Predictive modeling of cholera outbreaks in Bangladesh

DOI10.1214/16-AOAS908zbMATH Open1400.62271arXiv1402.0536OpenAlexW1646553488WikidataQ39285591 ScholiaQ39285591MaRDI QIDQ312893FDOQ312893

Authors: Amanda A. Koepke, Ira M. jun. Longini, M. Elizabeth Halloran, Vladimir N. Ninin, Jon Wakefield 

Publication date: 9 September 2016

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Despite seasonal cholera outbreaks in Bangladesh, little is known about the relationship between environmental conditions and cholera cases. We seek to develop a predictive model for cholera outbreaks in Bangladesh based on environmental predictors. To do this, we estimate the contribution of environmental variables, such as water depth and water temperature, to cholera outbreaks in the context of a disease transmission model. We implement a method which simultaneously accounts for disease dynamics and environmental variables in a Susceptible-Infected-Recovered-Susceptible (SIRS) model. The entire system is treated as a continuous-time hidden Markov model, where the hidden Markov states are the numbers of people who are susceptible, infected, or recovered at each time point, and the observed states are the numbers of cholera cases reported. We use a Bayesian framework to fit this hidden SIRS model, implementing particle Markov chain Monte Carlo methods to sample from the posterior distribution of the environmental and transmission parameters given the observed data. We test this method using both simulation and data from Mathbaria, Bangladesh. Parameter estimates are used to make short-term predictions that capture the formation and decline of epidemic peaks. We demonstrate that our model can successfully predict an increase in the number of infected individuals in the population weeks before the observed number of cholera cases increases, which could allow for early notification of an epidemic and timely allocation of resources.

Full work available at URL: https://arxiv.org/abs/1402.0536

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zbMATH Keywords

BayesianMCMCSIRhidden Markov modelparticle filter

Mathematics Subject Classification ID

Markov processes: estimation; hidden Markov models (62M05) Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical epidemiology (92C60)

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Cited In (8)

• A linear noise approximation for stochastic epidemic models fit to partially observed incidence counts
• Predictive modeling of cholera outbreaks in Bangladesh
• Effect of cross-immunity in a two-strain cholera model with aquatic component
• Early warning forecasts for COVID-19 in Korea using Bayesian estimation of the transmission rate
• A hybrid approach to study and forecast climate-sensitive norovirus infections in the USA
• Impact of hygiene, famine and environment on transmission and spread of cholera
• Phenomenological forecasting of disease incidence using heteroskedastic Gaussian processes: a dengue case study
• Statistical modeling of computer malware propagation dynamics in cyberspace

Uses Software

• Rcpp

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