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

Imperial College London
Public Health England
Wellcome Trust Genome Campus
University of Edinburgh
University of Birmingham
Barking, Havering and Redbridge University Hospitals NHS Trust
Basingstoke Hospital
Forster Green Hospital
Betsi Cadwaladr University Health Board
University of Oxford
Brighton and Sussex University Hospitals
University of Cambridge
Cambridge University Hospitals NHS Foundation Trust
Cardiff and Vale University Health Board
Cardiff University
St Thomas' Hospital
Guys and St Thomas' NHS Foundation Trust
University of Portsmouth
University of Oxford
Queen's Medical Centre
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
East Kent Hospitals University NHS Foundation Trust
Ipswich Hospital NHS Trust
Gateshead Health NHS Foundation Trust
Gloucestershire Hospitals NHS Foundation Trust
UCL Institute of Child Health and Great Ormond Street Hospital for Children NHS Foundation Trust
Hampshire Hospitals NHS Foundation Trust
Health Data Research UK
Health Services Laboratories
East Birmingham Hospital
Ellison Building
Imperial College Healthcare NHS Trust
University of Glasgow, G11 6NT
Liverpool Clinical Laboratories
Maidstone and Tunbridge Wells NHS Trust
University Hospital of South Manchester
Wye valley NHS Trust
MRC-University of Glasgow Centre for Virus Research
Leeds Teaching Hospitals NHS Trust
Newcastle upon Tyne NHS Hospitals 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 Goole NHS Foundation Trust
Portsmouth Hospitals University NHS Trust
Princess Alexandra Hospital
Public Health Agency
Public Health Scotland
Public Health Wales
Quadram Institute Bioscience
Queen Elizabeth Hospital Birmingham
Queen's University of Belfast
Royal Devon and Exeter National Health Service Foundation Trust
Royal Free NHS Trust
Sandwell and West Birmingham 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 a Journal (Peer & Non Peer) › Article › peer-review

842 Citations (Scopus)

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
Publication status	Published - 13 May 2021
Externally published	Yes

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SDG 3 Good Health and Well-being

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10.1038/s41586-021-03470-x

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@article{e385497b8f6c41efb04f05e05c5c1237,

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 and Kathryn McCluggage and Michaela John and Robert Beer and Safiah Afifi and Sian Morgan and Angela Marchbank and Anna Price and Christine Kitchen and Huw Gulliver and Ian Merrick and Joel Southgate and Martyn Guest and Robert Munn and Trudy Workman and Connor, \{Thomas R.\} and William Fuller and Catherine Bresner and Snell, \{Luke B.\} and Amita Patel and Themoula Charalampous and Gaia Nebbia and Rahul Batra and Jonathan Edgeworth and Robson, \{Samuel C.\} and Beckett, \{Angela H.\} and Aanensen, \{David M.\} and Underwood, \{Anthony P.\} and Yeats, \{Corin A.\} and Khalil Abudahab and Taylor, \{Ben E.W.\} and Mirko Menegazzo and Gemma Clark and Wendy Smith and Manjinder Khakh and Fleming, \{Vicki M.\} and Lister, \{Michelle M.\} and Howson-Wells, \{Hannah C.\} and Louise Berry and Tim Boswell and Amelia Joseph and Iona Willingham and Carl Jones and Christopher Holmes and Paul Bird and Thomas Helmer and Karlie Fallon and Julian Tang and Veena Raviprakash and Sharon Campbell and Dorman, \{Matthew J.\}",

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 = "English",

volume = "593",

pages = "266--269",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7858",

}

TY - JOUR

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

AU - McCluggage, Kathryn

AU - John, Michaela

AU - Beer, Robert

AU - Afifi, Safiah

AU - Morgan, Sian

AU - Marchbank, Angela

AU - Price, Anna

AU - Kitchen, Christine

AU - Gulliver, Huw

AU - Merrick, Ian

AU - Southgate, Joel

AU - Guest, Martyn

AU - Munn, Robert

AU - Workman, Trudy

AU - Connor, Thomas R.

AU - Fuller, William

AU - Bresner, Catherine

AU - Snell, Luke B.

AU - Patel, Amita

AU - Charalampous, Themoula

AU - Nebbia, Gaia

AU - Batra, Rahul

AU - Edgeworth, Jonathan

AU - Robson, Samuel C.

AU - Beckett, Angela H.

AU - Aanensen, David M.

AU - Underwood, Anthony P.

AU - Yeats, Corin A.

AU - Abudahab, Khalil

AU - Taylor, Ben E.W.

AU - Menegazzo, Mirko

AU - Clark, Gemma

AU - Smith, Wendy

AU - Khakh, Manjinder

AU - Fleming, Vicki M.

AU - Lister, Michelle M.

AU - Howson-Wells, Hannah C.

AU - Berry, Louise

AU - Boswell, Tim

AU - Joseph, Amelia

AU - Willingham, Iona

AU - Jones, Carl

AU - Holmes, Christopher

AU - Bird, Paul

AU - Helmer, Thomas

AU - Fallon, Karlie

AU - Tang, Julian

AU - Raviprakash, Veena

AU - Campbell, Sharon

AU - Dorman, Matthew J.

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 - Article

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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