Understanding the early dynamics of the 2014 porcine epidemic diarrhea virus (PEDV) outbreak in Ontario using the incidence decay and exponential adjustment (IDEA) model

Abstract

BackgroundThe United States swine industry was first confronted with porcine epidemic diarrhea virus (PEDV) in 2013. In young pigs, the virus is highly pathogenic and the associated morbidity and mortality has a significant negative impact on the swine industry. We have applied the IDEA model to better understand the 2014 PEDV outbreak in Ontario, Canada. Using our simple, 2-parameter IDEA model, we have evaluated the early epidemic dynamics of PEDV on Ontario swine farms.ResultsWe estimated the best-fit R0 and control parameter (d) for the between farm transmission component of the outbreak by fitting the model to publically available cumulative incidence data. We used maximum likelihood to compare model fit estimates for different combinations of the R0 and d parameters. Using our initial findings from the iterative fitting procedure, we projected the time course of the epidemic using only a subset of the early epidemic data. The IDEA model projections showed excellent agreement with the observed data based on a 7-day generation time estimate. The best-fit estimate for R0 was 1.87 (95% CI: 1.52 – 2.34) and for the control parameter (d) was 0.059 (95% CI: 0.022 – 0.117). Using data from the first three generations of the outbreak, our iterative fitting procedure suggests that R0 and d had stabilized sufficiently to project the time course of the outbreak with reasonable accuracy.ConclusionsThe emergence and spread of PEDV represents an important agricultural emergency. The virus presents a significant ongoing threat to the Canadian swine industry. Developing an understanding of the important epidemiological characteristics and disease transmission dynamics of a novel pathogen such as PEDV is critical for helping to guide the implementation of effective, efficient, and economically feasible disease control and prevention strategies that are able to help decrease the impact of an outbreak.

Basic Reproduction Number as a Measure of the Rapidity of the Inter-farm Spread of Porcine Epidemic Diarrhea during the Initial Phase of the Epidemic in Japan in 2013-2014

“…Another study on estimating inter-farm R 0 for PED in Canada used IDEA model, which has been used for projecting epidemic process of ebola 5,6) and Middle East respiratory syndrome coronavirus (MERS) 13) infections in human populations. The structure of IDEA model for PED is simple and has only two parameters : fixed generation interval and control effect 7) . It successfully showed the change of control effect over time, but did not describe mechanic transmission process.…”

“…Although commonly applied at the individual level, R 0 is also useful for examining animal health at the farm level. Only one study on the farm level R 0 for PED has been reported from Canada 7) , which used the incidence decay and exponential adjustment (IDEA) model. At the animal level, a study in Japan 17) used a compartment model for understanding within-farm PED dynamics, without focusing on the estimation of R 0 .…”

Dynamic contact networks of swine movement in Manitoba, Canada: Characterization and implications for infectious disease spread

“…As truck sharing is a common source of disease transmission in animal shipment networks (Dee, Deen, Burns, Douthit, & Pijoan, ; Greer, Spence, & Gardner, ; Lowe et al, ), we construct two‐mode binary contact networks (location‐to‐truck networks) to investigate truck sharing practices in windows of days, weeks, months and for the entire study period. Each unique location and each unique truck are nodes, and edges are defined as the sharing of trucks by locations.…”

The Canadian 2014 porcine epidemic diarrhoea virus outbreak: Important risk factors that were not considered in the epidemiological investigation could change the conclusions

“…Withdrawal of the SDPP containing feed did not alter the rate of new PEDV outbreaks. Greer, Spence, and Gardner () reported the cumulative incidence for the Ontario PEDV outbreaks before and after the withdrawal of SDPP containing feed from the market. There was no change in increase in cumulative incidence rate after withdrawal of the SDPP‐containing feed (Figure ).…”

“…Cumulative incidence data for the Ontario porcine epidemic diarrhoea virus outbreak in 2014. Cases occurring prior to 20 February 2014 (dashed line) are assumed to be the result of a point source exposure through swine feed with cases occurring after 20 February 2014 being the result of direct farm‐to‐farm transmission (adapted from Greer et al, )…”