Cited by 76COVID-19 epidemiological studiesAcademic Publishing and Open AccessSARS-CoV-2 and COVID-19 Research

Modelling that shaped the early COVID-19 pandemic response in the UK

Open access
Brooks-Pollock, Ellen, Danon, Leon, Jombart, Thibaut, Pellis, Lorenzo·2021·Philosophical Transactions of the Royal Society B

Abstract

Infectious disease modelling has played an integral part of the scientific evidence used to guide the response to the COVID-19 pandemic. In the UK, modelling evidence used for policy is reported to the Scientific Advisory Group for Emergencies (SAGE) modelling subgroup, SPI-M-O (Scientific Pandemic Influenza Group on Modelling-Operational). This Special Issue contains 20 articles detailing evidence that underpinned advice to the UK government during the SARS-CoV-2 pandemic in the UK between January 2020 and July 2020. Here, we introduce the UK scientific advisory system and how it operates in practice, and discuss how infectious disease modelling can be useful in policy making. We examine the drawbacks of current publishing practices and academic credit and highlight the importance of transparency and reproducibility during an epidemic emergency. This article is part of the theme issue ‘Modelling that shaped the early COVID-19 pandemic response in the UK’.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1098/rstb.2021.0001

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Mathematical models of disease transmission and control are a key tool for responding to infectious disease outbreaks and guiding policy, for example by projecting epidemic trajectories, healthcare demand, and intervention impact.

    “Mathematical models of disease transmission and control are a key tool that can be deployed in response to infectious disease outbreaks and are used to guide policy, for example by projecting plausible epidemic trajectories and expected healthcare demand and assessing the potential impact of interventions (19,20).”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

No references could be resolved yet.

Research works printed but not linked: 37

  1. [9]Reichardt J, Bornholdt S. 2006 Statistical mechanics of community detection. Phys. Rev. E 74, 016110. (10.1103/PhysRevE.74.016110) 16907154 · DOI · Paper page
  2. [11]Medley GF. 2001 Epidemiology. Predicting the unpredictable. Science 294, 1663- 1664. (10.1126/science.1067669) 11721038 · DOI
  3. [12]Anderson RM, May RM. 1992 Infectious diseases of humans: dynamics and control. Oxford, UK: Oxford University Press.
  4. [13]Keeling MJ, Rohani P. 2011 Modeling infectious diseases in humans and animals. Princeton, NJ: Princeton University Press.
  5. [14]Pellis L et al. 2021 Challenges in control of COVID-19: short doubling time and long delay to effect of interventions. Phil. Trans. R. Soc. B 376, 20200264. (10.1098/rstb.2020.0264) 34053267 PMC8165602 · DOI
  6. [15]Read JM, Bridgen JRE, Cummings DAT, Ho A, Jewell CP. 2021 Novel coronavirus 2019-nCoV (COVID-19): early estimation of epidemiological parameters and epidemic size estimates. Phil. Trans. R. Soc. B 376, 20200265. (10.1098/rstb.2020.0265) 34053269 PMC8165596 · DOI
  7. [16]Fyles M, Fearon E, Overton C, University of Manchester COVID-19 Modelling Group, Wingfield T, Medley GF, Hall I, Pellis L, House T. 2021 Using a household-structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic. Phil. Trans. R. Soc. B 376, 20200267. (10.1098/rstb.2020.0267) 34053253 PMC8165594 · DOI
  8. [17]Danon L, Lacasa L, Brooks-Pollock E. 2021 Household bubbles and COVID-19 transmission: insights from percolation theory. Phil. Trans. R. Soc. B 376, 20200284. (10.1098/rstb.2020.0284) 34053262 PMC8165589 · DOI
  9. [18]Brooks-Pollock E, Danon L, Jombart T, Pellis L. 2021 Modelling that shaped the early COVID-19 pandemic response in the UK. Phil. Trans. R. Soc. B 376, 20210001. (10.1098/rstb.2021.0001) 34053252 PMC8165593
  10. [19]Challen R, Tsaneva-Atanasova K, Pitt M, Edwards T, Gompels L, Lacasa L, Brooks-Pollock E, Danon L. 2021 Estimates of regional infectivity of COVID-19 in the United Kingdom following imposition of social distancing measures. Phil. Trans. R. Soc. B 376, 20200280. (10.1098/rstb.2020.0280) 34053251 PMC8165582 · DOI
  11. [20]Sherratt K, Abbott S, Meakin SR, Hellewell J, Munday JD, Bosse N, CMMID COVID-19 Working Group, Jit M, Funk S. 2021 Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England. Phil. Trans. R. Soc. B 376, 20200283. (10.1098/rstb.2020.0283) 34053260 PMC8165604 · DOI
  12. [21]Jarvis CI et al. 2020 Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK. BMC Med. 18, 124. (10.1186/s12916-020-01597-8) 32375776 PMC7202922 · DOI · Paper page
  13. [22]Riley S et al. 2021 REACT-1 round 9 final report: continued but slowing decline of prevalence of SARS-CoV-2 during national lockdown in England in February 2021. MedRxiv.
  14. [23]Pouwels KB et al. 2021 Community prevalence of SARS-CoV-2 in England from April to November 2020: results from the ONS Coronavirus Infection Survey. Lancet Pub. Health 6, E30–E38. (10.1016/s2468-2667(20)30282-6) PMC7786000 33308423 · DOI
  15. [24]Whitty CJM. 2015 What makes an academic paper useful for health policy? BMC Med. 13, 301. (10.1186/s12916-015-0544-8) 26675206 PMC4682263 · DOI
  16. [25]Kaplan EH. 1989 Can bad models suggest good policies? Sexual mixing and the AIDS epidemic. J. Sex Res. 26, 301- 314. (10.1080/00224498909551517) · DOI
  17. [26]Anderson RM, Medley GF, May RM, Johnson AM. 1986 A preliminary study of the transmission dynamics of the human immunodeficiency virus (HIV), the causative agent of AIDS. IMA J. Math. Appl. Med. Biol. 3, 229- 263. (10.1093/imammb/3.4.229) 3453839 · DOI
  18. [27]Anderson RM, Medley GF, Blythe SP, Johnson AM. 1987 Is it possible to predict the minimum size of the acquired immunodeficiency syndrome (AIDS) epidemic in the United Kingdom? Lancet 1, 1073- 1075. (10.1016/S0140-6736(87)90493-4) 2883405 · DOI
  19. [28]Ghani AC, Ferguson NM, Donnelly CA, Anderson RM. 2000 Predicted vCJD mortality in Great Britain. Nature 406, 583- 584. (10.1038/35020688) 10949288 · DOI
  20. [29]Keeling MJ et al. 2001 Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape. Science 294, 813- 817. (10.1126/science.1065973) 11679661 · DOI
  21. [30]Baguelin M, Flasche S, Camacho A, Demiris N, Miller E, Edmunds WJ. 2013 Assessing optimal target populations for influenza vaccination programmes: an evidence synthesis and modelling study. PLoS Med. 10, e1001527. (10.1371/journal.pmed.1001527) 24115913 PMC3793005 · DOI
  22. [31]Gog JR, Hollingsworth TD. 2021 Epidemic interventions: insights from classic results. Phil. Trans. R. Soc. B 376, 20200263. (10.1098/rstb.2020.0263) 34053265 PMC8165583 · DOI
  23. [32]Kucharski AJ, Funk S, Eggo RM. 2020 The COVID-19 response illustrates that traditional academic reward structures and metrics do not reflect crucial contributions to modern science. PLoS Biol. 18, e3000913. (10.1371/journal.pbio.3000913) 33064730 PMC7592912 · DOI
  24. [33]Jombart T. 2021 Why development of outbreak analytics tools should be valued, supported, and funded. Lancet Infect. Dis. 21, 458- 459. (10.1016/S1473-3099(20)30996-8) PMC7832113 33444558 · DOI
  25. [34]Singh CD. 2020 Critiqued coronavirus simulation gets thumbs up from code-checking efforts. Nature 582, 323- 324. (10.1038/d41586-020-01685-y) 32546864 · DOI
  26. [36]Birrell P, Blake J, van Leeuwen E, Gent N, De Angelis D. 2021 Real-time nowcasting and forecasting of COVID-19 dynamics in England: the first wave. Phil. Trans. R. Soc. B 376, 20200279. (10.1098/rstb.2020.0279) 34053254 PMC8165585 · DOI
  27. [37]Jombart T et al. 2021 Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection. Phil. Trans. R. Soc. B 376, 20200266. (10.1098/rstb.2020.0266) 34053271 PMC8165581 · DOI
  28. [38]Brooks-Pollock E, Read JM, McLean AR, Keeling MJ, Danon L. 2021 Mapping social distancing measures to the reproduction number for COVID-19. Phil. Trans. R. Soc. B 376, 20200276. (10.1098/rstb.2020.0276) 34053268 PMC8165600 · DOI
  29. [39]Keeling MJ et al. 2021 The impact of school reopening on the spread of COVID-19 in England. Phil. Trans. R. Soc. B 376, 20200261. (10.1098/rstb.2020.0261) 34053259 PMC8165595 · DOI
  30. [40]Brooks-Pollock E, Read JM, House T, Medley GF, Keeling MJ, Danon L. 2021 The population attributable fraction of cases due to gatherings and groups with relevance to COVID-19 mitigation strategies. Phil. Trans. R. Soc. B 376, 20200273. (10.1098/rstb.2020.0273) 34053263 PMC8165584 · DOI
  31. [41]Stage HB, Shingleton J, Ghosh S, Scarabel F, Pellis L, Finnie T. 2021 Shut and re-open: the role of schools in the spread of COVID-19 in Europe. Phil. Trans. R. Soc. B 376, 20200277. (10.1098/rstb.2020.0277) 34053270 PMC8165592 · DOI
  32. [42]Danon L, Brooks-Pollock E, Bailey M, Keeling M. 2021 A spatial model of COVID-19 transmission in England and Wales: early spread, peak timing and the impact of seasonality. Phil. Trans. R. Soc. B 376, 20200272. (10.1098/rstb.2020.0272) 34053261 PMC8165591 · DOI
  33. [43]Lucas TCD et al. 2021 Engagement and adherence trade-offs for SARS-CoV-2 contact tracing. Phil. Trans. R. Soc. B 376, 20200270. (10.1098/rstb.2020.0270) 34053257 PMC8165588 · DOI
  34. [44]Evans S, Agnew E, Vynnycky E, Stimson J, Bhattacharya A, Rooney C, Warne B, Robotham J. 2021 The impact of testing and infection prevention and control strategies on within-hospital transmission dynamics of COVID-19 in English hospitals. Phil. Trans. R. Soc. B 376, 20200268. (10.1098/rstb.2020.0268) 34053255 PMC8165586 · DOI
  35. [45]Hall I, Lewkowicz H, Webb L, House T, Pellis L, Sedgwick J, Gent N on behalf of the University of Manchester COVID-19 Modelling Group and the Public Health England Modelling Team. 2021 Outbreaks in care homes may lead to substantial disease burden if not mitigated. Phil. Trans. R. Soc. B 376, 20200269. (10.1098/rstb.2020.0269) 34053256 PMC8165603 · DOI
  36. [46]van Bunnik BAD et al. 2021 Segmentation and shielding of the most vulnerable members of the population as elements of an exit strategy from COVID-19 lockdown. Phil. Trans. R. Soc. B 376, 20200275. (10.1098/rstb.2020.0275) 34053266 PMC8165590 · DOI
  37. [47]Crellen T et al. 2021 Dynamics of SARS-CoV-2 with waning immunity in the UK population. Phil. Trans. R. Soc. B 376, 20200274. (10.1098/rstb.2020.0274) 34053264 PMC8165597 · DOI

Cited by

Sorted by citations

Authors
Brooks-Pollock, E., Danon, L., Jombart, T., & Pellis, L.
Affiliations
  • 1 Bristol Veterinary School, University of Bristol, Bristol BS40 5DU, UK
  • 3 Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TW, UK
  • London School of Hygiene & Tropical Medicine (GB)
  • University of Manchester (GB)
Venue
Philosophical Transactions of the Royal Society B
Published
2021-05-31
Volume
376
Issue
1829
Pages
20210001-20210001
ISSN
  • 0962-8436 (ISSN-L)
  • 1471-2970
OpenAlex
W3164986408
Cited by
76
References
0
Citations by year
2026: 5 · 2025: 15 · 2024: 17 · 2023: 16 · 2022: 16 · 2021: 7
FWCI
5.41
Type
journal article
Language
en
Open access
Locations
  • Philosophical Transactions of the Royal Society B Biological Sciences (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research Explorer (The University of Manchester) (publishedVersion, other-oa)
  • Bristol Research (University of Bristol) (publishedVersion, cc-by)
  • LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
  • Explore Bristol Research (submittedVersion, cc-by)
Funders
  • Medical Research Council (MC/PC/19067, MR/V038613/1)
  • Engineering and Physical Sciences Research Council (EP/N510129/1, EP/V051555/1)
Topics
  • Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
  • Social Sciences › Decision Sciences › Information Systems and Management › Academic Publishing and Open Access
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Keywords
COVID-19 pandemic response, epidemic modeling, sage, science-policy interface, transparency and reproducibility, academic publishing practices, academic credit
MeSH terms
COVID-19, SARS-CoV-2, United Kingdom, Humans, Pandemics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review