Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Paul Elliott; David Haw; Haowei Wang; Oliver Eales; Caroline E. Walters; Kylie E. C. Ainslie; Christina Atchison; Claudio Fronterre; Peter J. Diggle; Andrew J Page; Alexander J. Trotter; Sophie J. Prosolek; The COVID-19 Genomics UK (COG-UK) Consortium; Deborah Ashby; Christl A. Donnelly; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Steven Riley; Samuel C Robson; Nicholas J. Loman; Thomas R. Connor; Tanya Golubchik; Rocio T Martinez Nunez; Catherine Ludden; Sally Corden; Ian Johnston; David Bonsall; Colin P. Smith; Giselda Bucca; M Estee Torok; Kordo Saeed; Jacqui A Prieto; David K Jackson; William L Hamilton; Luke B Snell; Catherine Moore; Ewan M. Harrison; Rachel J Williams; Hannah Jones; John A Hartley; Chris Williams; Darren L Smith; Matthew Bashton; Andrew Nelson; Gregory R Young; Clare M McCann; Wen C Yew

doi:10.1126/science.abl9551

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Paul Elliott^*, David Haw, Haowei Wang, Oliver Eales, Caroline E. Walters, Kylie E. C. Ainslie, Christina Atchison, Claudio Fronterre, Peter J. Diggle, Andrew J Page, Alexander J. Trotter, Sophie J. Prosolek, The COVID-19 Genomics UK (COG-UK) Consortium, Deborah Ashby, Christl A. Donnelly, Wendy Barclay, Graham Taylor, Graham Cooke, Helen Ward, Ara DarziSteven Riley^*, Samuel C Robson, Nicholas J. Loman, Thomas R. Connor, Tanya Golubchik, Rocio T Martinez Nunez, Catherine Ludden, Sally Corden, Ian Johnston, David Bonsall, Colin P. Smith, Giselda Bucca, M Estee Torok, Kordo Saeed, Jacqui A Prieto, David K Jackson, William L Hamilton, Luke B Snell, Catherine Moore, Ewan M. Harrison, Rachel J Williams, Hannah Jones, John A Hartley, Chris Williams, Darren L Smith, Matthew Bashton, Andrew Nelson, Gregory R Young, Clare M McCann, Wen C Yew

^*Corresponding author for this work

Applied Sciences Department

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

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Abstract

SARS-CoV-2 infections were rising during early summer 2021 in many countries associated with the Delta variant. We assessed RT-PCR swab-positivity in the REal-time Assessment of Community Transmission-1 (REACT-1) study in England. We observed sustained exponential growth with average doubling time (June-July 2021) of 25 days driven by complete replacement of Alpha variant by Delta, and by high prevalence at younger less-vaccinated ages. Unvaccinated people were three times more likely than double-vaccinated people to test positive. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.

Original language	English
Article number	abl9551
Number of pages	15
Journal	Science
Volume	374
Issue number	6574
Early online date	2 Nov 2021
DOIs	https://doi.org/10.1126/science.abl9551
Publication status	Published - 17 Dec 2021

Keywords

Adolescent
Adult
Age Factors
Aged
COVID-19 Nucleic Acid Testing
COVID-19 Vaccines/administration & dosage
COVID-19/diagnosis
Child
Child, Preschool
England/epidemiology
Ethnicity
Family Characteristics
Female
Hospitalization
Humans
Male
Middle Aged
Prevalence
SARS-CoV-2
Self Report
Socioeconomic Factors
Vaccination Coverage
Vaccine Efficacy
Young Adult

UN SDGs

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

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10.1126/science.abl9551Licence: CC BY

Final published versionFinal published version, 1.61 MBLicence: CC BY
Advance online versionFinal published version, 1.35 MBLicence: CC BY

Cite this

Elliott, P., Haw, D., Wang, H., Eales, O., Walters, C. E., Ainslie, K. E. C., Atchison, C., Fronterre, C., Diggle, P. J., Page, A. J., Trotter, A. J., Prosolek, S. J., The COVID-19 Genomics UK (COG-UK) Consortium, Ashby, D., Donnelly, C. A., Barclay, W., Taylor, G., Cooke, G., Ward, H., ... Yew, W. C. (2021). Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant. Science, 374(6574), Article abl9551. https://doi.org/10.1126/science.abl9551

@article{444fedd1906749b58654d0d999f41f9e,

title = "Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant",

abstract = "SARS-CoV-2 infections were rising during early summer 2021 in many countries associated with the Delta variant. We assessed RT-PCR swab-positivity in the REal-time Assessment of Community Transmission-1 (REACT-1) study in England. We observed sustained exponential growth with average doubling time (June-July 2021) of 25 days driven by complete replacement of Alpha variant by Delta, and by high prevalence at younger less-vaccinated ages. Unvaccinated people were three times more likely than double-vaccinated people to test positive. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.",

keywords = "Adolescent, Adult, Age Factors, Aged, COVID-19 Nucleic Acid Testing, COVID-19 Vaccines/administration & dosage, COVID-19/diagnosis, Child, Child, Preschool, England/epidemiology, Ethnicity, Family Characteristics, Female, Hospitalization, Humans, Male, Middle Aged, Prevalence, SARS-CoV-2, Self Report, Socioeconomic Factors, Vaccination Coverage, Vaccine Efficacy, Young Adult",

author = "Paul Elliott and David Haw and Haowei Wang and Oliver Eales and Walters, {Caroline E.} and Ainslie, {Kylie E. C.} and Christina Atchison and Claudio Fronterre and Diggle, {Peter J.} and Page, {Andrew J} and Trotter, {Alexander J.} and Prosolek, {Sophie J.} and {The COVID-19 Genomics UK (COG-UK) Consortium} and Deborah Ashby and Donnelly, {Christl A.} and Wendy Barclay and Graham Taylor and Graham Cooke and Helen Ward and Ara Darzi and Steven Riley and Robson, {Samuel C} and Loman, {Nicholas J.} and Connor, {Thomas R.} and Tanya Golubchik and {Martinez Nunez}, {Rocio T} and Catherine Ludden and Sally Corden and Ian Johnston and David Bonsall and Smith, {Colin P.} and Giselda Bucca and Torok, {M Estee} and Kordo Saeed and Prieto, {Jacqui A} and Jackson, {David K} and Hamilton, {William L} and Snell, {Luke B} and Catherine Moore and Harrison, {Ewan M.} and Williams, {Rachel J} and Hannah Jones and Hartley, {John A} and Chris Williams and Smith, {Darren L} and Matthew Bashton and Andrew Nelson and Young, {Gregory R} and McCann, {Clare M} and Yew, {Wen C}",

note = "Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann, Andrew Nelson and Wen Chyin Yew are members of the COVID-19 Genomics UK (COG-UK) Consortium. Funding information: The study was funded by the Department of Health and Social Care in England. Sequencing was provided through funding from the COVID-19 Genomics UK (COG-UK) Consortium. P.E. is Director of the Medical Research Council (MRC) Centre for Environment and Health (MR/L01341X/1, MR/S019669/1). P.E. acknowledges support from Health Data Research UK (HDR UK); the National Institute for Health Research (NIHR) Imperial Biomedical Research Centre; NIHR Health Protection Research Units (HPRUs) in Chemical and Radiation Threats and Hazards, and Environmental Exposures and Health; the British Heart Foundation Centre for Research Excellence at Imperial College London (RE/18/4/34215); and the UK Dementia Research Institute at Imperial (MC_PC_17114). S.R., C.A.D. acknowledge support: MRC Centre for Global Infectious Disease Analysis, NIHR HPRU in Modelling and Health Economics, Wellcome Trust (200861/Z/16/Z, 200187/Z/15/Z), and Centres for Disease Control and Prevention (US, U01CK0005-01-02). G.C. is supported by an NIHR Professorship. H.War. acknowledges support from an NIHR Senior Investigator Award and the Wellcome Trust (205456/Z/16/Z). We thank The Huo Family Foundation for their support of our work on COVID-19. Quadram authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352. We thank members of the COVID-19 Genomics Consortium UK (COG-UK) for their contributions to generating the genomic data used in this study. COG-UK is supported by funding from the MRC, part of UK Research & Innovation (UKRI), NIHR and Genome Research Limited, operating as the Wellcome Sanger Institute.",

year = "2021",

month = dec,

day = "17",

doi = "10.1126/science.abl9551",

language = "English",

volume = "374",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6574",

}

Elliott, P, Haw, D, Wang, H, Eales, O, Walters, CE, Ainslie, KEC, Atchison, C, Fronterre, C, Diggle, PJ, Page, AJ, Trotter, AJ, Prosolek, SJ, The COVID-19 Genomics UK (COG-UK) Consortium, Ashby, D, Donnelly, CA, Barclay, W, Taylor, G, Cooke, G, Ward, H, Darzi, A, Riley, S, Robson, SC, Loman, NJ, Connor, TR, Golubchik, T, Martinez Nunez, RT, Ludden, C, Corden, S, Johnston, I, Bonsall, D, Smith, CP, Bucca, G, Torok, ME, Saeed, K, Prieto, JA, Jackson, DK, Hamilton, WL, Snell, LB, Moore, C, Harrison, EM, Williams, RJ, Jones, H, Hartley, JA, Williams, C, Smith, DL , Bashton, M, Nelson, A, Young, GR, McCann, CM & Yew, WC 2021, 'Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant', Science, vol. 374, no. 6574, abl9551. https://doi.org/10.1126/science.abl9551

TY - JOUR

T1 - Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

AU - Elliott, Paul

AU - Haw, David

AU - Wang, Haowei

AU - Eales, Oliver

AU - Walters, Caroline E.

AU - Ainslie, Kylie E. C.

AU - Atchison, Christina

AU - Fronterre, Claudio

AU - Diggle, Peter J.

AU - Page, Andrew J

AU - Trotter, Alexander J.

AU - Prosolek, Sophie J.

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

AU - Ashby, Deborah

AU - Donnelly, Christl A.

AU - Barclay, Wendy

AU - Taylor, Graham

AU - Cooke, Graham

AU - Ward, Helen

AU - Darzi, Ara

AU - Riley, Steven

AU - Robson, Samuel C

AU - Loman, Nicholas J.

AU - Connor, Thomas R.

AU - Golubchik, Tanya

AU - Martinez Nunez, Rocio T

AU - Ludden, Catherine

AU - Corden, Sally

AU - Johnston, Ian

AU - Bonsall, David

AU - Smith, Colin P.

AU - Bucca, Giselda

AU - Torok, M Estee

AU - Saeed, Kordo

AU - Prieto, Jacqui A

AU - Jackson, David K

AU - Hamilton, William L

AU - Snell, Luke B

AU - Moore, Catherine

AU - Harrison, Ewan M.

AU - Williams, Rachel J

AU - Jones, Hannah

AU - Hartley, John A

AU - Williams, Chris

AU - Smith, Darren L

AU - Bashton, Matthew

AU - Nelson, Andrew

AU - Young, Gregory R

AU - McCann, Clare M

AU - Yew, Wen C

N1 - Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann, Andrew Nelson and Wen Chyin Yew are members of the COVID-19 Genomics UK (COG-UK) Consortium. Funding information: The study was funded by the Department of Health and Social Care in England. Sequencing was provided through funding from the COVID-19 Genomics UK (COG-UK) Consortium. P.E. is Director of the Medical Research Council (MRC) Centre for Environment and Health (MR/L01341X/1, MR/S019669/1). P.E. acknowledges support from Health Data Research UK (HDR UK); the National Institute for Health Research (NIHR) Imperial Biomedical Research Centre; NIHR Health Protection Research Units (HPRUs) in Chemical and Radiation Threats and Hazards, and Environmental Exposures and Health; the British Heart Foundation Centre for Research Excellence at Imperial College London (RE/18/4/34215); and the UK Dementia Research Institute at Imperial (MC_PC_17114). S.R., C.A.D. acknowledge support: MRC Centre for Global Infectious Disease Analysis, NIHR HPRU in Modelling and Health Economics, Wellcome Trust (200861/Z/16/Z, 200187/Z/15/Z), and Centres for Disease Control and Prevention (US, U01CK0005-01-02). G.C. is supported by an NIHR Professorship. H.War. acknowledges support from an NIHR Senior Investigator Award and the Wellcome Trust (205456/Z/16/Z). We thank The Huo Family Foundation for their support of our work on COVID-19. Quadram authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352. We thank members of the COVID-19 Genomics Consortium UK (COG-UK) for their contributions to generating the genomic data used in this study. COG-UK is supported by funding from the MRC, part of UK Research & Innovation (UKRI), NIHR and Genome Research Limited, operating as the Wellcome Sanger Institute.

PY - 2021/12/17

Y1 - 2021/12/17

N2 - SARS-CoV-2 infections were rising during early summer 2021 in many countries associated with the Delta variant. We assessed RT-PCR swab-positivity in the REal-time Assessment of Community Transmission-1 (REACT-1) study in England. We observed sustained exponential growth with average doubling time (June-July 2021) of 25 days driven by complete replacement of Alpha variant by Delta, and by high prevalence at younger less-vaccinated ages. Unvaccinated people were three times more likely than double-vaccinated people to test positive. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.

AB - SARS-CoV-2 infections were rising during early summer 2021 in many countries associated with the Delta variant. We assessed RT-PCR swab-positivity in the REal-time Assessment of Community Transmission-1 (REACT-1) study in England. We observed sustained exponential growth with average doubling time (June-July 2021) of 25 days driven by complete replacement of Alpha variant by Delta, and by high prevalence at younger less-vaccinated ages. Unvaccinated people were three times more likely than double-vaccinated people to test positive. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.

KW - Adolescent

KW - Adult

KW - Age Factors

KW - Aged

KW - COVID-19 Nucleic Acid Testing

KW - COVID-19 Vaccines/administration & dosage

KW - COVID-19/diagnosis

KW - Child

KW - Child, Preschool

KW - England/epidemiology

KW - Ethnicity

KW - Family Characteristics

KW - Female

KW - Hospitalization

KW - Humans

KW - Male

KW - Middle Aged

KW - Prevalence

KW - SARS-CoV-2

KW - Self Report

KW - Socioeconomic Factors

KW - Vaccination Coverage

KW - Vaccine Efficacy

KW - Young Adult

UR - http://www.scopus.com/inward/record.url?scp=85120291789&partnerID=8YFLogxK

U2 - 10.1126/science.abl9551

DO - 10.1126/science.abl9551

M3 - Article

C2 - 34726481

SN - 0036-8075

VL - 374

JO - Science

JF - Science

IS - 6574

M1 - abl9551

ER -

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Abstract

Keywords

UN SDGs

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