109/1, MR/S00291X/1, MC_PC_19012, COVID-19)
Engineering and Physical Sciences Research Council (EP/V002910/1, EP/V002910/2)
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
Keywords: SARS-CoV-2, B.1.1.7 lineage, variants of concern, transmissibility, S-gene target failure, time-varying reproduction number, viral genomic surveillance, COVID-19 pandemic, England
MeSH terms: COVID-19, SARS-CoV-2, Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, England, Humans, Infant, Infant, Newborn, Middle Aged, Phylogeny, Time Factors, Genome, Viral, Age Distribution, Evolution, Molecular, Basic Reproduction Number, Young Adult, Spike Glycoprotein, Coronavirus

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Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

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