Data from: Theory of infectious disease spillover at an ecological boundary: Impacts of seasonality and cross-boundary movement
Data files
Sep 05, 2025 version files 63.81 KB
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CTMC_Ebola_V02.R
8.50 KB
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CTMC_Movement_BA_Persistence.R
10.92 KB
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CTMC_SeasonPersistence.R
10.30 KB
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MainDeterministicStochastic.Rmd
32.94 KB
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README.md
1.15 KB
Abstract
Ecological boundaries are a key site for the spillover of wildlife pathogens into human and domestic livestock populations. Ebola virus is a zoonotic pathogen that is periodically introduced into humans causing outbreaks of a highly fatal hemorrhagic disease. There is evidence that spillover risk varies seasonally. Here we hypothesize that this seasonality may be due to periodic variations in pathogen-host interactions, host social behaviors, movement and contact rates, and demography. To better understand the dynamics of such a system, we studied a two-patch SIR compartmental model for the spillover of Ebola virus with seasonal and demographic variability. The model is expressed as a system of coupled ordinary differential equations (ODE) with periodic disease transmission and dispersal between supercritical and subcritical patches. The periodic ODE system is generalized to a stochastic Continuous-Time Markov Chain (CTMC) model. The basic reproduction number of the two-patch SIR model is derived at the disease-free equilibrium to illustrate the impact of seasonality and movement on Ebola virus outbreaks. Several numerical examples are investigated. We find that the seasonality strength and human movement are two potentially leading factors that are responsible for the intensity of periodic spillover risk from pathogen reservoirs to human settlement regions.
(Kaniz Fatema Nipa, Mozzamil Mohammed, Patrick R. Stephens, John M. Drake)
The numerical implementation of a two-patch deterministic and stochastic model and the results are presented in the above-mentioned paper.
- The deterministic ODE system is coded in Two-patch_Ebola_ODE_Model.R.
- The Continuous-Time Markov Chain (CTMC) Model is coded in CTMC_Ebola_V02.R.
- The main script MainDeterministicStochastic.Rmd is where these functions are called and the manuscript results are produced.
- CTMC_SeasonPersistence.R codes the effect of seasonality strength on the persistence probability of the disease.
- CTMC_Movement_BA_Persistence.R codes the effect of movement strength of human settlement (Patch B) to the reservoir region (Patch A) on the persistence probability of the disease.
To reproduce results of the paper, compile MainDeterministicStochastic.Rmd using knitr or run the code chunks individually in a session.
Compiled with R version 5.4.1
Dependencies: deSolve
