Science Page: 2017 summary of the Morrison Swine Health Monitoring Project

diagram MSHMP 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.

Key points:

  • We will remember 2017 for the loss of Dr. Morrison, in whose honor the program us now named. Dr. Andres Perez led the transition of the program and now Dr. Corzo, the new Leman Chair in Swine health and Productivity is leading the project.
  • MSHMP acknowledges and thanks all participants for their willingness to share their data to support the US industry.
  • The Swine Health Information Center (SHIC) has been instrumental for the execution of this project.

Four new participants joined MSHMP increasing the representativeness of the project by adding 64 sow farms accounting for 220,000 sows.
The weekly report capturing the changes in incidence and prevalence of important pathogens has been shared to participants (n=33) and non-participants (n=185). Now we report on PRRS, PEDv, SVA and novel viruses associated with atypical central nervous system disease.
The weekly science page featured authors from 18 institutions who explained cutting edge research findings, recent publication summaries, and breakdowns of MSHMP data.

Take a look at the report to see the 6 peer-reviewed publications generated thanks to this collaborative work.

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.

 

pig-flow-and-sources-of-influenza-genetic-diversity.gif
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)

Abstract

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.

Science Page: EWMA by State

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 by our MSHMP team regarding the evolution of the EWMA by state. The states of Illinois, Iowa, Minnesota, Nebraska, North Carolina, and Oklahoma are presented in today’s analysis.

Reminder: What is the EWMA?

The Exponential Weighted Moving Average (EMWA) is a statistical method that averages data over time, continually decreasing the weight of data as it moves further back in time.  An EWMA chart is particularly good at monitoring processes that drift over time and is used to detect small shifts in a trend.

In our project, EWMA is used to follow the evolution of the % of farms at risk that broke with PRRSV every week. EWMA incorporates all the weekly percentages recorded since the beginning of the project and gives less and less weight to the results as they are more removed in time. Therefore, the % of farms at risk that broke with PRRSV last week will have much more influence on the EMWA than the % of farms at risk that broke with PRRSV during the same week last year.

Key Points of the report:

  • Different states continue to have different EWMA patterns.
  • Even though winter is the high risk season, biosecurity measures should be enhanced during the whole year.
  • The state of Minnesota suffered two unusual peaks, one in spring and another one during the summer.
EWMA patterns by state
EWMA patterns by state

New position in Swine Health, Production and Economics at the UMN

Join the swine group at the College of Veterinary Medicine, University of Minnesota!

job opening UMN swineThe University of Minnesota has a new position open in swine health, production and economics.  We consider it an important position as we strive to integrate all our work into strategies and training that protect and improve the profitability of swine farms.  For those that are interested, please apply or contact John Deen.  If you know of someone who could be a good fit, please urge her or him to apply.  We appreciate the support that the swine group has received and we look forward to welcoming this new member to UMN.

You can read more about the position here or apply here.

We are excited to meet with you!

Science Page: Why are we not making more progress to decrease PRRS incidence?

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 by Dr. Clayton Johnson from Carthage Veterinary Services on PRRSV incidence and why it has not been decreasing as expected at the past few years.

Key points

  • Enhancing biosecurity increases the chances to prevent PRRS.
  • We have learnt to deal better with the disease and that is reflected by the reduction of the economic impact of PRRS
  • Choose the level of biosecurity that economically better fits to your risk.

In his report, Dr. Johnson identifies 3 main causes that PRRSV incidence is not decreasing.

  1. We can’t Prevent PRRS Infections
  2. PRRS Cost is Decreasing: Tools and Technologies for PRRS Infection Management are Improving
  3. PRRS Prevention Strategies aren’t Cost Effective

To learn more you can read the full report or take a look at Dr. Johnson’s presentation on this very same topic during the 2017 Leman conference:

Identification of antigenically important sites in Rotavirus B

Happy New Year to all of you readers of this blog! We appreciate your presence here. In 2018, we will bring you even more quality content related to swine health and production.

Our first publication of the year features the work of Frances Shepherd, a PhD student (who recently received an award at the CRWAD meeting) with Drs. Michael Murtaugh and Douglas Marthaler. The paper is in open access in the journal Pathogens and you can read it here.

Shepherd antigenically important sites in rotaviruses B

In this experiment, 174 clinical samples from US and Canadian swine herds and positive for rotavirus B by PCR were used to sequence the gene for the protein VP7.
VP7 is a protein of interest in rotaviruses B because it is structural and can be found on the outer layer of the virus capsid. Along with VP4, they stimulate the creation of neutralizing antibodies in pigs.

Based on those sequences, 169 of the viruses were allocated to 8 defined genotypes: G8, G11, G12, G14, G16, G17, G18, and G20. However, five strains had less than 80% similarity with those genotypes and were assigned to the new genotypes G22, G23 (2 strains), G24, and G25. The G16 genotype was the most prevalent genotype each year. The predominant genotypes clustered geographically, with G12 being predominant on the east coast, G16 in the Midwest, and G20 within the Great Plains states.

Rotaviruses B geographical distribution US
Distribution of Rotavirus B genotypes per state

Investigation of the variability within the VP7 proteins identified 8 variable regions. However, those regions did not align with the sites of high antigenicity detected in the predominant groups. Indeed, surface-exposed antigenic residues underwent negative selection more often than positive selection.

Abstract

Rotavirus B (RVB) is an important swine pathogen, but control and prevention strategies are limited without an available vaccine. To develop a subunit RVB vaccine with maximal effect, we characterized the amino acid sequence variability and predicted antigenicity of RVB viral protein 7 (VP7), a major neutralizing antibody target, from clinically infected pigs in the United States and Canada. We identified genotype-specific antigenic sites that may be antibody neutralization targets. While some antigenic sites had high amino acid functional group diversity, nine antigenic sites were completely conserved. Analysis of nucleotide substitution rates at amino acid sites (dN/dS) suggested that negative selection appeared to be playing a larger role in the evolution of the identified antigenic sites when compared to positive selection, and was identified in six of the nine conserved antigenic sites. These results identified important characteristics of RVB VP7 variability and evolution and suggest antigenic residues on RVB VP7 that are negatively selected and highly conserved may be good candidate regions to include in a subunit vaccine design due to their tendency to remain stable.