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

Abstract

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.

Keywords: disease surveillance; herd-level incidence; herd-level prevalence; porcine deltacoronavirus (PDCoV); porcine epidemic diarrhoea virus (PEDV).

Figure 1

Venn diagram representing overlap among the three surveillance components for identification of new cases of the porcine epidemic diarrhoea virus (PEDV) in Ontario (Canada) between 2014 and 2016—The Animal Health Laboratory (AHL), Ontario Ministry of Agriculture Food and Rural Affairs (OMAFRA) and the Ontario Swine Health Advisory Board (OSHAB). The size of individual circles should be proportional to the number of positive cases recorded by a specific surveillance component. The overlapping areas should represent cases that were identified by as many surveillance components as are being overlapped. The numbers listed in a specific area represent number of cases that are identified by a specific surveillance component or combination thereof

Figure 2

Cumulative weekly confirmed and presumed positive cases for porcine epidemic diarrhoea virus (PEDV) in Ontario (Canada) for 2014–2016, based on data provided in the Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP) database (average number of herds for 2014–2016 = 1093)

Figure 3

Cumulative weekly confirmed and presumed positive cases for porcine deltacoronavirus (PDCoV) in Ontario (Canada) for 2014–2016, based on data provided in the Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP) database (average number of herds for 2014–2016 = 1093)

Figure 4

Number of Herds with confirmed positive, presumed positive, presumed negative or confirmed negative status for porcine epidemic diarrhoea virus (PEDV) in Ontario (Canada) for 2014–2016, based on data provided in the Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP) database (average number of herds for 2014–2016 = 1093)

Figure 5

Percentage of Herds with confirmed positive, presumed positive, presumed negative or confirmed negative status for porcine epidemic diarrhoea virus (PEDV) in Ontario (Canada) for 2014–2016, based on data provided in the Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP) database (average number of herds for 2014–2016 = 1093)

Figure 6

Number of Herds with confirmed positive, presumed positive, presumed negative or confirmed negative status for porcine deltacoronavirus (PDCoV) in Ontario (Canada) for 2014–2016, based on data provided in the Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP) database (average number of herds for 2014–2016 = 1093)

Figure 7

Percentage of Herds with confirmed positive, presumed positive, presumed negative or confirmed negative status for porcine deltacoronavirus (PDCoV) in Ontario (Canada) for 2014–2016, based on data provided in the Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP) database (average number of herds for 2014–2016 = 1093)