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

Erik Volz; Swapnil Mishra; Meera Chand; Jeffrey C. Barrett; Robert Johnson; Lily Geidelberg; Wes R. Hinsley; Daniel J. Laydon; Gavin Dabrera; Áine O’Toole; Robert Amato; Manon Ragonnet-Cronin; Ian Harrison; Ben Jackson; Cristina V. Ariani; Olivia Boyd; Nicholas J. Loman; John T. McCrone; Sónia Gonçalves; David Jorgensen; Richard Myers; Verity Hill; David K. Jackson; Katy Gaythorpe; Natalie Groves; John Sillitoe; Dominic P. Kwiatkowski; Cherian Koshy; Amy Ash; Emma Wise; Nathan Moore; Matilde Mori; Nick Cortes; Jessica Lynch; Stephen Kidd; Derek J. Fairley; Tanya Curran; James P. McKenna; Helen Adams; Christophe Fraser; The COVID-19 Genomics UK (COG-UK) Consortium; Darren L. Smith; Matthew Bashton; Gregory R. Young; Andrew Nelson; Clare M. McCann; Wen C. Yew; Hannah Jones; Seth Flaxman; Oliver Ratmann; Samir Bhatt; Susan Hopkins; Axel Gandy; Andrew Rambaut; Neil M. Ferguson

doi:10.1038/s41586-021-03470-x

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

Erik Volz^*, Swapnil Mishra, Meera Chand, Jeffrey C. Barrett, Robert Johnson, Lily Geidelberg, Wes R. Hinsley, Daniel J. Laydon, Gavin Dabrera, Áine O’Toole, Robert Amato, Manon Ragonnet-Cronin, Ian Harrison, Ben Jackson, Cristina V. Ariani, Olivia Boyd, Nicholas J. Loman, John T. McCrone, Sónia Gonçalves, David JorgensenRichard Myers, Verity Hill, David K. Jackson, Katy Gaythorpe, Natalie Groves, John Sillitoe, Dominic P. Kwiatkowski, Cherian Koshy, Amy Ash, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Jessica Lynch, Stephen Kidd, Derek J. Fairley, Tanya Curran, James P. McKenna, Helen Adams, Christophe Fraser, The COVID-19 Genomics UK (COG-UK) Consortium, Darren L. Smith, Matthew Bashton, Gregory R. Young, Andrew Nelson, Clare M. McCann, Wen C. Yew, Hannah Jones, Seth Flaxman, Oliver Ratmann, Samir Bhatt, Susan Hopkins, Axel Gandy, Andrew Rambaut, Neil M. Ferguson^*

^*Corresponding author for this work

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

820 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
Early online date	25 Mar 2021
DOIs	https://doi.org/10.1038/s41586-021-03470-x
Publication status	Published - 13 May 2021

Keywords

Population genetics
SARS-CoV-2
Viral infection

UN SDGs

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

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10.1038/s41586-021-03470-x

https://eprints.whiterose.ac.uk/175263/

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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., ... Ferguson, N. M. (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), 266-269. https://doi.org/10.1038/s41586-021-03470-x

@article{e881032a6e4b45ce99bc9dda92aeeafa,

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.",

keywords = "Population genetics, SARS-CoV-2, Viral infection",

author = "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 \{The COVID-19 Genomics UK (COG-UK) Consortium\} and Smith, \{Darren L.\} and Matthew Bashton and Young, \{Gregory R.\} and Andrew Nelson and McCann, \{Clare M.\} and Yew, \{Wen C.\} and Chris Williams and Hannah Jones and Hartley, \{John A.\} and Seth Flaxman and Oliver Ratmann and Samir Bhatt and Susan Hopkins and Axel Gandy and Andrew Rambaut and Ferguson, \{Neil M.\}",

note = "Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium. Funding information: 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.",

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",

}

Volz, E, Mishra, S, Chand, M, Barrett, JC, Johnson, R, Geidelberg, L, Hinsley, WR, Laydon, DJ, Dabrera, G, O’Toole, Á, Amato, R, Ragonnet-Cronin, M, Harrison, I, Jackson, B, Ariani, CV, Boyd, O, Loman, NJ, McCrone, JT, Gonçalves, S, Jorgensen, D, Myers, R, Hill, V, Jackson, DK, Gaythorpe, K, Groves, N, Sillitoe, J, Kwiatkowski, DP, Koshy, C, Ash, A, Wise, E, Moore, N, Mori, M, Cortes, N, Lynch, J, Kidd, S, Fairley, DJ, Curran, T, McKenna, JP, Adams, H, Fraser, C, The COVID-19 Genomics UK (COG-UK) Consortium, Smith, DL , Bashton, M, Young, GR, Nelson, A , McCann, CM , Yew, WC, Jones, H, Flaxman, S, Ratmann, O, Bhatt, S, Hopkins, S, Gandy, A, Rambaut, A & Ferguson, NM 2021, 'Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England', Nature, vol. 593, no. 7858, pp. 266-269. https://doi.org/10.1038/s41586-021-03470-x

TY - JOUR

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

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

AU - Smith, Darren L.

AU - Bashton, Matthew

AU - Young, Gregory R.

AU - Nelson, Andrew

AU - McCann, Clare M.

AU - Yew, Wen C.

AU - Williams, Chris

AU - Jones, Hannah

AU - Hartley, John A.

AU - Flaxman, Seth

AU - Ratmann, Oliver

AU - Bhatt, Samir

AU - Hopkins, Susan

AU - Gandy, Axel

AU - Rambaut, Andrew

AU - Ferguson, Neil M.

N1 - Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium. Funding information: 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.

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.

KW - Population genetics

KW - SARS-CoV-2

KW - Viral infection

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

U2 - 10.1038/s41586-021-03470-x

DO - 10.1038/s41586-021-03470-x

M3 - Article

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

Keywords

UN SDGs

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