Response to the COVID-19 pandemic

As part of an MRC funded project "Mathematical modelling and adaptive control to inform real time decision making for the COVID-19 pandemic at the local, regional and national scale", our team at the Zeeman Institute:SBIDER (Systems Biology & Infectious Disease Epidemiology Research) at the University of Warwick used real time data on the UK SARS-CoV-2 outbreak to provide robust predictions, gauging the ability of a model to predict future epidemic behaviour.

The team includes Matt Keeling, Michael Tildesley, Louise Dyson, Ben Atkins and several colleagues in SBIDER. For further details on the research undertaken by members of the Zeeman Institute:SBIDER, contributing to the COVID-19 modelling response both in the UK and abroad, visit the SBIDER COVID-19 modelling response webpage.

I was also a participant of the Scientific Pandemic Influenza Group on Modelling, Operational subgroup (SPI-M-O) of the Scientific Advisory Group for Emergencies (SAGE), providing advice (based on infectious disease modelling and epidemiology) on scientific matters related to the UK’s response to the COVID-19 pandemic.

Listed below are associated peer-reviewed publications and preprints, split into twelve broad themes (in alphabetical order): Contact tracing mobile apps, fitting to the UK outbreak, higher education, households, immune escape, impact on other pathogens, impact on the infectious disease modelling community, precautionary breaks (circuit breakers), schools, vaccination, Variants of Concern (VOCs), workplaces.

Contact tracing mobile apps

• The effect of notification window length on the epidemiological impact of COVID-19 contact tracing mobile applications.
  Trystan Leng, Edward M Hill, Matt J Keeling, Michael J Tildesley, Robin N Thompson. (2022)
  Communications Medicine. doi:10.1038/s43856-022-00143-2
  

Fitting to the UK outbreak

• Predictions of COVID-19 dynamics in the UK: short-term forecasting and analysis of potential exit strategies
  Matt J Keeling, Edward M Hill, Erin E Gorsich, Bridget Penman, Glen Guyver-Fletcher, Alex Holmes, Trystan Leng, Hector McKimm, Massimiliano Tamborrino, Louise Dyson, Michael J Tildesley. (2021)
  PLoS Comput Biol, 17(1): e1008619. doi:10.1371/journal.pcbi.1008619
  

• Fitting to the UK COVID-19 outbreak, short-term forecasts and estimating the reproductive number
  Matt J Keeling, Louise Dyson, Glen Guyver-Fletcher, Alex Holmes, Malcolm G Semple, ISARIC4C Investigators, Michael J Tildesley, Edward M Hill. (2022)
  Statistical Methods in Medical Research, 31(9): 1716-1737. doi:10.1177/09622802211070257
  

• Short-term forecasts to inform the response to the COVID-19 epidemic in the UK
  Sebastian Funk et al. (2020)
  medRxiv. doi:10.1101/2020.11.11.20220962
  

• Short-term Projections based on Early Omicron Variant Dynamics in England
  Matt J Keeling, Ellen Brooks-Pollock, Robert J Challen, Leon Danon, Louise Dyson, Julia R Gog, Laura Guzman-Rincon, Edward M Hill, Lorenzo M Pellis, Jonathan M Read, Michael J Tildesley. (2021)
  medRxiv. doi:10.1101/2021.12.30.21268307
  

• Bayesian estimation of real-time epidemic growth rates using Gaussian processes: local dynamics of SARS-CoV-2 in England
  Laura Guzman-Rincon, Edward M Hill, Louise Dyson, Michael J Tildesley, Matt J Keeling. (2023)
  Journal of the Royal Statistical Society Series C: Applied Statistics, qlad056. doi:10.1093/jrsssc/qlad056
  

• Comparison of the 2021 COVID-19 roadmap projections against public health data in England
  Matt J Keeling, Louise Dyson, Michael J Tildesley, Edward M Hill, Sam Moore. (2022)
  Nature Communications, 13: 4924. doi:10.1038/s41467-022-31991-0
  

Higher education

• Modelling SARS-CoV-2 transmission in a UK university setting
  Edward M Hill, Benjamin D Atkins, Matt J Keeling, Michael J Tildesley, Louise Dyson. (2021)
  Epidemics, 36: 100476. doi:10.1016/j.epidem.2021.100476
  

• SARS-CoV-2 infection in UK university students: Lessons from September-December 2020 and modelling insights for future student return.
  Jessica Enright*, Edward M Hill*, Helena B Stage, Kirsty J Bolton, Emily J Nixon, Emma Fairbanks, Maria L Tang, Ellen Brooks-Pollock, Louise Dyson, Chris J Budd, Rebecca B Hoyle, Lars Schewe, Julia R Gog, Michael J Tildesley. (2021)
  Royal Society Open Science, 8(8): 210310. doi:10.1098/rsos.210310
  * denotes joint first authors

• Coughs, colds and “freshers’ flu” survey in the University of Cambridge, 2007-2008
  Ken TD Eames, Maria L Tang, Edward M Hill, Michael J Tildesley, Jonathan M Read, Matt J Keeling, Julia R Gog. (2022)
  Epidemics, 42: 100659. doi:10.1016/j.epidem.2022.100659
  

Households

• Modelling the epidemiological implications for SARS-CoV-2 of Christmas household bubbles in England
  Edward M Hill. (2022)
  Journal of Theoretical Biology, 557: 111331. doi:10.1016/j.jtbi.2022.111331
  

Immune escape

• SARS-CoV-2 incidence and vaccine escape
  Robin N Thompson, Edward M Hill, Julia R Gog. (2021)
  Lancet Infectious Diseases, 21(7): 913-914. doi:10.1016/S1473-3099(21)00202-4
  

• Vaccine escape in a heterogeneous population: insights for SARS-CoV-2 from a simple model
  Julia R Gog, Edward M Hill, Leon Danon, Robin N Thompson. (2021)
  Royal Society Open Science, 8(7): 210530. doi:10.1098/rsos.210530
  

Impact on other pathogens

• Scenario modelling for diminished influenza seasons during 2020/2021 and 2021/2022 in England
  Edward M Hill, Matt J Keeling. (2022)
  medRxiv. doi:10.1101/2022.10.27.22281628
  

Impact on the infectious disease modelling community

• Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic
  Katharine Sherratt, Anna C Carnegie, Adam Kucharski, Anne Cori, Carl AB Pearson, Christopher I Jarvis, Christopher Overton, Dale Weston, Edward M Hill, Edward Knock, Elizabeth Fearon, Emily Nightingale, Joel Hellewell, W John Edmunds, Julian Villabona Arenas, Kiesha Prem, Li Pi, Marc Baguelin, Michelle Kendall, Neil Ferguson, Nicholas Davies, Rosalind M Eggo, Sabine van Elsland, Timothy Russell, Sebastian Funk, Yang Liu, Sam Abbott. (2023)
  bioRxiv. doi:10.1101/2023.06.12.544667
  

Precautionary breaks (circuit breakers)

• Precautionary breaks: Planned, limited duration circuit breaks to control the prevalence of SARS-CoV-2 and the burden of COVID-19 disease
  Matt J Keeling, Glen Guyver-Fletcher, Alex Holmes, Louise Dyson, Michael J Tildesley, Edward M Hill, Graham F Medley. (2021)
  Epidemics, 37: 100526. doi:10.1016/j.epidem.2021.100526
  

• Optimal health and economic impact of non-pharmaceutical intervention measures prior and post vaccination in England: a mathematical modelling study
  Michael J Tildesley, Anna Vassall, Steven Riley, Mark Jit, Frank Sandmann, Edward M Hill, Robin N Thompson, Benjamin D Atkins, John Edmunds, Louise Dyson, Matt J Keeling. (2022)
  Royal Society Open Science, 9(8): 211746. doi:10.1098/rsos.211746
  

Schools

• An analysis of school absences in England during the Covid-19 pandemic
  Emma R Southall, Alex Holmes, Edward M Hill, Benjamin D Atkins, Trystan Leng, Robin N Thompson, Louise Dyson, Matt J Keeling, Michael J Tildesley. (2021)
  BMC Medicine, 19: 137. doi:10.1186/s12916-021-01990-x
  

• The impact of school reopening on the spread of COVID-19 in England
  Matt J Keeling, Michael J Tildesley, Benjamin D Atkins, Bridget Penman, Emma Southall, Glen Guyver-Fletcher, Alex Holmes, Hector McKimm, Erin E Gorsich, Edward M Hill, Louise Dyson. (2021)
  Phil Trans B, 376(1829): 20200261. doi:10.1098/rstb.2020.0261
  

• Assessing the impact of lateral flow testing strategies on within-school SARS-CoV-2 transmission and absences: A modelling study.
  Trystan Leng, Edward M Hill, Robin N Thompson, Michael J Tildesley, Matt J Keeling, Louise Dyson. (2022)
  PLoS Comput Biol, 18(6): e1010158. doi:10.1371/journal.pcbi.1010158
  

• Quantifying within-school SARS-CoV-2 transmission and the impact of lateral flow testing in secondary schools in England.
  Trystan Leng, Edward M Hill, Alex Holmes, Emma Southall, Robin N Thompson, Michael J Tildesley, Matt J Keeling, Louise Dyson. (2022)
  Nature Communications, 13: 1106. doi:10.1038/s41467-022-28731-9
  

Vaccination

• Modelling optimal vaccination strategy for SARS-CoV-2 in the UK
  Sam Moore, Edward M Hill, Louise Dyson, Michael J Tildesley, Matt J Keeling. (2021)
  PLoS Comput Biol, 17(5): e1008849. doi:10.1371/journal.pcbi.1008849
  

• Vaccination and non-pharmaceutical interventions for COVID-19: a mathematical modelling study
  Sam Moore, Edward M Hill, Michael J Tildesley, Louise Dyson, Matt J Keeling. (2021)
  Lancet Infectious Diseases, 21(6): 793-802. doi:10.1016/S1473-3099(21)00143-2
  

• Comparison between one and two dose SARS-CoV-2 vaccine prioritization for a fixed number of vaccine doses
  Edward M Hill, Matt J Keeling. (2021)
  J. R. Soc. Interface, 18(182): 20210214. doi:10.1098/rsif.2021.0214
  

• Waning, Boosting and a Path to Endemicity for SARS-CoV-2
  Matt J Keeling, Amy C Thomas, Edward M Hill, Robin N Thompson, Louise Dyson, Michael J Tildesley, Sam Moore. (2021)
  medRxiv. doi:10.1101/2021.11.05.21265977
  

• Retrospectively modeling the effects of increased global vaccine sharing on the COVID-19 pandemic
  Sam Moore, Edward M Hill, Louise Dyson, Michael J Tildesley, Matt J Keeling. (2022)
  Nature Medicine, 28: 2416-2423. doi:10.1038/s41591-022-02064-y
  

• The impacts of SARS-CoV-2 vaccine dose separation and targeting on the COVID-19 epidemic in England
  Matt J Keeling, Sam Moore, Bridget Penman, Edward M Hill. (2023)
  Nature Communications, 14: 740. doi:10.1038/s41467-023-35943-0
  

Variants of Concern (VOCs)

• Short-term Projections based on Early Omicron Variant Dynamics in England
  Matt J Keeling, Ellen Brooks-Pollock, Robert J Challen, Leon Danon, Louise Dyson, Julia R Gog, Laura Guzman-Rincon, Edward M Hill, Lorenzo M Pellis, Jonathan M Read, Michael J Tildesley. (2021)
  medRxiv. doi:10.1101/2021.12.30.21268307
  

• Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics
  Louise Dyson*, Edward M Hill*, Sam Moore, Jacob Curran-Sebastian, Michael J Tildesley, Katrina A Lythgoe, Thomas House, Lorenzo Pellis, Matt J Keeling. (2021)
  Nature Communications, 12: 5730. doi:10.1038/s41467-021-25915-7
  * denotes joint first authors

• Early epidemiological signatures of novel SARS-CoV-2 variants: establishment of B.1.617.2 in England
  Robert Challen et al. (2021)
  medRxiv. doi:10.1101/2021.06.05.21258365
  

• Emergence of SARS-CoV-2 Delta Variant and Effect of Nonpharmaceutical Interventions, British Columbia, Canada
  Y.L. Elaine Chan, Michael A. Irvine, Natalie Prystajecky, Hind Sbihi, Marsha Taylor, Yayuk Joffres, Andrea Schertzer, Caren Rose, Louise Dyson, Edward M. Hill, Michael Tildesley, John R. Tyson, Linda M.N. Hoang, Eleni Galanis. (2023)
  Emerging Infectious Diseases, 29(10): 1999-2007. doi:10.3201/eid2910.230055
  

Workplaces

• A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2
  Edward M Hill*, Benjamin D Atkins*, Matt J Keeling, Louise Dyson, Michael J Tildesley. (2021)
  PLoS Comput Biol, 17(6): e1009058. doi:10.1371/journal.pcbi.1009058
  * denotes joint first authors