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Epidemiological investigations aimed towards understanding the incursion of porcine epidemic diarrhea virus into Canada

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Title: Epidemiological investigations aimed towards understanding the incursion of porcine epidemic diarrhea virus into Canada
Author: Perri, Amanda
Department: Department of Population Medicine
Program: Population Medicine
Advisor: O'Sullivan, TerriPoljak, Zvonimir
Abstract: This thesis aims to evaluate and describe the early phase of the 2014 Canadian porcine epidemic diarrhea virus (PEDV) outbreak using various epidemiological methods to improve our understanding of the outbreak. The epidemiological methods used include a case-control study using various types of logistic regressions (Firth, exact conditional and mixed), network analysis, random forest modelling and survival analysis. The source of data for chapters 2-4 was a questionnaire that was designed to obtain detailed information on herd demographics, animal and people movements on- and off-sites and biosecurity practices of PED-positive and matched PED-negative herds. Producers from the herds completed the questionnaire either by a face-to-face interview or by telephone. PED-positive herds were any swine herd with a positive diagnostic test (RT-PCR) from the Animal Health Laboratory at the University of Guelph. Contaminated feed from a single feed supplier, specifically contaminated spray-dried porcine plasma, was found to be a significant risk factor for the transmission of PEDV after adjusting for the effect of herd biosecurity. After evaluating the contact structure and animal movement patterns of the herds using descriptive network measures, the outgoing contact chain and out-degree; the same feed supplier was found to play an important role in multiple networks, indicating its importance in disease transmission. Also, when using randomly permuted networks, a common-source outbreak through feed supply was the most plausible explanation for the outbreak. However, transportation companies and semen suppliers as well as herd-to-herd spread through animal movement or transportation were not found to be important during the study period. After removing variables reflective of the common source of infection, random forest modelling provided a unique perspective on determining the most important variables for predicating herd status. The most important variables found to predict herd status included herd size and variables related to feed management. The model had a moderate predictive accuracy (72%). Lastly, time to PEDV elimination in Ontario swine herds infected between 2014 and 2017 was evaluated, using a disease control program database (DCP) to identify factors associated with the likelihood of elimination.
URI: http://hdl.handle.net/10214/14732
Date: 2018-12-19
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