Journal publications

Comparison between one and two dose SARS-CoV-2 vaccine prioritization for a fixed number of vaccine doses

Edward M. Hill1,2 and Matt J. Keeling, R. Soc Interface, Aug 2021

High COVID-19 transmission potential associated with re-opening universities can be mitigated with layered interventions

Ellen Brooks-Pollock, Hannah Christensen, Adam Trickey, Gibran Hemani, Emily Nixon, Amy C. Thomas, Katy Turner, Adam Finn, Matt Hickman, Caroline Relton & Leon Danon, Nature Communications, Aug 2021

Hospital-acquired SARS-CoV-2 infection in the UK's first COVID-19 pandemic wave

Jonathan M Read, Chris A Green, Ewen M Harrison, Annemarie B Docherty, Sebastian Funk, Janet Harrison, Michelle Girvan, Hayley E Hardwick, Lance Turtle, Jake Dunning, Jonathan S Nguyen-Van-Tam, Peter JM Openshaw, J Kenneth Baillie, Malcolm G Semple and the ISARIC4C investigators, The Lancet correspondence, Aug 2021

University students and staff able to maintain low daily contact numbers during various COVID-19 guideline periods

Adam Trickey, Emily Nixon, Hannah Christensen, Adam Finn, Amy Thomas, Caroline Relton, Clara Montgomery, Gibran Hemani, Jane Metz, Josephine G Walker, Katy Turner, Rachel Kwiatkowska, Sarah Sauchelli, Leon Danon, Ellen Brooks-Pollock, Epidemiology and Infection, Aug 2021

Hospital length of stay for COVID-19 patients: Data-driven methods for forward planning

Bindu Vekaria , Christopher Overton, Arkadiusz Wis ́niowski, Shazaad Ahmad, Andrea Aparicio-Castro, Jacob Curran-Sebastian, Jane Eddleston, Neil A Hanley, Thomas House, Jihye Kim, Wendy Olsen, Maria Pampaka, Lorenzo Pellis, Diego Perez Ruiz, John Schofield, Nick Shryane and Mark J. Elliot BMC Infectious Diseases, July 2021

SARS-CoV-2 antigen testing: weighing the false positives against the costs of failing to control transmission

Elizabeth Fearon, Iain E Buchan, Rajenki Das, Emma L Davis, Martyn Fyles, Ian Hall, T Deirdre Hollingsworth, Thomas House, Caroline Jay, Graham F Medley, Lorenzo Pellis, Billy J Quilty, Miguel E P Silva, Helena B Stage, Tom Wingfield, The Lancet Respiratory Medicine, Comment, vol 9, issue 7, p685-687, July, 2021

Vaccine escape in a heterogeneous population: insights for SARS-CoV-2 from a simple model

Julia R. Gog, Edward M. Hill, Leon Danon, and Robin N. Thompson, R. Soc. Open Science, July 2021

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 L. Fairbanks, Maria L. Tang, Ellen Brooks-Pollock, Louise Dyson, Chris J. Budd, Rebecca B. Hoyle, Lars Schewe, Julia R. Gog and Michael J. Tildesley, R. Soc Open Sci. July 2021

Spatially resolved simulations of the spread of COVID-19 in three European countries

Andrea Parisi, Samuel P. C. Brand, Joe Hilton, Rabia Aziza, Matt J. Keeling, D. James Nokes, PLOS COMP BIO, July 2021

Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values

Massimo Cavallaro, Haseeb Moiz, Matt J Keeling, Noel D McCarthy, PLOS Computational Biology, June 2021

Contacts and behaviours of university students during the COVID-19 pandemic at the start of the 2020/2021 academic year

Emily Nixon, Adam Trickey, Hannah Christensen, Adam Finn, Amy Thomas, Caroline Relton, Clara Montgomery, Gibran Hemani, Jane Metz, Josephine G. Walker, Katy Turner, Rachel Kwiatkowska, Sarah Sauchelli, Leon Danon and Ellen Brooks‐Pollock, Scientific Reports, June 2021

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, The Lancet Infectious Diseases, vol 21, issue 6, June 2021

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, PloS Comp Bio, June 2021

An analysis of school absences in England during the COVID-19 pandemic SARS-CoV-2 incidence and vaccine escape

Emma Southall, Alex Holmes, Edward M. Hill, Benjamin D. Atkins, Trystan Leng, Robin N. Thompson, Louise Dyson, Matt J. Keeling and Michael J. Tildesley, BMC Medicine, June 2021

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

Ellen Brooks-Pollock, Leon Danon, Thibaut Jombart and Lorenzo Pellis, R. Soc. Phil. Trans. B, May 2021

Novel coronavirus 2019-nCoV (COVID-19): early estimation of epidemiological parameters and epidemic size estimates

Jonathan M. Read, Jessica R. E. Bridgen, Derek A. T. Cummings, Antonia Ho and Chris P. Jewell, R. Soc. Phil. Trans. B, May 2021

Challenges in control of COVID-19: short doubling time and long delay to effect of interventions

Lorenzo Pellis, Francesca Scarabel, Helena B. Stage, Christopher E. Overton, Lauren H. K. Chappell, Elizabeth Fearon, Emma Bennett, Katrina A. Lythgoe, Thomas A. House, Ian Hall and University of Manchester COVID-19 Modelling Group, R. Soc. Phil. Trans. B, May 2021

A spatial model of COVID-19 transmission in England and Wales: early spread, peak timing and the impact of seasonality

Leon Danon, Ellen Brooks-Pollock, Mick Bailey and Matt Keeling, R. Soc. Phil. Trans. B, May 2021

Epidemic interventions: insights from classic results

Julia R. Gog and T. Déirdre Hollingsworth, R. Soc. Phil. Trans. B, May 2021

Estimates of regional infectivity of COVID-19 in the United Kingdom following imposition of social distancing measures

Robert Challen, Krasimira Tsaneva-Atanasova, Martin Pitt, Tom Edwards, Luke Gompels, Lucas Lacasa, Ellen Brooks-Pollock and Leon Danon, R. Soc. Phil. Trans. B, May 2021

The population attributable fraction of cases due to gatherings and groups with relevance to COVID-19 mitigation strategies

Ellen Brooks-Pollock, Jonathan M. Read, Thomas House, Graham F. Medley, Matt J. Keeling and Leon Danon, R. Soc. Phil. Trans. B, May 2021

Real-time nowcasting and forecasting of COVID-19 dynamics in England: the first wave

Paul Birrell, Joshua Blake, Edwin van Leeuwen, Nick Gent and Daniela De Angelis, R. Soc. Phil. Trans. B, May 2021

Mapping social distancing measures to the reproduction number for COVID-19

Ellen Brooks-Pollock, Jonathan M. Read, Angela R. McLean, Matt J. Keeling and Leon Danon, R. Soc. Phil. Trans. B, May 2021

Outbreaks in care homes may lead to substantial disease burden if not mitigated

Ian Hall, Hugo Lewkowicz, Luke Webb, Thomas House, Lorenzo Pellis, James Sedgwick4 and Nick Gent, on behalf of the University of Manchester COVID-19 Modelling Group and the Public Health England Modelling Team, R. Soc. Phil. Trans. B, May 2021

Shut and re-open: the role of schools in the spread of COVID-19 in Europe

Helena B. Stage1, Joseph Shingleton2, Sanmitra Ghosh3, Francesca Scarabel, Lorenzo Pellis and Thomas Finnie, R. Soc. Phil. Trans. B, May 2021

Using a household-structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic

Martyn Fyles, Elizabeth Fearon, Christopher Overton, University of Manchester COVID-19 Modelling Group, Tom Wingfield5, Graham F. Medley, Ian Hall, Lorenzo Pellis and Thomas House, R. Soc. Phil. Trans. B, May 2021

Household bubbles and COVID-19 transmission: insights from percolation theory

Leon Danon, Lucas Lacasa and Ellen Brooks-Pollock, R. Soc. Phil. Trans. B, May 2021

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 and Louise Dyson, R. Soc. Phil. Trans. B, May 2021

Engagement and adherence trade-offs for SARS-CoV-2 contact tracing

Tim C. D. Lucas, Emma L. Davis, Diepreye Ayabina, Anna Borlase, Thomas Crellen, Li Pi, Graham F. Medley, Lucy Yardley, Petra Klepac, Julia Gog and T. Déirdre Hollingsworth, R. Soc. Phil. Trans. B, May 2021

Dynamics of SARS-CoV-2 with waning immunity in the UK population

Thomas Crellen, Li Pi, Emma L. Davis, Timothy M. Pollington, Tim C. D. Lucas, Diepreye Ayabina, Anna Borlase, Jaspreet Toor, Kiesha Prem, Graham F. Medley, Petra Klepac, and T. Déirdre Hollingsworth, R. Soc. Phil. Trans. B, May 2021

Modelling optimal vaccination strategy for SARS-CoV-2 in the UK

Sam Moore, Edward M. Hill, Louise Dyson, Michael J. Tildesley, Matt J. Keeling, PloS Comp Bio, May 2021

Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data

John Ojal, Samuel PC Brand, Vincent Were, Emelda A Okiro, Ivy K Kombe, Caroline Mburu, Rabia Aziza, Morris Ogero, Ambrose Agweyu, George M Warimwe, Sophie Uyoga, Ifedayo MO Adetifa, J Anthony G Scott, Edward Otieno, Lynette I Ochola-Oyier, Charles N Agoti, Kadondi Kasera, Patrick Amoth, Mercy Mwangangi, Rashid Aman, Benjamin Tsofa, Philip Bejon, Edwine Barasa, Matt J Keeling, D James Nokes, Wellcome Open Research, vol 6, issue 127, May 2021

COVID-19 testing in outbreak-free care homes: what are the public health benefits?

R Green, JSP Tulloch, C Tunnah, E Coffey, K Lawrenson, A Fox, J Mason, R Barnett, A Constantine, W Shepherd, M Ashton, MBJ Beadsworth, Roberto Vivancos, I Hall, Naomi Walker, Samuel Ghebrehewet, Journal of Hospital Infection, May 2021

A renewal equation model to assess roles and limitations of contact tracing for disease outbreak control

Francesca Scarabel, Lorenzo Pellis, Nicholas H. Ogden and Jianhong Wu, Royal Society Open Science, 8, April 2021

The effectiveness of social bubbles as part of a Covid-19 lockdown exit strategy, a modelling study

Trystan Leng, Connor White, Joe Hilton, Adam Kucharski, Lorenzo Pellis, Helena Stage, Nicholas G. Davies, Centre for Mathematical Modelling of Infectious Disease 2019 nCoV Working Group, Matt J. Keeling, Stefan Flasche, Wellcome Open Research, March 2021

Excess mortality for care home residents during the first 23 weeks of the COVID-19 pandemic in England: a national cohort study

Marcello Morciano, Jonathan Stokes, Evangelos Kontopantelis, Ian Hall, Alex J Turner, BMC Medicine, March 2021

Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study

Robert Challen, Ellen Brooks-Pollock, Jonathan M Read, Louise Dyson, Krasimira Tsaneva-Atanasova, Leon Danon, BMJ, March 2021

Superinfection and the evolution of an initial asymptomatic stage

Chadi M. Saad-Roy, Bryan T. Grenfell, Simon A. Levin, Lorenzo Pellis, Helena B. Stage, P. van den Driessche and Ned S. Wingreen, Royal Society Open Science, Jan 2021

Developing a Framework for Public Involvement in Mathematical and Economic Modelling: Bringing New Dynamism to Vaccination Policy Recommendations

Sophie Staniszewska, Edward M Hill, Richard Grant, Peter Grove, Jarina Porter, Tinevimbo Shiri, Sue Tulip, Jane Whitehurst, Claire Wright, Samik Datta, Stavros Petrou, Matt Keeling, The Patient - Patient-Centered Outcomes Research (Jan 2021) 14:435–445

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, PLOS COMP BIO, Jan 2021

A novel approach for evaluating contact patterns and risk mitigation strategies for COVID-19 in English primary schools with application of structured expert judgement

RSJ Sparks, WP Aspinall, E Brooks-Pollock, RM Cooke, L Danon, J Barclay, JH Scarrow, J Cox, R. Soc. Open Science, Jan 2021

Hospital bed capacity and usage across secondary healthcare providers in England during the first wave of the COVID-19pandemic: a descriptive analysis

Bilal Akhter Mateen, Harrison Wilde, John M Dennis, Andrew Duncan, Nick Thomas, Andrew McGovern, Spiros Denaxas, Matt Keeling, Sebastian Vollmer, BMJ Open Dec 2020

Assessing the impact of secondary school reopening strategies on within-school COVID-19 transmission and absences: a modelling study

Trystan Leng, Edward M Hill, Robin N Thompson, Michael J Tildesley, Matt J Keeling, Louise J Dyson, https://doi.org/10.1101/2021.02.11.21251587