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

This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.

This week, we are sharing a report regarding the prevalence of Porcine Deltacoronavirus and Porcine Epidemic Diarrhea virus in swine herds from Ontario.

Key Points

  • Cumulative incidence of PED and PDCoV in Canada is decreasing according to data coming from the industry for the year 2014, 2015 and 2016.
  • PED showed a cyclical pattern when looking at the number of farms infected. However, PDCoV showed a more erratic pattern with no clear trends.
  • Industry driven disease control programs provide useful information to understand temporal evolution and disease patterns.

The primary goal of this study was to estimate herd-level incidence and prevalence measures for PEDV and PDCoV in swine herds in Ontario (Canada) between January 2014 and December 2016, based on industry data (Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP)).

The full paper was published in the Transboundary and Emerging Diseases journal.

Ajayi PED Deltacoronavirus prevalence in swine herd Ontario

Herd-level incidence risk and rate of two novel porcine coronaviruses (PEDV and PDCoV) in Ontario swine herds between 2014 and 2016, and estimated prevalence of positive cases at the end of each year 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).

PED showed a cyclical pattern over the three years of the study while PDCoV showed a more erratic pattern. Incidence decreased over time between 2014 and 2016 in both, PED and PDCoV.

You can also read our report on the prevalence of PDCoV in the USA.

The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States

Today, we are sharing a recent publication on swine influenza in the Journal of General Virology. Dr. Marie Culhane from the University of Minnesota collaborated on this study of the genetic diversity of swine viruses in Canada and how it influences the strains found in the US.

The final data set included:

  • 168 genomes from Canadian swine influenza A viruses,
  • 5 genomes from highly under-represented US states (Alabama, Arkansas, Kentucky, Maryland and Montana),
  • 648 genomes from US and Canadian swine influenza A viruses (GenBank).

In total, these data represented 29 US states and 5 Canadian provinces.

Genetic diversity of influenza A viruses

In Canada, H1α viruses were the most frequently identified H1 viruses. In contrast, H1α viruses died out long ago in US herds, and have only been identified sporadically following new viral introductions from Canada. Notably, the two dominant H1 viruses in the United States, H1γ and H1δ-1, were not observed in any Canadian province during 2009–2016. In contrast to H1, H3 viruses are found in both the United States and Canada, with evidence of frequent cross-border transmission.

Sources of viral diversity

The study shows that the source of influenza viruses is aligned with pig movements. Indeed, Iowa and Minnesota receive around 87% of Manitoba swine exports. Therefore, the patterns of swine influenza viruses in those 2 US states correlate with the ones in Manitoba.

Similarly, viral gene patterns found in Illinois, Michigan, Wisconsin, or Ohio are influenced by the ones found in Ontario. Indeed, it only takes 3 hours to transport pigs from Ontario to Michigan. However, North Carolina and Virginia are the largest source of viruses for this region.


Left: Each region is shaded according to the proportion of total ‘Markov jump’ counts from that particular region into the Heartland: red, high proportion of jumps, important source of viruses; light yellow, low proportion of jumps, not an important source of viruses; black, destination. Right: US states are shaded according to the number of live swine imported from Manitoba in 2015 (per 1000 head)


Swine are a key reservoir host for influenza A viruses (IAVs), with the potential to cause global pandemics in humans. Gaps in surveillance in many of the world’s largest swine populations impede our understanding of how novel viruses emerge and expand their spatial range in pigs. Although US swine are intensively sampled, little is known about IAV diversity in Canada’s population of ~12 million pigs. By sequencing 168 viruses from multiple regions of Canada, our study reveals that IAV diversity has been underestimated in Canadian pigs for many years. Critically, a new H1 clade has emerged in Canada (H1α-3), with a two-amino acid deletion at H1 positions 146–147, that experienced rapid growth in Manitoba’s swine herds during 2014–2015. H1α-3 viruses also exhibit a higher capacity to invade US swine herds, resulting in multiple recent introductions of the virus into the US Heartland following large-scale movements of pigs in this direction. From the Heartland, H1α-3 viruses have disseminated onward to both the east and west coasts of the United States, and may become established in Appalachia. These findings demonstrate how long-distance trading of live pigs facilitates the spread of IAVs, increasing viral genetic diversity and complicating pathogen control. The proliferation of novel H1α-3 viruses also highlights the need for expanded surveillance in a Canadian swine population that has long been overlooked, and may have implications for vaccine design.

Characterizing Canadian rotavirus A strains and their similarity to a commercial vaccine


Rotaviruses A are genetically diverse.

Rotaviruses are responsible for increased mortality in neonatal swine populations. They are different genetically and more studies are needed to characterize their diversity. This is the objective of this study coordinated by Dr. Marthaler’s lab focusing on rotaviruses strains found in Canada.

Viral proteins 7 and 4 are used for rotavirus A classification.

Rotaviruses are classified based on two viral proteins (VP) found on their outer capsid called respectively VP7 and VP4. Those two proteins are also essential to induce an efficient immune response against the virus. This project characterized VP7 and VP4 sequences in 136 Canadian samples and compared them with the strains used in a rotavirus commercial vaccine.

The VP7 (n=32) and partial VP4 (n=25) were analyzed, identifying the G3P[13], G5P[7], G5P[x], G9P[7], G9P[13], G9P[19], and G9P[x] genotypes.
Minimal differences in the antigenic epitopes for the G5, G9, and P[7] strains were identified.
Major differences in the antigenic epitopes of the G3, P[13], and P[19] may question the effectiveness of the ProSystems RCE RVA.

Marthaler rotavirus A Canada 2017


Surveillance of Rotavirus A (RVA) infections in North America swine populations are limited and not performed over a significant time period to properly assess the diversity of RVA strains in swine. The VP7 (G) and VP4 (P) genes of 32 Canadian RVA strains, circulating between 2009 and 2015 were sequenced, identifying the G3P[13], G5P[7], G9P[7], G9[13], and G9[19] genotype combinations. The Canadian RVA strains were compared to the RVA strains present in the swine ProSystems RCE rotavirus vaccine. The comparison revealed multiple amino acid differences in the G and P antigenic epitopes, regardless of the G and P genotypes but specifically in the Canadian G3, P[13] and P[19] genotypes. Our study further contributes to the characterization of RVA’s evolution and disease mitigation among swine, which may optimize target vaccine design, thereby minimizing RVA disease in this economically important animal population.

Link to the full article