Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

The COVID-19 Genomics UK (COG-UK) Consortium; J Panovska-Griffiths; B Swallow; R Hinch; J Cohen; K Rosenfeld; R M Stuart; L Ferretti; F Di Lauro; C Wymant; A Izzo; W Waites; R Viner; C Bonell; C Fraser; D Klein; C C Kerr; Matthew Bashton; Darren Smith; Andrew Nelson; Gregory R. Young; Clare McCann

doi:10.1098/rsta.2021.0315

Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

The COVID-19 Genomics UK (COG-UK) Consortium, J Panovska-Griffiths, B Swallow, R Hinch, J Cohen, K Rosenfeld, R M Stuart, L Ferretti, F Di Lauro, C Wymant, A Izzo, W Waites, R Viner, C Bonell, C Fraser, D Klein, C C Kerr, Matthew Bashton, Darren Smith, Andrew NelsonGregory R. Young, Clare McCann

Applied Sciences Department

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15 Citations (Scopus)

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Abstract

The English SARS-CoV-2 epidemic has been affected by the emergence of new viral variants such as B.1.177, Alpha and Delta, and changing restrictions. We used statistical models and the agent-based model Covasim, in June 2021, to estimate B.1.177 to be 20% more transmissible than the wild type, Alpha to be 50-80% more transmissible than B.1.177 and Delta to be 65-90% more transmissible than Alpha. Using these estimates in Covasim (calibrated 1 September 2020 to 20 June 2021), in June 2021, we found that due to the high transmissibility of Delta, resurgence in infections driven by the Delta variant would not be prevented, but would be strongly reduced by delaying the relaxation of restrictions by one month and with continued vaccination. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Original language	English
Article number	20210315
Number of pages	19
Journal	Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
Volume	380
Issue number	2233
DOIs	https://doi.org/10.1098/rsta.2021.0315
Publication status	Published - 3 Oct 2022

Keywords

COVID-19
Humans
Models, Statistical
SARS-CoV-2/genetics
Systems Analysis

UN SDGs

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

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rsta.2021.0315Final published version, 1.47 MBLicence: CC BY

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The COVID-19 Genomics UK (COG-UK) Consortium, Panovska-Griffiths, J., Swallow, B., Hinch, R., Cohen, J., Rosenfeld, K., Stuart, R. M., Ferretti, L., Di Lauro, F., Wymant, C., Izzo, A., Waites, W., Viner, R., Bonell, C., Fraser, C., Klein, D., Kerr, C. C., Bashton, M., Smith, D., ... McCann, C. (2022). Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233), Article 20210315. https://doi.org/10.1098/rsta.2021.0315

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title = "Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions",

abstract = "The English SARS-CoV-2 epidemic has been affected by the emergence of new viral variants such as B.1.177, Alpha and Delta, and changing restrictions. We used statistical models and the agent-based model Covasim, in June 2021, to estimate B.1.177 to be 20% more transmissible than the wild type, Alpha to be 50-80% more transmissible than B.1.177 and Delta to be 65-90% more transmissible than Alpha. Using these estimates in Covasim (calibrated 1 September 2020 to 20 June 2021), in June 2021, we found that due to the high transmissibility of Delta, resurgence in infections driven by the Delta variant would not be prevented, but would be strongly reduced by delaying the relaxation of restrictions by one month and with continued vaccination. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.",

keywords = "COVID-19, Humans, Models, Statistical, SARS-CoV-2/genetics, Systems Analysis",

author = "{The COVID-19 Genomics UK (COG-UK) Consortium} and J Panovska-Griffiths and B Swallow and R Hinch and J Cohen and K Rosenfeld and Stuart, {R M} and L Ferretti and {Di Lauro}, F and C Wymant and A Izzo and W Waites and R Viner and C Bonell and C Fraser and D Klein and Kerr, {C C} and Matthew Bashton and Darren Smith and Andrew Nelson and Young, {Gregory R.} and Clare McCann",

note = "Matthew Bashton, Andrew Nelson, Clare McCann, Greg Young and Darren Smith are members of the COVID-19 Genomics UK consortium.",

year = "2022",

month = oct,

day = "3",

doi = "10.1098/rsta.2021.0315",

language = "English",

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The COVID-19 Genomics UK (COG-UK) Consortium, Panovska-Griffiths, J, Swallow, B, Hinch, R, Cohen, J, Rosenfeld, K, Stuart, RM, Ferretti, L, Di Lauro, F, Wymant, C, Izzo, A, Waites, W, Viner, R, Bonell, C, Fraser, C, Klein, D, Kerr, CC, Bashton, M , Smith, D , Nelson, A, Young, GR & McCann, C 2022, 'Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions', Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 380, no. 2233, 20210315. https://doi.org/10.1098/rsta.2021.0315

Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions. / The COVID-19 Genomics UK (COG-UK) Consortium; Panovska-Griffiths, J; Swallow, B et al.
In: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 380, No. 2233, 20210315, 03.10.2022.

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

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T1 - Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

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

AU - Panovska-Griffiths, J

AU - Swallow, B

AU - Hinch, R

AU - Cohen, J

AU - Rosenfeld, K

AU - Stuart, R M

AU - Ferretti, L

AU - Di Lauro, F

AU - Wymant, C

AU - Izzo, A

AU - Waites, W

AU - Viner, R

AU - Bonell, C

AU - Fraser, C

AU - Klein, D

AU - Kerr, C C

AU - Bashton, Matthew

AU - Smith, Darren

AU - Nelson, Andrew

AU - Young, Gregory R.

AU - McCann, Clare

N1 - Matthew Bashton, Andrew Nelson, Clare McCann, Greg Young and Darren Smith are members of the COVID-19 Genomics UK consortium.

PY - 2022/10/3

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N2 - The English SARS-CoV-2 epidemic has been affected by the emergence of new viral variants such as B.1.177, Alpha and Delta, and changing restrictions. We used statistical models and the agent-based model Covasim, in June 2021, to estimate B.1.177 to be 20% more transmissible than the wild type, Alpha to be 50-80% more transmissible than B.1.177 and Delta to be 65-90% more transmissible than Alpha. Using these estimates in Covasim (calibrated 1 September 2020 to 20 June 2021), in June 2021, we found that due to the high transmissibility of Delta, resurgence in infections driven by the Delta variant would not be prevented, but would be strongly reduced by delaying the relaxation of restrictions by one month and with continued vaccination. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

AB - The English SARS-CoV-2 epidemic has been affected by the emergence of new viral variants such as B.1.177, Alpha and Delta, and changing restrictions. We used statistical models and the agent-based model Covasim, in June 2021, to estimate B.1.177 to be 20% more transmissible than the wild type, Alpha to be 50-80% more transmissible than B.1.177 and Delta to be 65-90% more transmissible than Alpha. Using these estimates in Covasim (calibrated 1 September 2020 to 20 June 2021), in June 2021, we found that due to the high transmissibility of Delta, resurgence in infections driven by the Delta variant would not be prevented, but would be strongly reduced by delaying the relaxation of restrictions by one month and with continued vaccination. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

KW - COVID-19

KW - Humans

KW - Models, Statistical

KW - SARS-CoV-2/genetics

KW - Systems Analysis

U2 - 10.1098/rsta.2021.0315

DO - 10.1098/rsta.2021.0315

M3 - Article

C2 - 35965458

SN - 0962-8428

VL - 380

JO - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

JF - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

IS - 2233

M1 - 20210315

ER -

The COVID-19 Genomics UK (COG-UK) Consortium, Panovska-Griffiths J, Swallow B, Hinch R, Cohen J, Rosenfeld K et al. Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2022 Oct 3;380(2233):20210315. doi: 10.1098/rsta.2021.0315

Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

Abstract

Keywords

UN SDGs

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