1
|
Dangerfield CE, David Abrahams I, Budd C, Butchers M, Cates ME, Champneys AR, Currie CS, Enright J, Gog JR, Goriely A, Déirdre Hollingsworth T, Hoyle RB, INI Professional Services, Isham V, Jordan J, Kaouri MH, Kavoussanakis K, Leeks J, Maini PK, Marr C, Merritt C, Mollison D, Ray S, Thompson RN, Wakefield A, Wasley D. 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. J Theor Biol 2023; 557:111332. [PMID: 36323393 PMCID: PMC9618296 DOI: 10.1016/j.jtbi.2022.111332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022]
Abstract
In March 2020 mathematics became a key part of the scientific advice to the UK government on the pandemic response to COVID-19. Mathematical and statistical modelling provided critical information on the spread of the virus and the potential impact of different interventions. The unprecedented scale of the challenge led the epidemiological modelling community in the UK to be pushed to its limits. At the same time, mathematical modellers across the country were keen to use their knowledge and skills to support the COVID-19 modelling effort. However, this sudden great interest in epidemiological modelling needed to be coordinated to provide much-needed support, and to limit the burden on epidemiological modellers already very stretched for time. In this paper we describe three initiatives set up in the UK in spring 2020 to coordinate the mathematical sciences research community in supporting mathematical modelling of COVID-19. Each initiative had different primary aims and worked to maximise synergies between the various projects. We reflect on the lessons learnt, highlighting the key roles of pre-existing research collaborations and focal centres of coordination in contributing to the success of these initiatives. We conclude with recommendations about important ways in which the scientific research community could be better prepared for future pandemics. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".
Collapse
Affiliation(s)
- Ciara E. Dangerfield
- Isaac Newton Institute to Mathematical Sciences, University of Cambridge, United Kingdom,Joint UNIversities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom1,Corresponding author
| | - I. David Abrahams
- Department for Applied Mathematics and Theoretical Physics, University of Cambridge, United Kingdom
| | - Chris Budd
- Department of Mathematics, University of Bath, United Kingdom
| | - Matt Butchers
- Department of Mathematics, University of Bath, United Kingdom
| | - Michael E. Cates
- Department for Applied Mathematics and Theoretical Physics, University of Cambridge, United Kingdom
| | - Alan R. Champneys
- Department of Engineering Mathematics, University of Bristol, United Kingdom
| | | | - Jessica Enright
- School of Computing Science, University of Glasgow, United Kingdom
| | - Julia R. Gog
- Joint UNIversities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom1,Department for Applied Mathematics and Theoretical Physics, University of Cambridge, United Kingdom
| | - Alain Goriely
- Mathematical Institute, University of Oxford, United Kingdom
| | - T. Déirdre Hollingsworth
- Joint UNIversities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom1,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, United Kingdom
| | - Rebecca B. Hoyle
- School of Mathematical Sciences, University of Southampton, United Kingdom
| | | | - Valerie Isham
- Department of Statistical Science, University College London, United Kingdom
| | | | - Maha H. Kaouri
- Isaac Newton Institute to Mathematical Sciences, University of Cambridge, United Kingdom
| | | | - Jane Leeks
- Isaac Newton Institute to Mathematical Sciences, University of Cambridge, United Kingdom
| | - Philip K. Maini
- Mathematical Institute, University of Oxford, United Kingdom
| | - Christie Marr
- Isaac Newton Institute to Mathematical Sciences, University of Cambridge, United Kingdom
| | - Clare Merritt
- Isaac Newton Institute to Mathematical Sciences, University of Cambridge, United Kingdom
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, United Kingdom
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, United Kingdom
| | - Robin N. Thompson
- Mathematics Institute, University of Warwick, United Kingdom,Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, United Kingdom
| | | | - Dawn Wasley
- International Centre for Mathematical Sciences, University of Edinburgh & Heriot-Watt University, United Kingdom
| |
Collapse
|
2
|
Vegvari C, Abbott S, Ball F, Brooks-Pollock E, Challen R, Collyer BS, Dangerfield C, Gog JR, Gostic KM, Heffernan JM, Hollingsworth TD, Isham V, Kenah E, Mollison D, Panovska-Griffiths J, Pellis L, Roberts MG, Scalia Tomba G, Thompson RN, Trapman P. Commentary on the use of the reproduction number R during the COVID-19 pandemic. Stat Methods Med Res 2022; 31:1675-1685. [PMID: 34569883 PMCID: PMC9277711 DOI: 10.1177/09622802211037079] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Since the beginning of the COVID-19 pandemic, the reproduction number [Formula: see text] has become a popular epidemiological metric used to communicate the state of the epidemic. At its most basic, [Formula: see text] is defined as the average number of secondary infections caused by one primary infected individual. [Formula: see text] seems convenient, because the epidemic is expanding if [Formula: see text] and contracting if [Formula: see text]. The magnitude of [Formula: see text] indicates by how much transmission needs to be reduced to control the epidemic. Using [Formula: see text] in a naïve way can cause new problems. The reasons for this are threefold: (1) There is not just one definition of [Formula: see text] but many, and the precise definition of [Formula: see text] affects both its estimated value and how it should be interpreted. (2) Even with a particular clearly defined [Formula: see text], there may be different statistical methods used to estimate its value, and the choice of method will affect the estimate. (3) The availability and type of data used to estimate [Formula: see text] vary, and it is not always clear what data should be included in the estimation. In this review, we discuss when [Formula: see text] is useful, when it may be of use but needs to be interpreted with care, and when it may be an inappropriate indicator of the progress of the epidemic. We also argue that careful definition of [Formula: see text], and the data and methods used to estimate it, can make [Formula: see text] a more useful metric for future management of the epidemic.
Collapse
Affiliation(s)
- Carolin Vegvari
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, 4615Imperial College London, London, UK
| | - Sam Abbott
- Center for the Mathematical Modelling of Infectious Diseases, 4906London School of Hygiene & Tropical Medicine, UK
| | - Frank Ball
- School of Mathematical Sciences, 6123University of Nottingham, UK
| | - Ellen Brooks-Pollock
- Bristol Veterinary School, 1980University of Bristol, UK.,NIHR Health Protection Research Unit in Behavioural Science and Evaluation at the University of Bristol, UK
| | - Robert Challen
- EPSRC Centre for Predictive Modelling in Healthcare, 3286University of Exeter, UK.,Somerset NHS Foundation Trust, UK
| | - Benjamin S Collyer
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, 4615Imperial College London, London, UK
| | | | - Julia R Gog
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK
| | - Katelyn M Gostic
- Department of Ecology and Evolution, 2462University of Chicago, USA
| | - Jane M Heffernan
- Centre for Disease Modelling, Mathematics & Statistics, 7991York University, Canada.,COVID Modelling Task-Force, The Fields Institute, Canada
| | - T Déirdre Hollingsworth
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, 6396University of Oxford, UK
| | - Valerie Isham
- Department of Statistical Science, 4919University College London, UK
| | - Eben Kenah
- Division of Biostatistics, College of Public Health, 2647The Ohio State University, USA
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, UK
| | - Jasmina Panovska-Griffiths
- The Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Wolfson Centre for Mathematical Biology, Mathematical Institute and The Queen's College, University of Oxford, Oxford, UK
| | - Lorenzo Pellis
- Department of Mathematics, 5292The University of Manchester, UK.,The Alan Turing Institute, UK
| | - Michael G Roberts
- School of Natural and Computational Sciences and New Zealand Institute for Advanced Study, Massey University, New Zealand
| | | | - Robin N Thompson
- Mathematics Institute, 2707University of Warwick, Coventry, UK.,Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, 2707University of Warwick, Coventry, UK
| | - Pieter Trapman
- Department of Mathematics, 7675Stockholm University, Sweden
| |
Collapse
|
3
|
Mollison D, Isham V, Dangerfield C, Hollingsworth D. Preface: Challenges for future pandemics. Epidemics 2022; 40:100621. [PMID: 36030185 DOI: 10.1016/j.epidem.2022.100621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Scotland.
| | - Valerie Isham
- Department of Statistical Science, University College London, UK.
| | - Ciara Dangerfield
- Isaac Newton Institute for Mathematical Sciences, University of Cambridge, UK.
| | - Deirdre Hollingsworth
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK.
| |
Collapse
|
4
|
Marion G, Hadley L, Isham V, Mollison D, Panovska-Griffiths J, Pellis L, Tomba GS, Scarabel F, Swallow B, Trapman P, Villela D. Modelling: Understanding pandemics and how to control them. Epidemics 2022; 39:100588. [PMID: 35679714 DOI: 10.1016/j.epidem.2022.100588] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/22/2022] [Accepted: 05/26/2022] [Indexed: 12/11/2022] Open
Abstract
New disease challenges, societal demands and better or novel types of data, drive innovations in the structure, formulation and analysis of epidemic models. Innovations in modelling can lead to new insights into epidemic processes and better use of available data, yielding improved disease control and stimulating collection of better data and new data types. Here we identify key challenges for the structure, formulation, analysis and use of mathematical models of pathogen transmission relevant to current and future pandemics.
Collapse
Affiliation(s)
- Glenn Marion
- Biomathematics and Statistics Scotland, Edinburgh, UK; Scottish COVID-19 Response Consortium, UK.
| | - Liza Hadley
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, UK
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, UK
| | - Jasmina Panovska-Griffiths
- The Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; The Queen's College, Oxford University, UK
| | - Lorenzo Pellis
- Department of Mathematics, University of Manchester, UK; The Alan Turing Institute, London, UK; Joint UNIversities Pandemic and Epidemiological Research, UK
| | | | - Francesca Scarabel
- Department of Mathematics, University of Manchester, UK; Joint UNIversities Pandemic and Epidemiological Research, UK; CDLab - Computational Dynamics Laboratory, Department of Mathematics, Computer Science and Physics, University of Udine, Italy
| | - Ben Swallow
- Scottish COVID-19 Response Consortium, UK; School of Mathematics and Statistics, University of Glasgow, UK
| | - Pieter Trapman
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | - Daniel Villela
- Program of Scientific Computing, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| |
Collapse
|
5
|
Hadley L, Challenor P, Dent C, Isham V, Mollison D, Robertson DA, Swallow B, Webb CR. Challenges on the interaction of models and policy for pandemic control. Epidemics 2021; 37:100499. [PMID: 34534749 PMCID: PMC8404384 DOI: 10.1016/j.epidem.2021.100499] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/30/2021] [Accepted: 08/28/2021] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic has seen infectious disease modelling at the forefront of government decision-making. Models have been widely used throughout the pandemic to estimate pathogen spread and explore the potential impact of different intervention strategies. Infectious disease modellers and policymakers have worked effectively together, but there are many avenues for progress on this interface. In this paper, we identify and discuss seven broad challenges on the interaction of models and policy for pandemic control. We then conclude with suggestions and recommendations for the future.
Collapse
Affiliation(s)
- Liza Hadley
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, United Kingdom.
| | - Peter Challenor
- Department of Mathematics, University of Exeter, United Kingdom
| | - Chris Dent
- School of Mathematics, University of Edinburgh, United Kingdom; Alan Turing Institute, United Kingdom
| | - Valerie Isham
- Department of Statistical Science, University College London, United Kingdom
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, United Kingdom
| | - Duncan A Robertson
- School of Business and Economics, Loughborough University, United Kingdom; St Catherine's College, University of Oxford, United Kingdom
| | - Ben Swallow
- School of Mathematics and Statistics, University of Glasgow, United Kingdom
| | - Cerian R Webb
- Department of Plant Sciences, University of Cambridge, United Kingdom
| |
Collapse
|
6
|
Isham V. Contribution to the discussion of AIDS and Covid-19: A tale of two pandemics and the role of statisticians by Ellenberg and Morris. Stat Med 2021; 40:2518-2520. [PMID: 33963577 DOI: 10.1002/sim.8938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/13/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Valerie Isham
- Department of Statistical Science, University College London, London, UK
| |
Collapse
|
7
|
Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Glendinning P, Gog JR, Hart WS, Heesterbeek H, House T, Keeling M, Kiss IZ, Kretzschmar ME, Lloyd AL, McBryde ES, McCaw JM, McKinley TJ, Miller JC, Morris M, O'Neill PD, Parag KV, Pearson CAB, Pellis L, Pulliam JRC, Ross JV, Tomba GS, Silverman BW, Struchiner CJ, Tildesley MJ, Trapman P, Webb CR, Mollison D, Restif O. Key questions for modelling COVID-19 exit strategies. Proc Biol Sci 2020; 287:20201405. [PMID: 32781946 PMCID: PMC7575516 DOI: 10.1098/rspb.2020.1405] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.
Collapse
Affiliation(s)
- Robin N. Thompson
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
- Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | | | - Valerie Isham
- Department of Statistical Science, University College London, Gower Street, London WC1E 6BT, UK
| | - Daniel Arribas-Bel
- School of Environmental Sciences, University of Liverpool, Brownlow Street, Liverpool L3 5DA, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, North Road, Bath BA2 7AY, UK
| | - Tom Britton
- Department of Mathematics, Stockholm University, Kräftriket, 106 91 Stockholm, Sweden
| | - Peter Challenor
- College of Engineering, Mathematical and Physical Sciences, University of Exeter, Exeter EX4 4QE, UK
| | - Lauren H. K. Chappell
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Hannah Clapham
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore117549, Singapore
| | - Nik J. Cunniffe
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - A. Philip Dawid
- Statistical Laboratory, University of Cambridge, Wilberforce Road, Cambridge CB3 0WB, UK
| | - Christl A. Donnelly
- Department of Statistics, University of Oxford, St Giles', Oxford OX1 3LB, UK
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial CollegeLondon, Norfolk Place, London W2 1PG, UK
| | - Rosalind M. Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Sebastian Funk
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Nigel Gilbert
- Department of Sociology, University of Surrey, Stag Hill, Guildford GU2 7XH, UK
| | - Paul Glendinning
- Department of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Julia R. Gog
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - William S. Hart
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
| | - Hans Heesterbeek
- Department of Population Health Sciences, Utrecht University, Yalelaan, 3584 CL Utrecht, The Netherlands
| | - Thomas House
- IBM Research, The Hartree Centre, Daresbury, Warrington WA4 4AD, UK
- Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Matt Keeling
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - István Z. Kiss
- School of Mathematical and Physical Sciences, University of Sussex, Falmer, Brighton BN1 9QH, UK
| | - Mirjam E. Kretzschmar
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
| | - Alun L. Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
| | - Emma S. McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia
| | - James M. McCaw
- School of Mathematics and Statistics, University of Melbourne, Carlton, Victoria 3010, Australia
| | - Trevelyan J. McKinley
- College of Medicine and Health, University of Exeter, Barrack Road, Exeter EX2 5DW, UK
| | - Joel C. Miller
- Department of Mathematics and Statistics, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Martina Morris
- Department of Sociology, University of Washington, Savery Hall, Seattle, WA 98195, USA
| | - Philip D. O'Neill
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial CollegeLondon, Norfolk Place, London W2 1PG, UK
| | - Carl A. B. Pearson
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Jonkershoek Road, Stellenbosch 7600, South Africa
| | - Lorenzo Pellis
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Juliet R. C. Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Jonkershoek Road, Stellenbosch 7600, South Africa
| | - Joshua V. Ross
- School of Mathematical Sciences, University of Adelaide, South Australia 5005, Australia
| | | | - Bernard W. Silverman
- Department of Statistics, University of Oxford, St Giles', Oxford OX1 3LB, UK
- Rights Lab, University of Nottingham, Highfield House, Nottingham NG7 2RD, UK
| | - Claudio J. Struchiner
- Escola de Matemática Aplicada, Fundação Getúlio Vargas, Praia de Botafogo, 190 Rio de Janeiro, Brazil
| | - Michael J. Tildesley
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Pieter Trapman
- Department of Mathematics, Stockholm University, Kräftriket, 106 91 Stockholm, Sweden
| | - Cerian R. Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| |
Collapse
|
8
|
Abstract
Abstract
Interrupted time series are increasingly being used to evaluate the population-wide implementation of public health interventions. However, the resulting estimates of intervention impact can be severely biased if underlying disease trends are not adequately accounted for. Control series offer a potential solution to this problem, but there is little guidance on how to use them to produce trend-adjusted estimates. To address this lack of guidance, we show how interrupted time series can be analysed when the control and intervention series share confounders, i. e. when they share a common trend. We show that the intervention effect can be estimated by subtracting the control series from the intervention series and analysing the difference using linear regression or, if a log-linear model is assumed, by including the control series as an offset in a Poisson regression with robust standard errors. The methods are illustrated with two examples.
Collapse
Affiliation(s)
- Christian Bottomley
- MRC Tropical Epidemiology Group, London School of Hygiene & Tropical Medicine , London , UK
- Department of Infectious Disease Epidemiology , London School of Hygiene & Tropical Medicine , London , UK
| | - J. Anthony G. Scott
- Department of Infectious Disease Epidemiology , London School of Hygiene & Tropical Medicine , London , UK
- KEMRI-Wellcome Trust Research Programme , Kilifi , Kenya
| | - Valerie Isham
- Department of Statistical Science , University College London , London , UK
| |
Collapse
|
9
|
Buckingham-Jeffery E, Isham V, House T. Gaussian process approximations for fast inference from infectious disease data. Math Biosci 2018; 301:111-120. [PMID: 29471011 DOI: 10.1016/j.mbs.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 02/13/2018] [Accepted: 02/17/2018] [Indexed: 10/18/2022]
Abstract
We present a flexible framework for deriving and quantifying the accuracy of Gaussian process approximations to non-linear stochastic individual-based models of epidemics. We develop this for the SIR and SEIR models, and we show how it can be used to perform quick maximum likelihood inference for the underlying parameters given population estimates of the number of infecteds or cases at given time points. We also show how the unobserved processes can be inferred at the same time as the underlying parameters.
Collapse
Affiliation(s)
- Elizabeth Buckingham-Jeffery
- Centre for Complexity Science, University of Warwick, Coventry, CV4 7AL, UK; School of Mathematics, University of Manchester, Manchester M13 9PL, UK.
| | - Valerie Isham
- Department of Statistical Science, University College London, London, WC1E 6BT, UK
| | - Thomas House
- School of Mathematics, University of Manchester, Manchester M13 9PL, UK
| |
Collapse
|
10
|
Bottomley C, Isham V, Vivas-Martínez S, Kuesel AC, Attah SK, Opoku NO, Lustigman S, Walker M, Basáñez MG. Response to the Letter to the Editor by Eberhard et al. Parasit Vectors 2017; 10:240. [PMID: 28511662 PMCID: PMC5434579 DOI: 10.1186/s13071-017-2125-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 12/02/2022] Open
Abstract
In a Letter to the Editor, Eberhard et al. question the validity of our model of skin snip sensitivity and argue against the use of skin snips to evaluate onchocerciasis elimination by mass drug administration. Here we discuss their arguments and compare model predictions with observed data to assess the validity of our model.
Collapse
Affiliation(s)
- Christian Bottomley
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Valerie Isham
- Department of Statistical Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sarai Vivas-Martínez
- Cátedra de Salud Pública. Facultad de Medicina (Escuela Luis Razetti), Universidad Central de Venezuela, Caracas, Venezuela
| | - Annette C Kuesel
- UNICEF/UNDP/World Bank/WHO, Special Programme for Research and Training in Tropical Diseases, World Health Organization, Geneva, Switzerland
| | - Simon K Attah
- Department of Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Nicholas O Opoku
- University of Health and Allied Sciences Research Centre (UHASRC) Hohoe, Volta Region, Ghana
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th St, New York, NY10065, USA
| | - Martin Walker
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Norfolk Place, London, W2 1PG, UK.,Department of Pathobiology and Population Sciences and London Centre for Neglected Tropical Disease Research, Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Maria-Gloria Basáñez
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Norfolk Place, London, W2 1PG, UK
| |
Collapse
|
11
|
Abstract
A birth process is studied in which the birth rate at any time is a function of the difference between the current population size and a target corresponding to unit growth rate. If this controlling function is a decreasing function of its argument a stabilizing effect is to be expected. By supposing that the controlling function varies very slowly, series expansions for the properties of the process are obtained, the leading term corresponding to a diffusion approximation. The sequence of births considered as a point process of controlled variability is examined and approximations to the interval distribution and covariance density obtained.
Collapse
|
12
|
Abstract
A class of point processes is considered, in which the locations of the points are independent random variables. In particular some properties of the process in which the distribution function of the position of the nth event is the n-fold convolution of some distribution function F, are investigated. It is shown that, under fairly general conditions, the process remote from the origin will be asymptotically Poisson. It is also shown that the variance of the number of events in the interval (0, t] is . Some generalisations are discussed.
Collapse
|
13
|
Abstract
A sequence of finite point processes {Pn} is constructed in using a Markov sequence of points. Essentially, in the process Pn consisting of n events, the coordinates of these events are simply the first n points of a Markov sequence suitably scaled so that the average density of the process is independent of n. The second-order properties of Pn are discussed and sufficient conditions are found for Pn to converge in distribution to a Poisson process as n →∞. A simple example involving the cardioid distribution is described.
Collapse
|
14
|
Abstract
A point process, N, on the real line, is thinned using a k -dependent Markov sequence of binary variables, and is rescaled. Second-order properties of the thinned process are described when k = 1. For general k, convergence to a compound Poisson process is demonstrated.
Collapse
|
15
|
Abstract
The virtual waiting-time process of Takács is one of the simplest examples of a stochastic process with a continuous state space in continuous time in which jump transitions interrupt periods of deterministic decay. Properties of the process are reviewed, and the transient behaviour examined in detail. Several generalizations of the process are studied. These include two-sided jumps, periodically varying ‘arrival’ rate and the presence of a state-dependent decay rate; the last case is motivated by the properties of soil moisture in hydrology. Throughout, the emphasis is on the derivation of simple interpretable results.
Collapse
|
16
|
Bottomley C, Isham V, Vivas-Martínez S, Kuesel AC, Attah SK, Opoku NO, Lustigman S, Walker M, Basáñez MG. Modelling Neglected Tropical Diseases diagnostics: the sensitivity of skin snips for Onchocerca volvulus in near elimination and surveillance settings. Parasit Vectors 2016; 9:343. [PMID: 27301567 PMCID: PMC4908809 DOI: 10.1186/s13071-016-1605-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The African Programme for Onchocerciasis Control has proposed provisional thresholds for the prevalence of microfilariae in humans and of L3 larvae in blackflies, below which mass drug administration (MDA) with ivermectin can be stopped and surveillance started. Skin snips are currently the gold standard test for detecting patent Onchocerca volvulus infection, and the World Health Organization recommends their use to monitor progress of treatment programmes (but not to verify elimination). However, if they are used (in transition and in parallel to Ov-16 serology), sampling protocols should be designed to demonstrate that programmatic goals have been reached. The sensitivity of skin snips is key to the design of such protocols. METHODS We develop a mathematical model for the number of microfilariae in a skin snip and parameterise it using data from Guatemala, Venezuela, Ghana and Cameroon collected before the start of ivermectin treatment programmes. We use the model to estimate sensitivity as a function of time since last treatment, number of snips taken, microfilarial aggregation and female worm fertility after exposure to 10 annual rounds of ivermectin treatment. RESULTS The sensitivity of the skin snip method increases with time after treatment, with most of the increase occurring between 0 and 5 years. One year after the last treatment, the sensitivity of two skin snips taken from an individual infected with a single fertile female worm is 31 % if there is no permanent effect of multiple ivermectin treatments on fertility; 18 % if there is a 7 % reduction per treatment, and 0.6 % if there is a 35 % reduction. At 5 years, the corresponding sensitivities are 76 %, 62 % and 4.7 %. The sensitivity improves significantly if 4 skin snips are taken: in the absence of a permanent effect of ivermectin, the sensitivity of 4 skin snips is 53 % 1 year and 94 % 5 years after the last treatment. CONCLUSIONS Our model supports the timelines proposed by APOC for post-MDA follow-up and surveillance surveys every 3-5 years. Two skin snips from the iliac region have reasonable sensitivity to detect residual infection, but the sensitivity can be significantly improved by taking 4 snips. The costs and benefits of using four versus two snips should be evaluated.
Collapse
Affiliation(s)
- Christian Bottomley
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Valerie Isham
- Department of Statistical Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sarai Vivas-Martínez
- Cátedra de Salud Pública. Facultad de Medicina (Escuela Luis Razetti), Universidad Central de Venezuela, Caracas, Venezuela
| | - Annette C Kuesel
- UNICEF/UNDP/World Bank/WHO, Special Programme for Research and Training in Tropical Diseases, World Health Organization, Geneva, Switzerland
| | - Simon K Attah
- Department of Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Nicholas O Opoku
- University of Health and Allied Sciences Research Centre (UHASRC) Hohoe, Volta Region, Ghana
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th St, New York, NY, 10065, USA
| | - Martin Walker
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Norfolk Place, London, W2 1PG, UK
| | - Maria-Gloria Basáñez
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Norfolk Place, London, W2 1PG, UK
| |
Collapse
|
17
|
Heesterbeek H, Anderson RM, Andreasen V, Bansal S, De Angelis D, Dye C, Eames KTD, Edmunds WJ, Frost SDW, Funk S, Hollingsworth TD, House T, Isham V, Klepac P, Lessler J, Lloyd-Smith JO, Metcalf CJE, Mollison D, Pellis L, Pulliam JRC, Roberts MG, Viboud C. Modeling infectious disease dynamics in the complex landscape of global health. Science 2015; 347:aaa4339. [PMID: 25766240 PMCID: PMC4445966 DOI: 10.1126/science.aaa4339] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational, and spatial scales, which span hours to months, cells to ecosystems, and local to global spread. Moreover, some pathogens are directly transmitted between individuals of a single species, whereas others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity and changeable human behavior, elevate prevention and control from matters of national policy to international challenge. In the face of this complexity, mathematical models offer valuable tools for synthesizing information to understand epidemiological patterns, and for developing quantitative evidence for decision-making in global health.
Collapse
Affiliation(s)
- Hans Heesterbeek
- Faculty of Veterinary Medicine, University of Utrecht, Utrecht, Netherlands.
| | | | | | | | | | | | - Ken T D Eames
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene Tropical Medicine, London, UK
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene Tropical Medicine, London, UK
| | | | | | - T Deirdre Hollingsworth
- School of Life Sciences, University of Warwick, UK. School of Tropical Medicine, University of Liverpool, UK
| | - Thomas House
- Warwick Mathematics Institute, University of Warwick, Coventry, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, London, UK
| | | | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - C Jessica E Metcalf
- Department of Zoology, University of Oxford, Oxford, UK, and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Lorenzo Pellis
- Warwick Mathematics Institute, University of Warwick, Coventry, UK
| | - Juliet R C Pulliam
- Department of Biology-Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. Division of International Epidemiology and Population Studies, Fogarty International Center, NIH, Bethesda, MD, USA
| | - Mick G Roberts
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, NIH, Bethesda, MD, USA
| |
Collapse
|
18
|
Abstract
Infectious disease incidence data are increasingly available at the level of the individual and include high-resolution spatial components. Therefore, we are now better able to challenge models that explicitly represent space. Here, we consider five topics within spatial disease dynamics: the construction of network models; characterising threshold behaviour; modelling long-distance interactions; the appropriate scale for interventions; and the representation of population heterogeneity.
Collapse
Affiliation(s)
- Steven Riley
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK.
| | - Ken Eames
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, London, UK
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK
| | - Pieter Trapman
- Department of Mathematics, Stockholm University, Stockholm 106 91, Sweden
| |
Collapse
|
19
|
Hollingsworth TD, Pulliam JRC, Funk S, Truscott JE, Isham V, Lloyd AL. Seven challenges for modelling indirect transmission: vector-borne diseases, macroparasites and neglected tropical diseases. Epidemics 2014; 10:16-20. [PMID: 25843376 PMCID: PMC4383804 DOI: 10.1016/j.epidem.2014.08.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/22/2014] [Accepted: 08/23/2014] [Indexed: 12/04/2022] Open
Abstract
Many of the challenges which face modellers of directly transmitted pathogens also arise when modelling the epidemiology of pathogens with indirect transmission – whether through environmental stages, vectors, intermediate hosts or multiple hosts. In particular, understanding the roles of different hosts, how to measure contact and infection patterns, heterogeneities in contact rates, and the dynamics close to elimination are all relevant challenges, regardless of the mode of transmission. However, there remain a number of challenges that are specific and unique to modelling vector-borne diseases and macroparasites. Moreover, many of the neglected tropical diseases which are currently targeted for control and elimination are vector-borne, macroparasitic, or both, and so this article includes challenges which will assist in accelerating the control of these high-burden diseases. Here, we discuss the challenges of indirect measures of infection in humans, whether through vectors or transmission life stages and in estimating the contribution of different host groups to transmission. We also discuss the issues of “evolution-proof” interventions against vector-borne disease.
Collapse
Affiliation(s)
- T Déirdre Hollingsworth
- Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
| | - Juliet R C Pulliam
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - James E Truscott
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, W2 1PG London, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, WC1E 6BT, UK
| | - Alun L Lloyd
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; Department of Mathematics and Biomathematics Graduate Program, North Carolina State University, NC 27695, USA
| |
Collapse
|
20
|
Ball F, Britton T, House T, Isham V, Mollison D, Pellis L, Scalia Tomba G. Seven challenges for metapopulation models of epidemics, including households models. Epidemics 2014; 10:63-7. [PMID: 25843386 DOI: 10.1016/j.epidem.2014.08.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 08/05/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022] Open
Abstract
This paper considers metapopulation models in the general sense, i.e. where the population is partitioned into sub-populations (groups, patches,...), irrespective of the biological interpretation they have, e.g. spatially segregated large sub-populations, small households or hosts themselves modelled as populations of pathogens. This framework has traditionally provided an attractive approach to incorporating more realistic contact structure into epidemic models, since it often preserves analytic tractability (in stochastic as well as deterministic models) but also captures the most salient structural inhomogeneity in contact patterns in many applied contexts. Despite the progress that has been made in both the theory and application of such metapopulation models, we present here several major challenges that remain for future work, focusing on models that, in contrast to agent-based ones, are amenable to mathematical analysis. The challenges range from clarifying the usefulness of systems of weakly-coupled large sub-populations in modelling the spread of specific diseases to developing a theory for endemic models with household structure. They include also developing inferential methods for data on the emerging phase of epidemics, extending metapopulation models to more complex forms of human social structure, developing metapopulation models to reflect spatial population structure, developing computationally efficient methods for calculating key epidemiological model quantities, and integrating within- and between-host dynamics in models.
Collapse
Affiliation(s)
- Frank Ball
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Tom Britton
- Department of Mathematics, Stockholm University, Stockholm 106 91, Sweden
| | - Thomas House
- Warwick Infectious Disease Epidemiology Research Centre (WIDER) and Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, London WC1E 6BT, UK
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK
| | - Lorenzo Pellis
- Warwick Infectious Disease Epidemiology Research Centre (WIDER) and Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
| | | |
Collapse
|
21
|
Pellis L, Ball F, Bansal S, Eames K, House T, Isham V, Trapman P. Eight challenges for network epidemic models. Epidemics 2014; 10:58-62. [PMID: 25843385 DOI: 10.1016/j.epidem.2014.07.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 11/29/2022] Open
Abstract
Networks offer a fertile framework for studying the spread of infection in human and animal populations. However, owing to the inherent high-dimensionality of networks themselves, modelling transmission through networks is mathematically and computationally challenging. Even the simplest network epidemic models present unanswered questions. Attempts to improve the practical usefulness of network models by including realistic features of contact networks and of host-pathogen biology (e.g. waning immunity) have made some progress, but robust analytical results remain scarce. A more general theory is needed to understand the impact of network structure on the dynamics and control of infection. Here we identify a set of challenges that provide scope for active research in the field of network epidemic models.
Collapse
Affiliation(s)
- Lorenzo Pellis
- Warwick Infectious Disease Epidemiology Research Centre (WIDER) and Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK.
| | - Frank Ball
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, DC 20057, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Ken Eames
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Thomas House
- Warwick Infectious Disease Epidemiology Research Centre (WIDER) and Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, London WC1E 6BT, UK
| | - Pieter Trapman
- Department of Mathematics, Stockholm University, Stockholm 106 91, Sweden
| |
Collapse
|
22
|
Abstract
A number of childhood vaccination programmes have recently introduced vaccination against Streptococcus pneumoniae, the pneumococcus, a major cause of pneumonia and meningitis. The pneumococcal conjugate vaccines (PCVs) that are currently in use only protect against some serotypes of the bacterium, and there is now strong evidence that those serotypes not included in the vaccine increase in prevalence among most vaccinated populations. We present a mathematical model for the dynamics of nasopharyngeal carriage of S. pneumoniae that allows for carriage with multiple serotypes. The model is used to predict the prevalence of vaccine type (VT) and non-VT (NVT) serotypes following the introduction of PCV. Parameter estimates for the model are obtained by maximum likelihood using pre-vaccination data from The Gambia. The model predicts that low (1, 6A and 9V) and medium (4, 5, 7F, 14, 18C, 19A and 19F) prevalence serotypes can be eliminated through vaccination, but that the overall prevalence of carriage will be reduced only slightly because of an increase in the prevalence of NVT serotypes. Serotype replacement will be sequential, with high and medium prevalence NVT serotypes dominating initially, followed by an increase of serotypes of low prevalence. We examine the impact of a hypothetical vaccine that provides partial protection against all serotypes, and find that this reduces overall carriage, but is unable to eliminate low or medium prevalence serotypes.
Collapse
|
23
|
Isham V, Kaczmarska J, Nekovee M. Spread of information and infection on finite random networks. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 83:046128. [PMID: 21599261 DOI: 10.1103/physreve.83.046128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Indexed: 05/30/2023]
Abstract
The modeling of epidemic-like processes on random networks has received considerable attention in recent years. While these processes are inherently stochastic, most previous work has been focused on deterministic models that ignore important fluctuations that may persist even in the infinite network size limit. In a previous paper, for a class of epidemic and rumor processes, we derived approximate models for the full probability distribution of the final size of the epidemic, as opposed to only mean values. In this paper we examine via direct simulations the adequacy of the approximate model to describe stochastic epidemics and rumors on several random network topologies: homogeneous networks, Erdös-Rényi (ER) random graphs, Barabasi-Albert scale-free networks, and random geometric graphs. We find that the approximate model is reasonably accurate in predicting the probability of spread. However, the position of the threshold and the conditional mean of the final size for processes near the threshold are not well described by the approximate model even in the case of homogeneous networks. We attribute this failure to the presence of other structural properties beyond degree-degree correlations, and in particular clustering, which are present in any finite network but are not incorporated in the approximate model. In order to test this "hypothesis" we perform additional simulations on a set of ER random graphs where degree-degree correlations and clustering are separately and independently introduced using recently proposed algorithms from the literature. Our results show that even strong degree-degree correlations have only weak effects on the position of the threshold and the conditional mean of the final size. On the other hand, the introduction of clustering greatly affects both the position of the threshold and the conditional mean. Similar analysis for the Barabasi-Albert scale-free network confirms the significance of clustering on the dynamics of rumor spread. For this network, though, with its highly skewed degree distribution, the addition of positive correlation had a much stronger effect on the final size distribution than was found for the simple random graph.
Collapse
Affiliation(s)
- Valerie Isham
- Department of Statistical Science, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | | | | |
Collapse
|
24
|
Royston P, Barthel FMS, Parmar MK, Choodari-Oskooei B, Isham V. Designs for clinical trials with time-to-event outcomes based on stopping guidelines for lack of benefit. Trials 2011; 12:81. [PMID: 21418571 PMCID: PMC3078872 DOI: 10.1186/1745-6215-12-81] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 03/18/2011] [Indexed: 11/24/2022] Open
Abstract
background The pace of novel medical treatments and approaches to therapy has accelerated in recent years. Unfortunately, many potential therapeutic advances do not fulfil their promise when subjected to randomized controlled trials. It is therefore highly desirable to speed up the process of evaluating new treatment options, particularly in phase II and phase III trials. To help realize such an aim, in 2003, Royston and colleagues proposed a class of multi-arm, two-stage trial designs intended to eliminate poorly performing contenders at a first stage (point in time). Only treatments showing a predefined degree of advantage against a control treatment were allowed through to a second stage. Arms that survived the first-stage comparison on an intermediate outcome measure entered a second stage of patient accrual, culminating in comparisons against control on the definitive outcome measure. The intermediate outcome is typically on the causal pathway to the definitive outcome (i.e. the features that cause an intermediate event also tend to cause a definitive event), an example in cancer being progression-free and overall survival. Although the 2003 paper alluded to multi-arm trials, most of the essential design features concerned only two-arm trials. Here, we extend the two-arm designs to allow an arbitrary number of stages, thereby increasing flexibility by building in several 'looks' at the accumulating data. Such trials can terminate at any of the intermediate stages or the final stage. Methods We describe the trial design and the mathematics required to obtain the timing of the 'looks' and the overall significance level and power of the design. We support our results by extensive simulation studies. As an example, we discuss the design of the STAMPEDE trial in prostate cancer. Results The mathematical results on significance level and power are confirmed by the computer simulations. Our approach compares favourably with methodology based on beta spending functions and on monitoring only a primary outcome measure for lack of benefit of the new treatment. Conclusions The new designs are practical and are supported by theory. They hold considerable promise for speeding up the evaluation of new treatments in phase II and III trials.
Collapse
|
25
|
Abstract
A conceptual stochastic model of rainfall is proposed in which storm origins occur in a Poisson process, where each storm has a random lifetime during which rain cell origins occur in a secondary Poisson process. In addition, each cell has a random lifetime during which instantaneous random depths (or ‘pulses’) of rain occur in a further Poisson process. A key motivation behind the model formulation is to account for the variability in rainfall data over small (e.g. 5 min) and larger time intervals. Time-series properties are derived to enable the model to be fitted to aggregated rain gauge data. These properties include moments up to third order, the probability that an interval is dry, and the autocovariance function. To allow for distinct storm types (e.g. convective and stratiform), several processes may be superposed. Using the derived properties, a model consisting of two storm types is fitted to 60 years of 5 min rainfall data taken from a site near Wellington, New Zealand, using sample estimates taken at 5 min, 1 hour, 6 hours and daily levels of aggregation. The model is found to fit moments of the depth distribution up to third order very well at these time scales. Using the fitted model, 5 min series are simulated, and annual maxima are extracted and compared with equivalent values taken from the historical record. A good fit in the extremes is found at both 1 and 24 hour levels of aggregation, although at the 5 min level there is some underestimation of the historical values. Proportions of time intervals with depths below various low thresholds are extracted from the simulated and historical series and compared. A tendency for underestimation of the historical values is evident at some time scales, with a close fit being obtained as the threshold is increased.
Collapse
Affiliation(s)
- Paul Cowpertwait
- Institute of Information and Mathematical Sciences, Massey UniversityAuckland 0745, New Zealand
| | - Valerie Isham
- Department of Statistical Science, University College LondonLondon WC1E 6BT, UK
| | - Christian Onof
- Department of Civil and Environmental Engineering, Imperial College LondonLondon SW7 2AZ, UK
| |
Collapse
|
26
|
Bottomley C, Isham V, Basáñez MG. Population biology of multispecies helminth infection: Competition and coexistence. J Theor Biol 2007; 244:81-95. [DOI: 10.1016/j.jtbi.2006.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2006] [Revised: 06/09/2006] [Accepted: 07/19/2006] [Indexed: 11/25/2022]
|
27
|
Abstract
1. The epidemiology of sexually transmitted diseases (STDs) in human and domesticated populations is well documented. However, there has been less study of STDs in natural populations. 2. We investigated STD dynamics in the model system involving a host from the most speciose group of animals: the insects. We investigated temporal variation in the prevalence of the sexually transmitted mite Coccipolipus hippodamiae on its ladybird host, Adalia bipunctata. 3. Field surveys over two seasons showed a repeated pattern of a profound epidemic in the overwintered cohort and a later prevalence decline. 4. In order to understand the key factors in the dynamics of this system we studied the phenology of the host and simulated parasite dynamics in the overwintered cohort using a model with within-sex homogeneity in mating rate and field-measured parameter values. The similarity of natural and simulation prevalence levels allowed us to carry out sensitivity analysis and hence to identify the key determinants of the dynamics. 5. The observed pattern of periodic extreme prevalence combined with system persistence probably results from time lags in host recruitment and widespread promiscuity. 6. Our findings improve our understanding of STDs in natural populations and illustrate the importance of examining seasonality and time delays in population dynamics in order to fully understand the characteristics of natural populations and their parasites.
Collapse
|
28
|
Abstract
A simplified spatial-temporal soil moisture model driven by stochastic spatial rainfall forcing is proposed. The model is mathematically tractable, and allows the spatial and temporal structure of soil moisture fields, induced by the spatial-temporal variability of rainfall and the spatial variability of vegetation, to be explored analytically. The influence of the main model parameters, reflecting the spatial scale of rain cells, the soil storage capacity, the rainfall interception and the soil water loss rate (representing evaporation and deep infiltration) is investigated. The variabilities of the spatially averaged soil moisture process, and that averaged in both space and time, are derived. The present analysis focuses on spatially uniform vegetation conditions; a follow-up paper will incorporate stochastically heterogeneous vegetation.
Collapse
Affiliation(s)
- V Isham
- Department of Statistical Science, University College LondonGower Street, London WC1E 6BT, UK
| | - D.R Cox
- Nuffield College, University of OxfordOxford OX1 1NF, UK
| | - I Rodríguez-Iturbe
- Department of Civil and Environmental Engineering, Princeton UniversityPrinceton, NJ 08540, USA
| | - A Porporato
- Department of Civil and Environmental Engineering, Duke UniversityDurham, NC 27708, USA
| | - S Manfreda
- Department of Civil and Environmental Engineering, Princeton UniversityPrinceton, NJ 08540, USA
- Dipartimento di Ingegneria e Fisica dell'Ambiente (DIFA), Università degli Studi della BasilicataPotenza 85100, Italy
| |
Collapse
|
29
|
Abstract
Despite evidence for the existence of interspecific interactions between helminth species, there has been no theoretical exploration of their effect on the distribution of the parasite species in a host population. We use a deterministic model for the accumulation and loss of adult worms of 2 interacting helminth species to motivate an individual-based stochastic model. The mean worm burden and variance[ratio ]mean ratio (VMR) of each species, and the correlation between the two species are used to describe the distribution within different host age classes. We find that interspecific interactions can produce convex age-intensity profiles and will impact the level of aggregation (as measured by the VMR). In the absence of correlated exposure, the correlation in older age classes may be close to zero when either intra- or interspecific synergistic effects are strong. We therefore suggest examining the correlation between species in young hosts as a possible means of identifying interspecific interaction. The presence of correlation between the rates of exposure makes the interpretation of correlations between species more difficult. Finally we show that in the absence of interaction, strong positive correlations are generated by averaging across most age classes.
Collapse
Affiliation(s)
- C Bottomley
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), Wolfson House, 4 Stephenson Way, London NW1 2HE.
| | | | | |
Collapse
|
30
|
Webberley KM, Hurst GDD, Husband RW, Schulenburg JHGVD, Sloggett JJ, Isham V, Buszko J, Majerus MEN. Host reproduction and a sexually transmitted disease: causes and consequences ofCoccipolipus hippodamiaedistribution on coccinellid beetles. J Anim Ecol 2004. [DOI: 10.1111/j.1365-2656.2004.00769.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
31
|
Bax R, Bywater R, Cornaglia G, Goossens H, Hunter P, Isham V, Jarlier V, Jones R, Phillips I, Sahm D, Senn S, Struelens M, Taylor D, White A. Surveillance of antimicrobial resistance--what, how and whither? Clin Microbiol Infect 2001; 7:316-25. [PMID: 11442565 DOI: 10.1046/j.1198-743x.2001.00239.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To express the views of a working party held to consider antibiotic resistance surveillance systems, their strengths and weaknesses, and their current and future applications. METHODS The participants, all of whom were experienced in this field, discussed the development of surveillance systems in relation to the increasing prevalence of resistance to antibacterial agents and the current interest in surveillance systems shown by many official bodies, in both the human and veterinary fields. The problems inherent in surveillance systems were considered together with the applications of different systems. RESULTS The properties of good antibiotic resistance surveillance systems were defined. Surveillance systems vary widely from those with a narrow base, focusing on few organisms in one disease area, to those covering many diseases, many organisms (including normal flora) and many compounds. Whatever their design, they should be able to detect significant differences and shifts in susceptibility to various antibacterial agents, and the information derived from them should reach as many interested parties as possible in a timely manner. In using this information to decide strategies, criteria for action need to be determined by pragmatic consensus. Funding remains a major problem, with few large studies being supported by official bodies in spite of their professed enthusiasm for surveillance. In consequence, many current systems are funded by the pharmaceutical industry and are of necessity restricted in their focus. CONCLUSIONS Antibiotic resistance surveillance studies should and can be well planned and well executed. Many current systems suffer from well-recognized but uncorrected biases. Consortium funding will be necessary for large schemes to be successful. There is no "ideal" surveillance system.
Collapse
Affiliation(s)
- R Bax
- Biosyn Inc., 3401 Market Street, Philadelphia, PA 19104-6273, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Herbert J, Isham V. A study of the role of the transmission mechanism in macroparasite aggregation. J Appl Probab 2001. [DOI: 10.1239/jap/1085496607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The dynamics of host-macroparasite infections pose considerable challenges for stochastic modelling because of the need to take into account a large number of relevant factors and many nonlinear interactions between them. This paper focuses attention on the infection transmission process and the effects of specific modelling assumptions about the mechanisms involved. Some dramatically simplified linear models are considered; they are based on multidimensional linear birth and death processes, and are designed to illuminate qualitative effects of interest. Both single and compound infections are allowed. It is shown that such simple models can generate and increase dispersion of parasite counts, even among homogeneous hosts.
Collapse
|
33
|
Abstract
We contribute to the discussion of causes and effects of aggregation (overdispersion) of macroparasite counts, focussing particularly upon the effects of clumped infections and parasite-induced host mortality. The simple nonlinear stochastic model for the evolution of the parasite load of a single host, investigated in Isham (1995), is extended to allow three parasite stages (larval, mature and offspring), and to allow durations of these stages to be non-exponentially distributed. As in the earlier work, exact algebraic results are possible, providing insight into the aggregation mechanisms, as long as the only source of interaction between host and parasites is an excess host mortality linearly related to the parasite load. Results are obtained on the distribution of parasite load and on host survival. In particular, although parasite-induced host mortality is usually thought of as a process that reduces parasite aggregation (Anderson and Gordon 1982), it is shown that, for this model, parasite-induced host mortality cannot cause the index of dispersion to fall below unity. Host heterogeneity and disease control are also discussed. An approximation based on moment assumptions appropriate to a specially-constructed multivariate negative binomial distribution is proposed. This approximation, which is applicable to other processes, and an alternative based on the multivariate normal distribution are compared with exact results.
Collapse
Affiliation(s)
- J Herbert
- Department of Statistical Science, University College London, UK
| | | |
Collapse
|
34
|
Rodriguez-Iturbe I, Porporato A, Ridolfi L, Isham V, Coxi DR. Probabilistic modelling of water balance at a point: the role of climate, soil and vegetation. Proc Math Phys Eng Sci 1999. [DOI: 10.1098/rspa.1999.0477] [Citation(s) in RCA: 445] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- I. Rodriguez-Iturbe
- Environmental Engineering and Water Resources Program and Princeton Environmental Institute, Princeton, NJ 08544, USA
| | - A. Porporato
- Dipartimento di Idraulica Trasporti e Infrastrutture Civili, Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Torino, Italy
| | - L. Ridolfi
- Dipartimento di Idraulica Trasporti e Infrastrutture Civili, Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Torino, Italy
| | - V. Isham
- Department of Statistical Science, University College London, Gower Street, London WC1E 6BT, UK
| | - D. R. Coxi
- Nuffield College, University of Oxford, Oxford OX1 1NF, UK
| |
Collapse
|
35
|
Smith G, Grenfell BT, Isham V, Cornell S. Anthelmintic resistance revisited: under-dosing, chemoprophylactic strategies, and mating probabilities. Int J Parasitol 1999; 29:77-91; discussion 93-4. [PMID: 10048821 DOI: 10.1016/s0020-7519(98)00186-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Deterministic and stochastic models are used to examine the evolution of anthelmintic resistance among trichostrongylid parasites of domestic ruminants. We find that the relative selection pressures exerted by chemoprophylactic (preventive) control strategies, chemotherapeutic (salvage) control strategies, and regimens involving "under-dosing" are critically dependent on a variety of host and parasite parameters (particularly host immunity and grazing behaviour, parasite fecundity, and the survival of the free-living stages on the pasture). Chemoprophylactic strategies are not necessarily more likely to exert a stronger selection pressure than chemotherapeutic strategies. Similarly, as one reduces dosage levels, there is a range of dose levels where under-dosing promotes resistance and a range of dose levels where under-dosing impedes resistance. The most dangerous dose is either that necessary to kill all the susceptible homozygotes, or that necessary to kill all the susceptible homozygotes and all the heterozygotes. Which one prevails depends upon model parameters. The stochastic formulation indicates that spatial heterogeneity in transmission may be a significant force in promoting the spread of resistant genotypes--at least when infection is at low levels.
Collapse
Affiliation(s)
- G Smith
- University of Pennsylvania School of Veterinary Medicine, Center for Infectious Disease and Food Safety, Kennett Square, PA 19348, USA.
| | | | | | | |
Collapse
|
36
|
Lyerla R, Isham V, Medley G. Models for Infectious Human Diseases: Their Structure and Relation to Data. J Am Stat Assoc 1997. [DOI: 10.2307/2965602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
37
|
|
38
|
|
39
|
Mollison D, Isham V, Grenfell B. Epidemics: models and data. J R Stat Soc Ser A Stat Soc 1994; 157:115-149. [PMID: 12159126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
"The problems of understanding and controlling disease raise a range of challenging mathematical and statistical research topics, from broad theoretical issues to specific practical ones. In particular, recent interest in acquired immune deficiency syndrome has stimulated much progress in diverse areas of epidemic modelling, particularly with regard to the treatment of heterogeneity, both between individuals and in mixing of subgroups of the population. At the same time better data and data analysis techniques have become available, and there have been exciting developments in relevant theory.... This progress in specific areas is now being matched by interdisciplinary cooperation aimed at elucidating relationships between the widely varying types of model that have been found useful, to determine their strengths and limitations in relation to basic aims such as understanding, prediction, and evaluation and implementation of control strategies."
Collapse
|
40
|
|
41
|
Abstract
In predicting the course of individual realizations of an epidemic it is important to know the magnitude of the variability of such realizations about their mean. In this paper and in the context of the general stochastic epidemic, some methods of obtaining approximate estimates of this variability are investigated; one is a multivariate normal approximation based on an asymptotic Gaussian diffusion process, and another uses an approximating linear stochastic process. The extension of these methods to the more detailed models used to describe the transmission dynamics of HIV infection and AIDS is discussed.
Collapse
Affiliation(s)
- V Isham
- University College London, England
| |
Collapse
|
42
|
Isham V. Stochastic processes in epidemic theory. (Lecture notes in biomathematics vol. 86). J-P. Gabriel, C. Lefevre and P. Picard (eds), Springer-Verlag, Berlin, 1990. No. of pages: viii + 197. Price: 44DM (paperback). ISBN: 3-540-52571-8. Stat Med 1991. [DOI: 10.1002/sim.4780101119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
43
|
Abstract
The aim of the method of 'back projection' is to provide estimates of the number of new infections with the human immunodeficiency virus (HIV) as a function of time, by using the numbers of diagnoses of the acquired immune deficiency syndrome (AIDS) together with information on the distribution of the incubation period between infection and diagnosis. Here, the method is investigated with particular reference to cases of HIV infection and AIDS in the United Kingdom.
Collapse
Affiliation(s)
- V Isham
- Department of Statistical Science, University College London, U.K
| |
Collapse
|
44
|
|
45
|
|
46
|
|
47
|
|
48
|
Abstract
The relation is investigated between the distributions of the total time until failure and the time of exposure to risk until failure, for individuals who are at risk only intermittently during their lifetimes. A specific example is considered in the case of computer failures.
Collapse
|