Herd‐level prevalence and incidence of porcine epidemic diarrhoea virus (PEDV) and porcine deltacoronavirus (PDCoV) in swine herds in Ontario, Canada.

Summary: Porcine epidemic diarrhoea virus (PEDV) and porcine deltacoronavirus (PDCoV) were first identified in Canada in 2014. Surveillance efforts have been instrumental in controlling both diseases. In this study, we provide an overview of surveillance components for the two diseases in Ontario (Canada), as well as PEDV and PDCoV incidence and prevalence measures. Swine herds located in the Province of Ontario, of any type, whose owners agreed to participate in a voluntary industry‐led disease control programme (DCP) and with associated diagnostic or epidemiological information about the two swine coronaviruses, were eligible to be included for calculation of disease frequency at the provincial level. PEDV and PDCoV data stored in the industry DCP database were imported into the R statistical software and analysed to produce weekly frequency of incidence counts and prevalence counts, in addition to yearly herd‐level incidence risk and prevalence between 2014 and 2016. The yearly herd‐level incidence risk of PEDV, based on industry data, was 13.5%, 3.0% and 1.4% (95% CI: 11.1–16.2, 2.0–4.2, 0.8–2.3), while the yearly herd‐level incidence risk of PDCoV was 1.1%, 0.3%, and 0.1% (95% CI: 0.5–2.2, 0.1–0.9, 0.0–0.5), for 2014, 2015 and 2016, respectively. Herd‐level prevalence estimates for PEDV in the last week of 2014, 2015 and 2016 were 4.4%, 2.3% and 1.4%, respectively (95% CI: 3.1–6.0, 1.5–3.3, 0.8–2.2), while herd‐level prevalence estimates for PDCoV in the last week of 2014, 2015 and 2016 were 0.5%, 0.2% and 0.2%, respectively (95% CI: 0.1–1.2, 0.0–0.6, 0.0–0.6). Collectively, our results point to low and decreasing incidence risk and prevalence for PEDV and PDCoV in Ontario, making both diseases possible candidates for disease elimination at the provincial level. [ABSTRACT FROM AUTHOR]