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

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

The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. 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.

Adolescent, Adult, Age Distribution, Aged, Aged, 80 and over, Basic Reproduction Number, COVID-19/diagnosis, Child, Child, Preschool, England/epidemiology, Evolution, Molecular, Genome, Viral/genetics, Humans, Infant, Infant, Newborn, Middle Aged, Phylogeny, SARS-CoV-2/classification, Spike Glycoprotein, Coronavirus/analysis, Time Factors, Young Adult
0028-0836
266-269
Volz, Erik
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Mishra, Swapnil
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Chand, Meera
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Barrett, Jeffrey C
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Johnson, Robert
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Geidelberg, Lily
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Hinsley, Wes R
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Laydon, Daniel J
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Dabrera, Gavin
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O'Toole, Áine
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Amato, Robert
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Ragonnet-Cronin, Manon
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Harrison, Ian
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Jackson, Ben
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Ariani, Cristina V
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Boyd, Olivia
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Loman, Nicholas J
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McCrone, John T
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Gonçalves, Sónia
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Jorgensen, David
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Myers, Richard
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Hill, Verity
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Jackson, David K
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Gaythorpe, Katy
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Groves, Natalie
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Sillitoe, John
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Kwiatkowski, Dominic P
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Flaxman, Seth
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Ratmann, Oliver
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Bhatt, Samir
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Hopkins, Susan
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Gandy, Axel
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Rambaut, Andrew
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Ferguson, Neil M
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Saeed, Kordo
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Prieto, Jacqui
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COVID-19 Genomics UK (COG-UK) consortium
Volz, Erik
b109616c-f061-49d8-87e8-ff9597bcf60e
Mishra, Swapnil
46a21337-415e-415e-a572-82b633e9231a
Chand, Meera
7a806b7b-d601-4c7b-b66e-95bbda6f7933
Barrett, Jeffrey C
34060616-1b70-4e97-9d2b-28541d6c2924
Johnson, Robert
3d94ab9e-b597-45d9-be5e-f9fbeadaf245
Geidelberg, Lily
cd130857-593b-4107-94ea-218de1ba7798
Hinsley, Wes R
1dc8932d-2af4-4a74-adc2-6d8782da1d43
Laydon, Daniel J
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Dabrera, Gavin
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O'Toole, Áine
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Amato, Robert
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Ragonnet-Cronin, Manon
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Harrison, Ian
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Jackson, Ben
db7789ed-ed9c-4d49-95c9-fac452c2e2bb
Ariani, Cristina V
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Boyd, Olivia
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Loman, Nicholas J
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McCrone, John T
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Gonçalves, Sónia
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Jorgensen, David
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Myers, Richard
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Hill, Verity
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Jackson, David K
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Gaythorpe, Katy
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Groves, Natalie
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Sillitoe, John
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Kwiatkowski, Dominic P
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Flaxman, Seth
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Ratmann, Oliver
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Bhatt, Samir
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Hopkins, Susan
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Gandy, Axel
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Rambaut, Andrew
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Ferguson, Neil M
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Saeed, Kordo
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Prieto, Jacqui
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Volz, Erik, Mishra, Swapnil, Chand, Meera, Barrett, Jeffrey C, Johnson, Robert and Geidelberg, Lily , COVID-19 Genomics UK (COG-UK) consortium (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593 (7858), 266-269. (doi:10.1038/s41586-021-03470-x).

Record type: Article

Abstract

The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. 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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More information

Published date: 25 March 2021
Additional Information: Funding Information: Acknowledgements We thank all partners and contributors to the COG-UK consortium who are listed at https://www.cogconsortium.uk/about/. We thank the Sanger Covid Team (https:// www.sanger.ac.uk/covid-team) for data preparation and feedback on the manuscript. 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. N.M.F., E.V., M.R. and S.B. acknowledge support from the MRC Centre for Global Infectious Disease Analysis (MR/R015600/1). R.J. and E.V. acknowledge funding from the European Commission (CoroNAb 101003653). D.J.L. and N.M.F. were supported by the NIHR VEEPED (PR-OD-1017-20002). S.B. received support from the NIHR BRC Imperial College NHS Trust Infection and COVID themes. S.B and N.M.F were supported by the UK Research and Innovation Fund MR/V038109/1. S.B. is supported by the Academy of Medical Sciences Springboard Award SBF004/1080. S.B. is supported by the Novo Nordisk Foundation Young Investigator Award NNF20OC0059309. O.R. and S.B. were supported by the Bill & Melinda Gates Foundation (OPP1175094, OPP1084362). Computational resources were provided by Amazon AWS and Microsoft AI for Health. Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature Limited. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.
Keywords: Adolescent, Adult, Age Distribution, Aged, Aged, 80 and over, Basic Reproduction Number, COVID-19/diagnosis, Child, Child, Preschool, England/epidemiology, Evolution, Molecular, Genome, Viral/genetics, Humans, Infant, Infant, Newborn, Middle Aged, Phylogeny, SARS-CoV-2/classification, Spike Glycoprotein, Coronavirus/analysis, Time Factors, Young Adult

Identifiers

Local EPrints ID: 453435
URI: http://eprints.soton.ac.uk/id/eprint/453435
ISSN: 0028-0836
PURE UUID: 6888fa64-df9c-4a68-a6b9-1248ca206ab0
ORCID for Kordo Saeed: ORCID iD orcid.org/0000-0003-0123-0302
ORCID for Jacqui Prieto: ORCID iD orcid.org/0000-0002-5524-6775

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Date deposited: 14 Jan 2022 17:42
Last modified: 17 Mar 2024 03:56

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Contributors

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

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