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Kirkeby C, Brookes VJ, Ward MP, Dürr S, Halasa T. A Practical Introduction to Mechanistic Modeling of Disease Transmission in Veterinary Science. Front Vet Sci 2021; 7:546651. [PMID: 33575275 PMCID: PMC7870987 DOI: 10.3389/fvets.2020.546651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Computer-based disease spread models are frequently used in veterinary science to simulate disease spread. They are used to predict the impacts of the disease, plan and assess surveillance, or control strategies, and provide insights about disease causation by comparing model outputs with real life data. There are many types of disease spread models, and here we present and describe the implementation of a particular type: individual-based models. Our aim is to provide a practical introduction to building individual-based disease spread models. We also introduce code examples with the goal to make these techniques more accessible to those who are new to the field. We describe the important steps in building such models before, during and after the programming stage, including model verification (to ensure that the model does what was intended), validation (to investigate whether the model results reflect the modeled system), and convergence analysis (to ensure models of endemic diseases are stable before outputs are collected). We also describe how sensitivity analysis can be used to assess the potential impact of uncertainty about model parameters. Finally, we provide an overview of some interesting recent developments in the field of disease spread models.
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Affiliation(s)
- Carsten Kirkeby
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark,*Correspondence: Carsten Kirkeby
| | - Victoria J. Brookes
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga, NSW, Australia,Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Wagga, NSW, Australia
| | - Michael P. Ward
- Faculty of Veterinary Science, Sydney School of Veterinary Science, University of Sydney, Sydney, NSW, Australia
| | - Salome Dürr
- Department of Clinical Research and Public Health, Veterinary Public Health Institute, University of Bern, Bern, Switzerland
| | - Tariq Halasa
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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Zaheer MU, Salman MD, Steneroden KK, Magzamen SL, Weber SE, Case S, Rao S. Challenges to the Application of Spatially Explicit Stochastic Simulation Models for Foot-and-Mouth Disease Control in Endemic Settings: A Systematic Review. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:7841941. [PMID: 33294003 PMCID: PMC7700052 DOI: 10.1155/2020/7841941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 10/20/2020] [Accepted: 10/30/2020] [Indexed: 11/17/2022]
Abstract
Simulation modeling has become common for estimating the spread of highly contagious animal diseases. Several models have been developed to mimic the spread of foot-and-mouth disease (FMD) in specific regions or countries, conduct risk assessment, analyze outbreaks using historical data or hypothetical scenarios, assist in policy decisions during epidemics, formulate preparedness plans, and evaluate economic impacts. Majority of the available FMD simulation models were designed for and applied in disease-free countries, while there has been limited use of such models in FMD endemic countries. This paper's objective was to report the findings from a study conducted to review the existing published original research literature on spatially explicit stochastic simulation (SESS) models of FMD spread, focusing on assessing these models for their potential use in endemic settings. The goal was to identify the specific components of endemic FMD needed to adapt these SESS models for their potential application in FMD endemic settings. This systematic review followed the PRISMA guidelines, and three databases were searched, which resulted in 1176 citations. Eighty citations finally met the inclusion criteria and were included in the qualitative synthesis, identifying nine unique SESS models. These SESS models were assessed for their potential application in endemic settings. The assessed SESS models can be adapted for use in FMD endemic countries by modifying the underlying code to include multiple cocirculating serotypes, routine prophylactic vaccination (RPV), and livestock population dynamics to more realistically mimic the endemic characteristics of FMD. The application of SESS models in endemic settings will help evaluate strategies for FMD control, which will improve livestock health, provide economic gains for producers, help alleviate poverty and hunger, and will complement efforts to achieve the Sustainable Development Goals.
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Affiliation(s)
- Muhammad Usman Zaheer
- Animal Population Health Institute, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins CO 80523, USA
- FMD Project Office, Food and Agriculture Organization of the United Nations, ASI Premises, NARC Gate # 2, Park Road, Islamabad 44000, Pakistan
| | - Mo D. Salman
- Animal Population Health Institute, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins CO 80523, USA
| | - Kay K. Steneroden
- Animal Population Health Institute, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins CO 80523, USA
| | - Sheryl L. Magzamen
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins CO 80523, USA
| | - Stephen E. Weber
- Animal Population Health Institute, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins CO 80523, USA
| | - Shaun Case
- Department of Civil and Environmental Engineering, Walter Scott, Jr. College of Engineering, Colorado State University, Fort Collins CO 80521, USA
| | - Sangeeta Rao
- Animal Population Health Institute, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins CO 80523, USA
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Evaluating vaccination strategies to control foot-and-mouth disease: a country comparison study. Epidemiol Infect 2018; 146:1138-1150. [DOI: 10.1017/s0950268818001243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractVaccination is increasingly being recognised as a potential tool to supplement ‘stamping out’ for controlling foot-and-mouth disease (FMD) outbreaks in non-endemic countries. Infectious disease simulation models provide the opportunity to determine how vaccination might be used in the face of an FMD outbreak. Previously, consistent relative benefits of specific vaccination strategies across different FMD simulation modelling platforms have been demonstrated, using a UK FMD outbreak scenario. We extended this work to assess the relative effectiveness of selected vaccination strategies in five countries: Australia, New Zealand, the USA, the UK and Canada. A comparable, but not identical, FMD outbreak scenario was developed for each country with initial seeding of Pan Asia type O FMD virus into an area with a relatively high density of livestock farms. A series of vaccination strategies (in addition to stamping out (SO)) were selected to evaluate key areas of interest from a disease response perspective, including timing of vaccination, species considerations (e.g. vaccination of only those farms with cattle), risk area vaccination and resources available for vaccination. The study found that vaccination used with SO was effective in reducing epidemic size and duration in a severe outbreak situation. Early vaccination and unconstrained resources for vaccination consistently outperformed other strategies. Vaccination of only those farms with cattle produced comparable results, with some countries demonstrating that this could be as effective as all species vaccination. Restriction of vaccination to higher risk areas was less effective than other strategies. This study demonstrates consistency in the relative effectiveness of selected vaccination strategies under different outbreak start up conditions conditional on the assumption that each of the simulation models provide a realistic estimation of FMD virus spread. Preferred outbreak management approaches must however balance the principles identified in this study, working to clearly defined outbreak management objectives, while having a good understanding of logistic requirements and the socio-economic implications of different control measures.
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