Journal Publications
Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes
S. Cotton, M.P. McHugh, R. Dewar, J.G. Haas, K. Templeton, The COVID-19 Genomics UK (COG-UK) Consortium, Journal of Hospital Infection, May 2023
Multiple models for outbreak decision support in the face of uncertainty
Katriona Shea, Rebecca K. Borchering, M.J. Tildesley +74, PNAS, Apr 2023
Views and perceptions of people aged 55+ on the vaccination programme for older adults in the UK: A qualitative study
Taru Silvonen, Jo Kesten, Christie Cabral, Jo Coast, Yoav Ben-Shlomo, Hannah Christensen, Vaccines, Apr 2023
A target-cell limited model can reproduce influenza infection dynamics in hosts with differing immune responses
Rahil Sachak-Patwa, Erin I. Lafferty, Claude J. Schmit, Robin N. Thompson, Journal of Theoretical Biology, Apr 2023
The importance of vaccinated individuals to population-level evolution of pathogens
M.A. Gutierrez Guillen, J. Gog, Journal of Theoretical Biology, Apr 2023
Evaluation of outpatient treatment for non-hospitalised patients with COVID-19: The experience of a regional centre in the UK
Amanda T. Goodwin, Jonathan S. Thompson, Ian P. Hall, PLOS One, Mar 2023
Infectious disease modelling of HIV prevention interventions: A systematic review and narrative synthesis of compartmental models
Rebecca Giddings, Pitchaya Indravudh, Graham F. Medley, Fiammetta Bozzani, Mitzy Gafos, Shelly Malhotra, Fern Terris-Prestholt, Segio Torres-Rueda, Matthew Quaife, PharmacoEconomics, Mar 2023
An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study
Lindsay M. Beck-Johnson, Erin E. Gorsich, Clayton Hallman, Michael J. Tildesley, Ryan S. Miller, Collen T. Webb, Epidemics, Mar 2023
The impacts of SARS-CoV-2 vaccine dose separation and targeting on the COVID-19 epidemic in England
Matt J. Keeling, Samuel Moore, Bridget S. Penman, Edward M. Hill, Nature Communications, Feb 2023
Transmission of Mpox: A narrative review of environmental, viral, host and population factors in relation to the 2022 international outbreak
Daniel Pan, Joshua Nazareth, Shirley Sze, Christopher A. Martin, Jonathan Decker, Eve Fletcher, T. Deirdre Hollingsworth, Michael R. Barer, Manesh Pareek, Julian W. Tang, J. Med Virology, Jan 2023
Voluntary risk mitigation behaviour can reduce impact of SARS-CoV-2: a real-time modelling study of the January 2022 Omicron wave in England
Ellen Brooks-Pollock, Kate Northstone, Lorenzo Pellis, Francesca Scarabel, Amy Thomas, Emily Nixon, David A. Matthews, Vicky Bowyer, Maria Paz Garcia, Claire J. Steves, Nicholas J. Timpson, Leon Danon, BMC Medicine, Jan 2023
Getting the most out of maths: How to coordinate mathematical modelling research to support a pandemic, lessons learnt from three initiatives that were part of the COVID-19 response in the UK
Ciara E. Dangerfield, I. David Abrahams, Chris Budd, Matt Butchers, Michael E. Cates, Alan R. Champneys, Christine S.M. Currie, Jessica Enright, Julia R. Gog, Alain Goriely, T. Déirdre Hollingsworth, Rebecca B. Hoyle, INI Professional Services, Valerie Isham, Joanna Jordan, Maha H. Kaouri, Kostas Kavoussanakis, Jane Leeks, Philip K. Maini, Christie Marr, Clare Merritt, Denis Mollison, Surajit Ray, Robin N. Thompson, Alexandra Wakefield, Dawn Wasley, J. Theor Bio, Jan 2023
Modelling the epidemiological implications for SARS-CoV-2 of Christmas household bubbles in England
Edward M. Hill, J. Theor. Bio., Jan 2023
Patterns of Reported Infection and Reinfection of SARS-CoV-2 in England
Matt J Keeling, J. Theor. Bio, Jan 2023
Authors’ reply to the discussion of ‘Estimation of reproduction numbers in real time: conceptual and statistical challenges’ by Pellis et al. in Session 3 of the Royal Statistical Society’s Special Topic Meeting on COVID-19 transmission: 11 June 2021. Journal of the Royal Statistical Society: Series A (Statistics in Society), 1–5
Lorenzo Pellis, Paul J. Birrell, Joshua Blake, Ian Hall, Thomas A. House, Christopher E. Overton, Francesca Scarabel, Helena B. Stage, Daniela De Angelis Available from: https://doi.org/10.1111/rssa.12984
Retrospectively modeling the effects of increased global vaccine sharing on the COVID-19 pandemic
Sam Moore, Edward M Hill, Louise J Dyson, Michael J Tildesley, Matt J Keeling, Nature Medicine, Oct 2022
A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic
Joe Hilton, Heather Riley, Lorenzo Pellis, Rabia Aziza, Sam Brand, Ivy K. Kombe, John Ojal, Andrea Parisi, Matt Keeling, D. James Nokes, Robert Manson-Sawko, Thomas House, PLOS Computational Biology, Sept 2022
EpiBeds: Data informed modelling of the COVID-19 hospital burden in England
Christopher E. Overton, Lorenzo Pellis, Helena B. Stage, Francesca Scarabel, Joshua Burton, Christophe Fraser, Ian Hall, Thomas A. House, Chris Jewell, Anel Nurtay, Filippo Pagani, Katrina A. Lythgoe, PLOS Computational Biology, Sept 2022
Inferring Risks of Coronavirus Transmission from Community Household Data
Thomas House, Heather Riley, Lorenzo Pellis, Koen B. Pouwels, Sebastian Bacon, Arturas Eidukas, Kaveh Jahanshahi, Rosalind M. Eggo, A. Sarah Walker, Statistical Methods in Medical Research, Sept 2022
Comparison of the 2021 COVID-19 ‘Roadmap’ Projections against Public Health Data
Matt J. Keeling, Louise Dyson, Michael J. Tildesley, Edward M. Hill, Samuel Moore, Nature Communications Aug 2022
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, R. Soc. Open Science, Aug 2022
Alternative COVID-19 mitigation measures in school classrooms: analysis using an agent-based model of SARS-CoV-2 transmission
M. J. Woodhouse, W. P. Aspinall, R. S. J. Sparks, E. Brooks-Pollock and C. Relton, R. Soc. Open Science, Aug 2022
Incidence of community acquired lower respiratory tract disease in Bristol, UK during the COVID-19 pandemic: A prospective cohort study
Catherine Hyams, Robert Challen, Elizabeth Begier, Jo Southern, Jade King, Anna Morley, Zsuzsa Szasz-Benczur, Maria Garcia Gonzalez, Jane Kinney, James Campling, Sharon Gray, Jennifer Oliver, Robin Hubler, Srinivas Valluri, Andrew Vyse, John M. McLaughlin, Gillian Ellsbury, Nick A. Maskell, Bradford D. Gessner, Leon Danon, Adam Finn On behalf of the Avon CAP Research Group, The Lancet Regional Health - Europe, Oct 2022, https://doi.org/10.1016/j.lanepe.2022.100473
Monkeypox in the UK: arguments for a broader case definition
Daniel Pan, Shirley Sze, Joshua Nazareth, Christopher A Martin, Amani Al-Oraibi, Rebecca F Baggaley, Laura B Nellums, T Déirdre Hollingsworth, Julian W Tang, Manish Pareek, The Lancet, June 2022
An assessment of the vaccination of school-aged children in England against SARS-CoV-2
Matt J. Keeling and Sam E. Moore, BMC Medicine, May 2022
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, Communications Medicine, June 2022
Agility and Sustainability: A Qualitative Evaluation of COVID-19 Non-pharmaceutical Interventions in the UK Logistics Sector
Hua Wei, Sarah Daniels, Carl A Whitfield, Yang Han, David W Denning, Ian Hall, Martyn Regan, Arpana Verma, Martie van Tongeren, Frontiers in Public Health, June 2022
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, PLOS Computational Biology, May 2022
Challenges for modelling interventions for future pandemics
Mirjam E. Kretzschmar, Ben Ashby, Elizabeth Fearon, Christopher E. Overton, Jasmina Panovska-Griffiths, Lorenzo Pellis, Matthew Quaife, Ganna Rozhnova, Francesca Scarabel, Helena B Stage, Ben Swallow, Robin N. Thompson, Michael J. Tildesley, Daniel Villela, Epidemics, March 2022
Effectiveness of the BNT162b2 (Pfizer-BioNTech) and the ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines for reducing susceptibility to infection with the Delta variant (B.1.617.2) of SARS-CoV-2
Karan Pattni, Daniel Hungerford, Sarah Adams, Iain Buchan, Christopher P. Cheyne, Marta García-Fiñana, Ian Hall, David M. Hughes, Christopher E. Overton, Xingna Zhang & Kieran J. Sharkey, BMC Infectious Diseases, March 2022
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, Nature Communications, March 2022
MetaWards: A flexible metapopulation framework for modelling disease spread
Christopher Woods, Lester Hedges, Christopher Edsall, Ellen Brooks-Pollock, Christopher Parton-Fenton, Trevelyan J McKinley, Matt J Keeling, and Leon Danon, The Journal of Open Source Software, Feb 2022
Modeling the factors that influence exposure to SARS-CoV-2 on a subway train carriage
Daniel Miller, Marco‐Felipe King, James Nally, Joseph R Drodge, Gary I Reeves, Andrew M Bate, Henry Cooper, Ursula Dalrymple, Ian Hall, Martín López‐García, Simon T Parker, Catherine J Noakes, Indoor Air, Feb 2022
Estimating the potential for global dissemination of pandemic pathogens using the global airline network and healthcare development indices
Margaux MI Meslé, Roberto Vivancos, Ian M Hall, Robert M Christley, Steve Leach, Jonathan M Read, Scientific Reports, Feb 2022
School Attendance Registers for the Syndromic Surveillance of Infectious Intestinal Disease in UK Children: Protocol for a Retrospective Analysis
Anna L Donaldson, John P Harris, Roberto Vivancos, Daniel Hungerford, Ian Hall, Sarah J O'Brien, JMIR Res Protoc, Jan 2022
Epidemiological modelling in refugee and internally displaced people settlements: challenges and ways forward
Joseph Aylett-Bullock, Robert Tucker Gilman, Ian Hall, David Kennedy, Egmond Samir Evers, Anjali Katta, Hussien Ahmed, Kevin Fong, Keyrellous Adib, Lubna Al Ariqi, Ali Ardalan, Pierre Nabeth, Kai von Harbou, Katherine Hoffmann Pham, Carolina Cuesta-Lazaro, Arnau Quera-Bofarull, Allen Gidraf Kahindo Maina, Tinka Valentijn, Sandra Harlass, Frank Krauss, Chao Huang, Rebeca Moreno Jimenez, Tina Comes, Mariken Gaanderse, Leonardo Milano, Miguel Luengo-Oroz, BMJ Global Health, Jan 2022
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, and Edward M. Hill, Statistical Methods in Medical Research, Jan 2022
Modelling pooling strategies for SARS-CoV-2 testing in a university setting
Gibran Hemani, Amy C Thomas, Josephine G Walker, Adam Trickey, Emily Nixon, David Ellis, Rachel Kwiatkowska, Caroline Relton, Leon Danon, Hannah Christensen, Ellen Brooks-Pollock, Wellcome Open Research, Jan 2022
Low uptake of COVID-19 lateral flow testing among university students: a mixed methods evaluation
C.E.French, S.Denford, E.Brooks-Pollock, H.Wehling, M.Hickman, Public Health, Jan 2022
Challenges in evaluating risks and policy options around endemic establishment or elimination of novel pathogens
C Jessica E Metcalf, Soa Fy Andriamandimby, Rachel E Baker, Emma E Glennon, Katie Hampson, T Deirdre Hollingsworth, Petra Klepac, Amy Wesolowski, Epidemics, Dec 2021
Precautionary breaks: Planned, limited duration circuit breaks to control the prevalence of SARS-CoV2 and the burden of COVID-19 disease
Matt J Keeling, Glen Guyver-Fletcher, Louise Dyson, Michael J Tildesley, Edward M Hill, Graham F Medley, Epidemics, 37, Dec 2021
Meta-analysis of the severe acute respiratory syndrome coronavirus 2 serial intervals and the impact of parameter uncertainty on the coronavirus disease 2019 reproduction number
Robert Challen, Ellen Brooks-Pollock, Krasimira Tsaneva-Atanasova and Leon Danon, Statistical Methods in Medical Research, Dec 2021
Limits of lockdown: characterising essential contacts during strict physical distancing
Amy Thomas, Leon Danon, Hannah Christensen, Kate Northstone, Daniel Smith, Emily Nixon, Adam Trickey, Gibran Hemani, Sarah Sauchelli, Adam Finn, Nicholas Timpson, Ellen Brooks-Pollock, Wellcome Open Research, Nov 2021
Covid-19 and ethnicity: we must seek to understand the drivers of higher transmission
Daniel Pan, Shirley Sze, Christopher A Martin, Joshua Nazareth, Katherine Woolf, Rebecca F Baggaley, T Déirdre Hollingsworth, Kamlesh Khunti, Laura B Nellums, Manish Pareek, BMJ, Nov 2021
Growth, reproduction numbers and factors affecting the spread of SARS-CoV-2 novel variants of concern in the UK from October 2020 to July 2021: a modelling analysis
Thomas Ward, Alex Glaser, Alexander Johnsen, Feng Xu, Ian Hall, Lorenzo Pellis, BMJ Open, Oct 2021
Insights gained from early modelling of COVID-19 to inform the management of outbreaks in UK prisons
Declan Bays, Hannah Williams, Lorenzo Pellis, Jacob Curran-Sebastian, Oscar O’Mara, PHE Joint Modelling Team and Thomas Finnie, INTERNATIONAL JOURNAL OF PRISONER HEALTH, VOL. 17 NO. 3 2021, pp. 380-397, Oct 2021
The SARS-CoV-2 pandemic: remaining uncertainties in our understanding of the epidemiology and transmission dynamics of the virus, and challenges to be overcome
Roy M Anderson, Carolin Vegvari, T Déirdre Hollingsworth, Li Pi, Rosie Maddren, Chi Wai Ng, Rebecca F Baggaley, Interface Focus, Oct 2021
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 and Matt J. Keeling, Nature Communications, 12, Sept 2021
Modelling SARS-CoV-2 transmission in a UK university setting
Edward M.Hill, Benjamin D.Atkins, Matt J.Keeling, Michael J.Tildesley, Louise Dyson, Epidemics, Sept 2021
Contact tracing is an imperfect tool for controlling COVID-19 transmission and relies on population adherence
Emma L. Davis, Tim C. D. Lucas, Anna Borlase, Timothy M. Pollington, Sam Abbott, Diepreye Ayabina, Thomas Crellen, Joel Hellewell, Li Pi, CMMID COVID-19 Working Group, Graham F. Medley, T. Déirdre Hollingsworth & Petra Klepac, Nature Communications, Sept 2021
Commentary on the use of the reproduction number R during the COVID-19 pandemic
Carolin Vegvari, Sam Abbott, Frank Ball, Ellen Brooks-Pollock, Robert Challen , Benjamin S Collyer, Ciara Dangerfield, Julia R Gog, Katelyn M Gostic, Jane M Heffernan, T Déirdre Hollingsworth, Valerie Isham, Eben Kenah, Denis Mollison, Jasmina Panovska-Griffiths, Lorenzo Pellis, Michael G Roberts, Gianpaolo Scalia Tomba, Robin N Thompson, and Pieter Trapman, Statistical Methods in Medical Research, Sept 2021
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
Preprints
Isolation may select for earlier and higher peak viral load but shorter isolation in SARS-CoV-2 evolution
Junya Sanagawa, Kwang Su Kim, Hyeongki Park, Ryo Komorizono, Sooyoun Choi, Lucia Ramirez Torres, Joohyeon Woo, Yong Dam Jeong, William S. Hart, Robin N. Thompson, Kazuyuki Aihara, Shingo Iwami, Ryo Yamaguchi, https://doi.org/10.1101/2023.02.23.529742
Incorporating heterogeneity in farmer disease control behaviour into a livestock disease transmission model
Edward Hill, Naomi Prosser, Paul Brown, Eamonn Ferguson, Martin Green, Jasmeet Kaler, Matt Keeling, Michael Tildesley, https://doi.org/10.21203/rs.3.rs-2547595/v1
The impacts of increased global vaccine sharing on the COVID-19 pandemic; a retrospective modelling study
Sam Moore, Edward M. Hill, Louise J. Dyson, Michael J. Tildesley, Matt J. Keeling
Calculation of epidemic first passage and peak time probability distributions
Jacob Curran-Sebastian, Lorenzo Pellis, Ian Hall, Thomas House, https://doi.org/10.48550/arXiv.2301.07058
Bayesian Estimation of real-time Epidemic Growth Rates using Gaussian Processes: local dynamics of SARS-CoV-2 in England
Laura Marcela Guzman Rincon, Edward M Hill, Louise Dyson, Michael J Tildesley, Matt J Keeling, https://doi.org/10.1101/2022.01.01.21268131
Coughs, Colds and “Freshers’ Flu” Survey in the University of Cambridge, 2007-2008
Ken TD Eames, Maria L Tang, Edward M Hill, Michael M Tildesley, Jonathan M Read, Matt J Keeling, Julia R Gog, https://doi.org/10.1101/2021.03.31.21251220
Short-term Projections based on Early Omicron Variant Dynamics in England
Matt J. Keeling, Ellen Brooks-Pollock, Rob Challen, Leon Danon, Louise Dyson, Julia R. Gog, Laura Guzmán Rincón, Edward M. Hill, Lorenzo Pellis, Jonathan M. Read, Michael J. Tildesley, doi: https://doi.org/10.1101/2021.12.30.21268307
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
Early signals of Omicron severity in sentinel UK hospitals
Christopher E. Overton, Shazaad Ahmad, Benjamin Brown, Andre Charlett, Emma Davies, Thomas House, Ben Kirkman, Nicholas Machin, Robert O’Hara, Rob Paton, Lorenzo Pellis, Tom Ward, Dec 2021, https://doi.org/10.21203/rs.3.rs-1203019/v1
Impacts of vaccination and asymptomatic testing on SARS-CoV-2 transmission dynamics in a university setting
Emily J Nixon, Amy C Thomas, Daniel A Stocks, Antoine M. G. Barreaux, Gibran Hemani, Adam Trickey, Rachel Kwiatkowska, Josephine G Walker, David Ellis, Leon Danon, Caroline Relton, Hannah Christensen, Ellen Brooks Pollock, doi: https://doi.org/10.1101/2021.11.22.21266565
Limited impact of contact tracing in a University setting for COVID-19 due to asymptomatic transmission and social distancing
Daniel Stocks, Emily Nixon, Adam Trickey, Martin Homer, Ellen Brooks-Pollock, https://doi.org/10.1101/2021.11.10.21265739
Waning, Boosting and a Path to Endemicity for SARS-CoV-2
Matt J. Keeling, Amy Thomas, Edward M. Hill, Robin N. Thompson, Louise Dyson, Michael J. Tildesley, Sam Moore, doi: https://doi.org/10.1101/2021.11.05.21265977
Total Effect Analysis of Vaccination on Household Transmission in the Office for National Statistics COVID-19 Infection Survey
Thomas House, Lorenzo Pellis, Emma Pritchard, Angela R. McLean, and A. Sarah Walker, arXiv:2107.06545
Early epidemiological signatures of novel SARS-CoV-2 variants: establishment of B.1.617.2 in England
Robert Challen, Louise Dyson, Christopher E. Overton, Laura M. Guzman-Rincon, Edward M. Hill, Helena B. Stage,Ellen Brooks-Pollock, Lorenzo Pellis, Francesca Scarabel, David J. Pascall, View ORCID ProfilePaula Blomquist, Michael Tildesley, Daniel Williamson, Stefan Siegert, Xiaoyu Xiong, Ben Youngman, Juniper, Jonathan M. Read, Julia R. Gog, View Matthew J. Keeling, Leon Danon, https://doi.org/10.1101/2021.06.05.21258365
Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK
William Waites, Carl AB Pearson, Katherine M Gaskell, Thomas House, Lorenzo Pellis, Marina Johnson, Victoria Gould, Adam Hunt, Neil RH Stone, Ben Kasstan, Tracey Chantler, Sham Lal, Chrissy h. Roberts, David Goldblatt, CMMID COVID-19 Working Group, Michael Marks, Rosalind M Eggo, https://doi.org/10.1101/2021.10.28.21265615
Modelling infectious disease transmission potential as a function of human behaviour
Caroline E Walters, Maria Bekker-Nielsen Dunbar, Dale Weston, Ian M Hall, https://doi.org/10.1101/2021.07.16.21260521
Statistical Design and Analysis of Diagnostic Tests for Mutating Viruses
Yang Han, Yujia Sun, Jason C Hsu, Thomas House, Nick Gent, Ian Hall, https://doi.org/10.1101/2021.04.07.21254917
A within-host model of SARS-CoV-2 infection
Jonathan Carruthers, Jingsi Xu, Thomas James Ronald Finnie, Ian Hall, https://doi.org/10.1101/2022.04.22.22274137
Modelling the impact of non-pharmaceutical interventions on workplace transmission of SARS-CoV-2 in the home-delivery sector
Carl A Whitfield, Martie Van Tongeren, Yang Han, Hua Wei, Sarah A Daniels, Martyn Regan, David W Denning, Arpana Verma, Lorenzo Pellis, Ian Hall, https://doi.org/10.1101/2022.03.17.22272414
Novel methods for estimating the instantaneous and overall COVID-19 case fatality risk among care home residents in England
Christopher E Overton, Luke Webb, Uma Datta, Mike Fursman, Jo Hardstaff, Iina Hiironen, Karthik Paranthaman, Heather Riley, James Sedgwick, Julia Verne, Steve Willner, Lorenzo Pellis, Ian Hall, arXiv:2202.07325
The role of vaccination and public awareness in medium-term forecasts of monkeypox incidence in the United Kingdom
SPC Brand, M Cavallaro, J Hilton, LM Guzman-Rincon, T House, MJ Keeling, DJ Nokes https://doi.org/10.1101/2022.08.15.22278788
Modelling the impact of repeat asymptomatic testing policies for staff on SARS-CoV-2 transmission potential
Carl A. Whitfield, Ian Hall arXiv:2210.08888
