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An Introduction to Infectious Disease Modelling by Emilia Vynnycky and Richard G White.
Drawing on examples from many diverse infections, the book guides readers step-by-step through the different types of models and the methods and data needed to set them up. It also covers the applications of modelling and the important insights that it has provided into the transmission and control of infections.
EpiModel: Mathematical Modeling of Infectious Disease Dynamics by Samuel M. Jenness, Steven M. Goodreau, Martina Morris [for R users]
The EpiModel package provides tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic agent-based models, and stochastic network models. Network models use the robust statistical methods of temporal exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims.
This overview article introduces the work of the Task Force, provides all the recommendations, and discusses some quandaries that require further elucidation. The audience for these articles includes those who build models, stakeholders who utilize their results, and, indeed, anyone concerned with the use of models to support decision making
GOOD PRACTICE: APPLICATIONS
Macroeconomic impact of a mild influenza pandemic and associated policies in Thailand, South Africa and Uganda: a computable general equilibrium analysis. Richard D. Smith, Marcus R. Keogh‐Brown Influenza Other Respir Viruses. 2013 Nov; 7(6): 1400–1408
Example of macro-economic modelling of a pandemic in LMICs
Objectives. To estimate the macroeconomic impact of pandemic influenza in Thailand, South Africa and Uganda with particular reference to pandemic (H1N1) 2009. Methods. A single‐country whole‐economy computable general equilibrium (CGE) model was set up for each of the three countries in question and used to estimate the economic impact of declines in labour attributable to morbidity, mortality and school closure. Results. Overall GDP impacts were less than 1% of GDP for all countries and scenarios. Uganda’s losses were proportionally larger than those of Thailand and South Africa. Labour‐intensive sectors suffer the largest losses. Conclusions. The economic cost of unavoidable absence in the event of an influenza pandemic could be proportionally larger for low‐income countries. The cost of mild pandemics, such as pandemic (H1N1) 2009, appears to be small, but could increase for more severe pandemics and/or pandemics with greater behavioural change and avoidable absence.
Exploring the Use of a General Equilibrium Method to Assess the Value of a Malaria Vaccine: An Application to Ghana. Erez Yerushalmi, Priscillia Hunt, Stijn Hoorens, Christophe Sauboin, Richard Smith. MDM Policy Pract. 2019 Jul-Dec; 4(2)
Example of integrated infectious disease model with a macro-economic model
Background. Malaria is an important health and economic burden in sub-Saharan Africa. Conventional economic evaluations typically consider only direct costs to the health care system and government budgets. This paper quantifies the potential impact of malaria vaccination on the wider economy, using Ghana as an example. Methods. We used a computable general equilibrium model of the Ghanaian economy to estimate the macroeconomic impact of malaria vaccination in children under the age of 5, with a vaccine efficacy of 50% against clinical malaria and 20% against malaria mortality. The model considered changes in demography and labor productivity, and projected gross domestic product (GDP) over a time frame of 30 years. Vaccine coverage ranging from 20% to 100% was compared with a baseline with no vaccination. Results. Malaria vaccination with 100% coverage was projected to increase the GDP of Ghana over 30 years by US$6.93 billion (in 2015 prices) above the baseline without vaccination, equivalent to an increase in annual GDP growth of 0.5%. Projected GDP per capita would increase in the first year due to immediate reductions in time lost from work by adults caring for children with malaria, then decrease for several years as reductions in child mortality increase the number of dependent children, then show a sustained increase after Year 11 due to long-term productivity improvements in adults resulting from fewer malaria episodes in childhood. Conclusion. Investing in improving childhood health by vaccinating against malaria could result in substantial long-term macroeconomic benefits when these children enter the workforce as adults. These macroeconomic benefits are not captured by conventional economic evaluations and constitute an important potential benefit of vaccination.
Empirical estimation of resource constraints for use in model-based economic evaluation: an example of TB services in South Africa Fiammetta M. Bozzani, Don Mudzengi, Tom Sumner, Gabriela B. Gomez, Piotr Hippner, Vicky Cardenas, Salome Charalambous, Richard White, Anna Vassall. Cost Eff Resour Alloc. 2018; 16:27.
Example of how to incorporate health system constraints in an economic evaluation of infectious disease case finding, using a dynamic transmission model
Background. Evidence on the relative costs and effects of interventions that do not consider ‘real-world’ constraints on implementation may be misleading. However, in many low- and middle-income countries, time and data scarcity mean that incorporating health system constraints in priority setting can be challenging. Methods. We developed a ‘proof of concept’ method to empirically estimate health system constraints for inclusion in model-based economic evaluations, using intensified case-finding strategies (ICF) for tuberculosis (TB) in South Africa as an example. As part of a strategic planning process, we quantified the resources (fiscal and human) needed to scale up different ICF strategies (cough triage and WHO symptom screening). We identified and characterised three constraints through discussions with local stakeholders: (1) financial constraint: potential maximum increase in public TB financing available for new TB interventions; (2) human resource constraint: maximum current and future capacity among public sector nurses that could be dedicated to TB services; and (3) diagnostic supplies constraint: maximum ratio of Xpert MTB/RIF tests to TB notifications. We assessed the impact of these constraints on the costs of different ICF strategies. Results. It would not be possible to reach the target coverage of ICF (as defined by policy makers) without addressing financial, human resource and diagnostic supplies constraints. The costs of addressing human resource constraints is substantial, increasing total TB programme costs during the period 2016–2035 by between 7% and 37% compared to assuming the expansion of ICF is unconstrained, depending on the ICF strategy chosen.
Catastrophic costs potentially averted by tuberculosis control in India and South Africa: a modelling study Stéphane Verguet, Carlos Riumallo-Herl, Gabriela B Gomez, Nicolas A Menzies, Rein M G J Houben, Tom Sumner, Marek Lalli, Richard G White, Joshua A Salomon, Ted Cohen, Nicola Foster, Susmita Chatterjee, Sedona Sweeney, Inés Garcia Baena, Knut Lönnroth, Diana E Weil, Anna Vassall. Lancet Glob Health. 2017 Nov; 5(11): e1123–e1132.
Example of how to conduct an equity analysis of infectious disease interventions, using a dynamic transmission model
Background. The economic burden on households affected by tuberculosis through costs to patients can be catastrophic. WHO’s End TB Strategy recognises and aims to eliminate these potentially devastating economic effects. We assessed whether aggressive expansion of tuberculosis services might reduce catastrophic costs. Methods. We estimated the reduction in tuberculosis-related catastrophic costs with an aggressive expansion of tuberculosis services in India and South Africa from 2016 to 2035, in line with the End TB Strategy. Using modelled incidence and mortality for tuberculosis and patient-incurred cost estimates, we investigated three intervention scenarios: improved treatment of drug-sensitive tuberculosis; improved treatment of multidrug-resistant tuberculosis; and expansion of access to tuberculosis care through intensified case finding (South Africa only). We defined tuberculosis-related catastrophic costs as the sum of direct medical, direct non-medical, and indirect costs to patients exceeding 20% of total annual household income. Intervention effects were quantified as changes in the number of households incurring catastrophic costs and were assessed by quintiles of household income. Findings. In India and South Africa, improvements in treatment for drug-sensitive and multidrug-resistant tuberculosis could reduce the number of households incurring tuberculosis-related catastrophic costs by 6–19%. The benefits would be greatest for the poorest households. In South Africa, expanded access to care could decrease household tuberculosis-related catastrophic costs by 5–20%, but gains would be seen largely after 5–10 years. Interpretation. Aggressive expansion of tuberculosis services in India and South Africa could lessen, although not eliminate, the catastrophic financial burden on affected households.