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

The COVID-19 Genomics UK (COG-UK) Consortium

doi:10.1038/s41586-021-03470-x

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

The COVID-19 Genomics UK (COG-UK) Consortium

Department of Medicine
Imperial College London
UK Health Security Agency
Wellcome Sanger Institute
University of Edinburgh
Liverpool Clinical Laboratories
University of Birmingham
Barking, Havering and Redbridge University Hospitals NHS Trust
Basingstoke Hospital
Belfast Health and Social Care Trust
Betsi Cadwaladr University Health Board
University of Oxford
University Hospitals Sussex NHS Foundation Trust
University of Cambridge
Cambridge University Hospitals NHS Foundation Trust
Cardiff & Vale University Health Board
Cardiff University
St Thomas’ Hospital and Kings College London
Guy's and St Thomas' NHS Foundation Trust
University of Portsmouth
Nottingham University Hospitals NHS Trust
University Hospitals of Leicester NHS Trust
County Durham and Darlington NHS Foundation Trust
University of Nottingham
London School of Hygiene and Tropical Medicine
King's College London
Kettering General Hospital NHS Trust
East Kent Hospitals University NHS Foundation Trust
East Suffolk and North Essex NHS Foundation Trust
Gateshead Health NHS Foundation Trust
Gloucestershire Hospitals NHS Foundation Trust
Great Ormond Street Hospital for Children NHS Foundation Trust
Hampshire Hospitals NHS Foundation Trust
Health Data Research UK
Health Services Laboratories
University Hospitals Birmingham NHS Foundation Trust
Northumbria University
Imperial College Healthcare NHS Trust
University of Glasgow
Maidstone and Tunbridge Wells NHS Trust
Manchester University NHS Foundation Trust
Wye Valley NHS Trust
MRC Biostatistics Unit
MRC-University of Glasgow Centre for Virus Research
Leeds Teaching Hospitals NHS Trust
Newcastle upon Tyne Hospitals NHS Foundation Trust
Newcastle University
NHS Greater Glasgow and Clyde
NHS Lothian
Norwich University Hospital
Norfolk County Council
North Cumbria Integrated Care NHS Foundation Trust
North Tees and Hartlepool NHS Foundation Trust
Oxford University Hospitals NHS Foundation Trust
Northern Lincolnshire and Goole NHS Foundation Trust
Portsmouth Hospitals University NHS Trust
The Princess Alexandra Hospital NHS Trust
Public Health Agency
Public Health Scotland
Public Health Wales
Quadram Institute
Queen's University Belfast
Royal Devon & Exeter NHS Foundation Trust
Royal Free London NHS Foundation Trust
Sandwell and West Birmingham Hospitals NHS Trust
Sheffield Teaching Hospitals NHS Foundation Trust
South Tees Hospitals NHS Foundation Trust
Swansea University
University Hospital Southampton NHS Foundation Trust
University College London
University Hospitals Coventry and Warwickshire NHS Trust
University of Brighton
University of East Anglia
University of Exeter
University of Liverpool
University of Sheffield
University of Warwick
Viapath
King's College Hospital NHS Foundation Trust
University of Copenhagen

Research output: Contribution to journal › Article › peer-review

851 Scopus citations

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.

Original language	English
Pages (from-to)	266-269
Number of pages	4
Journal	Nature
Volume	593
Issue number	7858
DOIs	https://doi.org/10.1038/s41586-021-03470-x
State	Published - 13 May 2021
Externally published	Yes

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1038/s41586-021-03470-x

Cite this

@article{8e9868e5ab7c49cbb815be922325551f,

title = "Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England",

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.",

author = "\{The COVID-19 Genomics UK (COG-UK) Consortium\} and Erik Volz and Swapnil Mishra and Meera Chand and Barrett, \{Jeffrey C.\} and Robert Johnson and Lily Geidelberg and Hinsley, \{Wes R.\} and Laydon, \{Daniel J.\} and Gavin Dabrera and {\'A}ine O{\textquoteright}Toole and Robert Amato and Manon Ragonnet-Cronin and Ian Harrison and Ben Jackson and Ariani, \{Cristina V.\} and Olivia Boyd and Loman, \{Nicholas J.\} and McCrone, \{John T.\} and S{\'o}nia Gon{\c c}alves and David Jorgensen and Richard Myers and Verity Hill and Jackson, \{David K.\} and Katy Gaythorpe and Natalie Groves and John Sillitoe and Kwiatkowski, \{Dominic P.\} and Cherian Koshy and Amy Ash and Emma Wise and Nathan Moore and Matilde Mori and Nick Cortes and Jessica Lynch and Stephen Kidd and Fairley, \{Derek J.\} and Tanya Curran and McKenna, \{James P.\} and Helen Adams and Christophe Fraser and Tanya Golubchik and David Bonsall and Hassan-Ibrahim, \{Mohammed O.\} and Malone, \{Cassandra S.\} and Cogger, \{Benjamin J.\} and Michelle Wantoch and Nicola Reynolds and Ben Warne and Joshua Maksimovic and Karla Spellman",

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature Limited.",

year = "2021",

month = may,

day = "13",

doi = "10.1038/s41586-021-03470-x",

language = "Ingl{\'e}s",

volume = "593",

pages = "266--269",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7858",

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T1 - Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

AU - The COVID-19 Genomics UK (COG-UK) Consortium

AU - Volz, Erik

AU - Mishra, Swapnil

AU - Chand, Meera

AU - Barrett, Jeffrey C.

AU - Johnson, Robert

AU - Geidelberg, Lily

AU - Hinsley, Wes R.

AU - Laydon, Daniel J.

AU - Dabrera, Gavin

AU - O’Toole, Áine

AU - Amato, Robert

AU - Ragonnet-Cronin, Manon

AU - Harrison, Ian

AU - Jackson, Ben

AU - Ariani, Cristina V.

AU - Boyd, Olivia

AU - Loman, Nicholas J.

AU - McCrone, John T.

AU - Gonçalves, Sónia

AU - Jorgensen, David

AU - Myers, Richard

AU - Hill, Verity

AU - Jackson, David K.

AU - Gaythorpe, Katy

AU - Groves, Natalie

AU - Sillitoe, John

AU - Kwiatkowski, Dominic P.

AU - Koshy, Cherian

AU - Ash, Amy

AU - Wise, Emma

AU - Moore, Nathan

AU - Mori, Matilde

AU - Cortes, Nick

AU - Lynch, Jessica

AU - Kidd, Stephen

AU - Fairley, Derek J.

AU - Curran, Tanya

AU - McKenna, James P.

AU - Adams, Helen

AU - Fraser, Christophe

AU - Golubchik, Tanya

AU - Bonsall, David

AU - Hassan-Ibrahim, Mohammed O.

AU - Malone, Cassandra S.

AU - Cogger, Benjamin J.

AU - Wantoch, Michelle

AU - Reynolds, Nicola

AU - Warne, Ben

AU - Maksimovic, Joshua

AU - Spellman, Karla

PY - 2021/5/13

Y1 - 2021/5/13

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85103190451

U2 - 10.1038/s41586-021-03470-x

DO - 10.1038/s41586-021-03470-x

M3 - Artículo

C2 - 33767447

AN - SCOPUS:85103190451

SN - 0028-0836

VL - 593

SP - 266

EP - 269

JO - Nature

JF - Nature

IS - 7858

ER -

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

Abstract

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