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Appears in Collections:Computing Science and Mathematics Journal Articles
Peer Review Status: Refereed
Title: When and why direct transmission models can be used for environmentally persistent pathogens
Author(s): Benson, Lee
Davidson, Ross S
Green, Darren M
Hoyle, Andrew
Hutchings, Mike R
Marion, Glenn
Keywords: Computational Theory and Mathematics
Cellular and Molecular Neuroscience
Molecular Biology
Modelling and Simulation
Ecology, Evolution, Behavior and Systematics
Issue Date: 2021
Date Deposited: 13-Dec-2021
Citation: Benson L, Davidson RS, Green DM, Hoyle A, Hutchings MR & Marion G (2021) When and why direct transmission models can be used for environmentally persistent pathogens. PLOS Computational Biology, 17 (12), Art. No.: e1009652.
Abstract: Variants of the susceptible-infected-removed (SIR) model of Kermack & McKendrick (1927) enjoy wide application in epidemiology, offering simple yet powerful inferential and predictive tools in the study of diverse infectious diseases across human, animal and plant populations. Direct transmission models (DTM) are a subset of these that treat the processes of disease transmission as comprising a series of discrete instantaneous events. Infections transmitted indirectly by persistent environmental pathogens, however, are examples where a DTM description might fail and are perhaps better described by models that comprise explicit environmental transmission routes, so-called environmental transmission models (ETM). In this paper we discuss the stochastic susceptible-exposed-infected-removed (SEIR) DTM and susceptible-exposed-infected-removed-pathogen (SEIR-P) ETM and we show that the former is the timescale separation limit of the latter, with ETM host-disease dynamics increasingly resembling those of a DTM when the pathogen’s characteristic timescale is shortened, relative to that of the host population. Using graphical posterior predictive checks (GPPC), we investigate the validity of the SEIR model when fitted to simulated SEIR-P host infection and removal times. Such analyses demonstrate how, in many cases, the SEIR model is robust to departure from direct transmission. Finally, we present a case study of white spot disease (WSD) in penaeid shrimp with rates of environmental transmission and pathogen decay (SEIR-P model parameters) estimated using published results of experiments. Using SEIR and SEIR-P simulations of a hypothetical WSD outbreak management scenario, we demonstrate how relative shortening of the pathogen timescale comes about in practice. With atttempts to remove diseased shrimp from the population every 24h, we see SEIR and SEIR-P model outputs closely conincide. However, when removals are 6-hourly, the two models’ mean outputs diverge, with distinct predictions of outbreak size and duration.
DOI Link: 10.1371/journal.pcbi.1009652
Rights: © 2021 Benson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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