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.