Implementation and applications of EMOD, an individual-based multi-disease modeling platform

Bershteyn, Anna; Gerardin, Jaline; Bridenbecker, Daniel; Lorton, Christopher; Bloedow, Jonathan; Baker, Robert S.; Chabot-Couture, Guillaume; Chen, Ye; Fischle, Thomas; Frey, Kurt; Gauld, Jillian; Hu, Hao; Izzo, Amanda S; Klein, Daniel J.; Lukacevic, Dejan; McCarthy, Kevin; Miller, Joel C.; Ouédraogo, André Lin; Perkins, T. Alex; Steinkraus, Jeffrey; Bosch, Quirine A. ten; Ting, Hung-Fu; Titova, Svetlana; Wagner, Bradley G.; Welkhoff, Philip A.; Wenger, E. A.; Wiswell, Christian N

doi:10.1093/femspd/fty059

Cited by 79 publications

(75 citation statements)

References 30 publications

(27 reference statements)

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“…Transmission probability of infection from human to mosquito 0.275 0.275 0.3 [1,6] Infection Cycle Parameters:…”

Section: Infection Transmission Cycle Parametersmentioning

confidence: 99%

“…Number of days a human spends in exposed state 2 to 6 days 4 to 10 days 10 to 15 days [12,11,2] Number of days a human spends in infected state 4 to 7 days 2 to 7 days 5 to 7 days [12,11,1,2] regular movements. This represents the situation where lockdowns are accompanied by continued operation of essential services such as hospitals and government services, or lax observance of lockdowns by some people.…”

Section: Infection Transmission Cycle Parametersmentioning

confidence: 99%

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Lockdowns to Contain COVID-19 Increase Risk and Severity of Mosquito-Borne Disease Outbreaks

Jindal

Rao

2020

Preprint

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Many countries are implementing lockdown measures to slow the COVID-19 pandemic, putting more than a third of the world's population under restrictions. The scale of such lockdowns is unprecedented, and while some effects of lockdowns are readily apparent, it is less clear what effects they may have on outbreaks of serious communicable diseases. We examine the impact of these lockdowns on outbreaks of mosquito-borne diseases. Using an agent-based model and simulations, we find that the risk and severity of such outbreaks is much greater under lockdown conditions, with the number of infected people doubling in some cases. This increase in number of cases varies by different mosquito-borne diseases, and is significantly higher for diseases spread by day-biting mosquitoes. We analysed various intervention strategies and found that during lockdowns, decentralised strategies such as insecticide-treated nets and indoor residual spraying are more effective than centralised strategies.

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“…Transmission probability of infection from human to mosquito 0.275 0.275 0.3 [1,6] Infection Cycle Parameters:…”

Section: Infection Transmission Cycle Parametersmentioning

confidence: 99%

Section: Infection Transmission Cycle Parametersmentioning

confidence: 99%

Lockdowns to Contain COVID-19 Increase Risk and Severity of Mosquito-Borne Disease Outbreaks

Jindal

Rao

2020

Preprint

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“…A previously-developed spatial model of malaria transmission in southern Zambia (20) was adapted for use in this study ( Figure 1A). This model is an agent-based patch model (40) where each patch represents a single household, and both humans and mosquitoes can move between households. Areas between households were not modeled.…”

Section: Simulation Frameworkmentioning

confidence: 99%

Effective strategies for preventing reestablishment of malaria in areas with recent elimination and high transmission potential

Gerardin

Bever

Bridenbecker

et al. 2019

Preprint

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Maintaining zero transmission after malaria elimination will be a challenging task for many countries where malaria is still endemic. When local transmission potential is high, and importation of malaria infections continues from neighboring areas with ongoing transmission, malaria programs must develop robust surveillance and outbreak response systems. However, the requirements for such systems remain unclear. Using an agent-based, spatial microsimulation model of two areas in southern Zambia, where elimination efforts are currently underway, we compare the ability of various routine and reactive intervention packages to maintain near-zero prevalence in the face of continued importation. We find that in formerly moderate-transmission areas, high treatment rate of symptomatic malaria is sufficient to prevent reestablishment of malaria. Routine redistributions of insecticide-treated nets and reactive case detection with antimalarial drugs cannot completely compensate for inadequate case management. In formerly high-transmission areas, excellent case management and maintenance of good bednet coverage are both required to prevent resurgence, and outbreak response with antimalarial drugs or additional vector control is also necessary. These results begin to describe the essential criteria for operations that successfully prevent reestablishment of malaria post-elimination and highlight the need for both long-term, sustainable excellence in primary care and comprehensive surveillance that feeds into rapid and flexible outbreak response. Author SummaryThe global community is working toward malaria elimination, but some areas will eliminate before others. Eliminated areas will need to develop intervention programs capable of preventing imported infections from leading to reestablishment, a particular challenge when transmission was previously very high. Past experience has shown that stopping elimination interventions leads to massive resurgence, but it is unclear which interventions must be continued, which can be stopped to conserve resources, and what new interventions should be deployed. Using a simulation model built to capture malaria transmission and intervention history of two areas that recently made enormous progress toward elimination, we tested how well different intervention programs were able to prevent reestablishment of malaria. We found that treating as many symptomatic cases as possible was the single most important intervention to implement. In some contexts, this intervention alone was sufficient to prevent reestablishment. Other areas with historically higher transmission required maintaining vector control to contain mosquito populations. Localized outbreak response with antimalarial drugs or additional vector control was also necessary and predicted to be a highly efficient use of resources. These findings provide quantitative guidance for policy-makers considering how to stratify eliminated areas and plan new operational modes for the post-elimination era.

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“…STDSIM for simulating transmission of HIV and other Sexually Transmitted Diseases 11 ) are not open source, other IBMs (e.g. EMOD 14 ) are relatively difficult to modify. Another limitation of EMOD is that it can only be used on computers running Windows 10, Windows Server 12, Windows HPC Server 12 or CentOS 7.1.…”

Section: Introductionmentioning

confidence: 99%

“…As a consequence they require ad-hoc assumptions and decisions about in what order people "go out" to find partners and can "be found". For example, in EMOD, males and females are placed in a separate queue, where they stay for a predefined period, after which they form a relationship 14 . In STDsim, the order of going out to search for a partner and for being available for a relationship are both determined by stochastic processes 11 .…”

Section: Introductionmentioning

confidence: 99%

SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces

Liesenborgs

Hendrickx

Kuylen

et al. 2018

Preprint

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SimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV infections in dynamic sexual networks are simulated by discrete events. A generic "intervention" event allows model parameters to be changed over time, and can be used to model medical and behavioural HIV prevention programmes. First, we describe a more efficient variant of the modified Next Reaction Method that drives our continuous-time simulator. Next, we outline key built-in features and assumptions of individual-based models formulated in SimpactCyan, and provide code snippets for how to formulate, execute and analyse models in SimpactCyan through its R and Python interfaces. Lastly, we give two examples of applications in HIV epidemiology: the first demonstrates how the software can be used to estimate the impact of progressive changes to the eligibility criteria for HIV treatment on HIV incidence. The second example illustrates the use of SimpactCyan as a data-generating tool for assessing the performance of a phylodynamic inference framework. 2/1610/16

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Implementation and applications of EMOD, an individual-based multi-disease modeling platform

Cited by 79 publications

References 30 publications

Lockdowns to Contain COVID-19 Increase Risk and Severity of Mosquito-Borne Disease Outbreaks

Lockdowns to Contain COVID-19 Increase Risk and Severity of Mosquito-Borne Disease Outbreaks

Effective strategies for preventing reestablishment of malaria in areas with recent elimination and high transmission potential

SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces

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