Science Page: Update on EWMA all versus EWMA original 13

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 an update on the EWMA comparison by the MSHMP team.

Key points:

  • Even though small differences between both EWMAs exist, the EWMA of the original 13 participating systems is still a good indicator of the overall PRRS EWMA.
  • Questions from participants are always welcome and help us to provide answers and insights to all of you.

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.

EWMA vs EWMA 13

Results from this year’s comparison

EWMA 13 is still a good representation of the overall EWMA. The reason that the EWMA 13 is still representative may be because they cover a wide area of the States and they still represent a high percentage of the final EWMA. A minor difference occurred in 2017’s summer as some farms of the 13 experienced outbreaks. However, as we have discussed in previous science pages each state or region seems to have a different EWMA pattern.

Last year comparison of the EMWA

Production Losses From an Endemic Animal Disease: PRRS in Selected Midwest US Sow Farms

In this publication in Frontiers in Veterinary Science, Drs. Valdes-Donoso from UC Davis and Andres Perez from the Center of Animal Health and Food Safety (CAHFS) at the University of Minnesota, measured the impact of Porcine Reproductive and Respiratory Syndrome (PRRS) on the production of weaned pigs.

To do so, they monitored 16 different sow farms, all parts of a single production system in the Midwest for 48 weeks and recorded a total of 8 indicators:

  • number of weaned pigs
  • number of stillbirths per litter
  • number of live births per litter
  • number of pre-weaned dead
  • number of sows farrowing
  • number of sows repeating service
  • number of sows aborting
  • number of sows dead

For each farm and each indicator, the 12 weeks before the outbreak served as a baseline for the farm performances and the data was recorded until 35 weeks post outbreaks. All of the outbreaks occurred during the second half of 2014. The inventory of the farms varied between 2,714 and 6,009 breeding females.

The following figure represented the weekly average for the 8 recorded parameters from 12 weeks pre-outbreak to 35-weeks post-outbreak.

Perez PRRS sow farm losses Midwest

Based on these results, it was estimated that a PRRS outbreak caused a 7.4% decrease in weaned pigs per sow year, i.e., 1.92 fewer weaned pigs per breeding unit. In an average sized farm of this firm, the slight reduction in farrowing yielded a decline of 249 fewer farrows per year. The chances that a sow repeats service increased by 37%, while aborted fetuses increased by 26% in a year with a PRRS outbreak.

The primary estimate (using 12 weeks as pre-outbreak period) is that PRRS reduced weaned pig production per farm by 7.4% on an annual basis, leading to a decrease in output value per sow year of $86.6, or $367,521 per farm year for an average sized farm. If instead we assume the outbreak began in t −1 (i.e., using 11 weeks as pre-outbreak period), the estimated reduction in weaned pig production was 7.6%, or $88.8 less per sow year and an average revenue loss of $376,773 among the farms studied.

Results showed that weaned pig production declined in week − 1, although statistically insignificant, as did several performance indicators. The data suggest that the average PRRS outbreak in this set of farms began at least one week before it was announced.”

The rise in abortions was the strongest signal of PRRSV activity in our data. Increased surveillance, particularly to rising abortions, may allow farms to identify PRRS more quickly.

The length of PRRS outbreaks, as well as their effects over time, is highly variable. The results of this study demonstrate that PRRS has a negative effect on weaned pig production for a longer time than previously estimated. Indeed, the estimated means of weaned pig production remained below the baseline throughout the 35 weeks that we are able to observe following the outbreak.

For more details, read the open-access publication on the Frontiers in Veterinary Science website.

Abstract:

Porcine reproductive and respiratory syndrome (PRRS) is an endemic disease causing important economic losses to the US swine industry. The complex epidemiology of the disease, along with the diverse clinical outputs observed in different types of infected farms, have hampered efforts to quantify PRRS’ impact on production over time. We measured the impact of PRRS on the production of weaned pigs using a log-linear fixed effects model to evaluate longitudinal data collected from 16 sow farms belonging to a specific firm. We measured seven additional indicators of farm performance to gain insight into disease dynamics. We used pre-outbreak longitudinal data to establish a baseline that was then used to estimate the decrease in production. A significant rise of abortions in the week before the outbreak was reported was the strongest signal of PRRSV activity. In addition, production declined slightly one week before the outbreak and then fell markedly until weeks 5 and 6 post-outbreak. Recovery was not monotonic, cycling gently around a rising trend. At the end of the study period (35 weeks post-outbreak), neither the production of weaned pigs nor any of the performance indicators had fully recovered to baseline levels. This result suggests PRSS outbreaks may last longer than has been found in most other studies. We assessed PRRS’ effect on farm efficiency as measured by changes in sow production of weaned pigs per year. We translated production losses into revenue losses assuming an average market price of $45.2/weaned pig. We estimate that the average PRSS outbreak reduced production by approximately 7.4%, relative to annual output in the absence of an outbreak. PRRS reduced production by 1.92 weaned pigs per sow when adjusted to an annual basis. This decrease is substantially larger than the 1.44 decrease of weaned pigs per sow/year reported elsewhere.

Science Page: Effective disease surveillance and response strategies depend on detailed swine shipment data

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 use of swine shipment data for effective disease surveillance by Drs. Amy Kinsley, Meggan Craft, Andres Perez, and Kim VanderWaal.

Key point:

  • A production system’s vulnerability to disease spread can be greatly reduced when selectively identifying a subset of farms as disease control targets.

What was done:

In this study, we used a network approach to describe annual movement patterns between swine farms in three multi-site production systems (1,063 farms) in the United States.

We measured:

  1. degree: number of farms to which a farm ships or receives pigs
  2. farm’s individual contribution to disease spread via its movements
  3. mean infection potential (MIP), which measures potential incoming and outgoing infection chains

What was found:

Removing farms based on their mean infection potential substantially reduced the potential for transmission of an infectious pathogen through the network when compared to removing farms at random, as shown by a reduction in the magnitude of R0 attributable to contact pattern.
The MIP was more efficient at identifying targets for disease control compared to degree and farm’s contribution to disease spread.

What does this mean?

By targeting disease interventions towards farms based on their mean infection potential, we can substantially reduce the potential for transmission of an infectious pathogen in the contact network, and performed consistently well across production systems.
Fine-scale temporal movement data is important and is necessary for in-depth understanding of the contact structure in developing more efficient disease

 

 

 

Science Page: Comparison of individual oral fluids, pooled oral fluids and Swiffer™ environmental samples of drinkers for the detection of influenza A virus and PRRS virus by PCR

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 study done by Taylor Homann, a DVM student at the University of Minnesota in collaboration with the Swine Vet Center and Boehringer Ingelheim, regarding the comparison of several sample types to detect PRRS and flu by PCR.

Key points:

  • Pooling oral fluid samples seems to be a good strategy to determine the status of a farm (positive/negative) for influenza A virus (IAV) and PRRSV.
  • Sampling water cups using environmental Swiffer™ samples appears to be a sensitive approach to detect IAV at the pen level.
  • However, sample size has been limited to one farm.

Objective:

The objective of this project was to compare the sensitivity of pooled pen oral fluids (OF) and environmental samples (Swiffer™ kits on water cups) using individual pen oral fluids as the standard.

Methods:

Fifteen paired environmental and individual pen OF were collected at days 3, 7, 10, 17, 24 and 31 post placement in two different nursery farms. Environmental samples (ES) were taken using Swiffer™ cloths to sample the bottom of water cups (both pans and bowls), focusing around nipples. After individual samples were collected, pen OF were pooled by 3.

Results:

There was an overall sensitivity of 71% (IAV) and 14% (PRRS) for the ES samples compared to individual OF. Pooled oral fluids samples had an overall sensitivity of 50%(IAV)and 80%(PRRSV)relative to individual pen OF.

Homann PRRS flu Oral fluid water cup sample comparison

In summary, ES appears to be a good strategy when sampling for IAV and not a reliable option when trying to diagnose PRRSV.

Science Page: PRRS incidence in status 4 sow farms

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 the MSHMP team on PRRS incidence in status 4 sow farms.

Key points

  • In the last 9 years, on average 10.2% (Range 3.7% – 22%) of status 4 farms have had a PRRS outbreak during the MSHMP season and in the 2017-2018 season, the cumulative incidence (July to April) is 9.6%.
  • The lowest PRRS incidence was observed during the 2013/2014 PRRS season; the year that PED entered the US.
  • PRRS incidence in status 4 farms during the current MSHMP season is not higher than the ones observed in the previous MSHMP seasons.

Reminder: Status 4 sow farms are the farms that considered negative both in shedding and exposure status in the classification document published by the AASV.

Objective

Has there been an increase in PRRS outbreaks incidence in status 4 sow farms?

Method

PRRS incidence in status 4 farms from 2009 to April 2018 was compiled and compared with the current MSHMP year using Fisher’s Exact test.

Results

During the current MSHMP year (July 2017- April 2018), 27 status 4 farms have had a PRRS outbreak (6.9% incidence). The average incidence of status 4 farms from 2009 to April 2018 was 9.6%. However, PRRS incidence have varied greatly among years (figure 1). PRRS incidence had its minimum value during the 2013/2014 MSHMP season with a 3.4%. This coincides with the year that porcine epidemic diarrhea virus (PEDv) entered the US.

When comparing the incidence during the 2017/2018 MSHMP year with the incidence observed during the 2015/2016 MSHMP year, a borderline significant difference (p=0.06) was observed.

PRRS incidence in status 4 sow farms
Figure 1. Percentage of PRRS incidence in Status 4 farms by year (July-April)

Summary

PRRS incidence in status 4 farms (July 2017 –April 2018) was overall similar to previous years, although slightly higher than July 2016-April 2017, and significantly lower than July 2015-April 2016. Other factors, such as region, may be contributing to the
perception of increased PRRS incidence in status 4 farms.Exploring these factors may help explain the perception of increased
incidence.

Science Page: Sow Farm PRRS status classification survey

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 survey from the MSHMP team on the different protocols used to classify PRRS status.

Key points

  • The majority of veterinarians consider it important to classify sow herd PRRS status.Our survey showed that 8/21 follow AASV guidelines, with the others using alternative criteria.
  • Half of the surveyed veterinarians use processing fluids as part of their testing protocol for determining sow herd PRRS status.
  • Most of the respondents mentioned that AASV PRRS classification guidelines should be re-visited.

Twenty-one veterinarians from 12 participant systems and 1 non-participant group completed the questionnaire accounting approximately for 1.5 million sows.

When asked how important it was to classify sow farm PRRS status, 12/21 (57%) answered very important, 8/21 (38%) answered important. Among the most important reasons requiring PRRS status were:

  • Commingling of pigs downstream,
  • Timing the Depopulation/Re-population of growing sites with continuous flow, and
  • Defining gilt acclimation and introduction procedures.

The testing protocol to classify a farm as stable varied across and within systems. However, the most frequent sample collected was due-to-wean blood sampling. Other samples are shown in the figure below.

PRRS classification survey

 

Science Page: Assessment of PRRS area spread for sow herd outbreaks in US swine dense regions

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 project from Dr. Andreia Arruda in collaboration with the MSHMP team regarding Porcine Reproductive and Respiratory Syndrome virus (PRRSV) area spread for sow herd outbreaks in US swine dense regions.

Dr. Arruda has also been investigating PRRS seasonality in the US and how topography surrounding a farm influences outbreak risk.

Key points

  • Strong evidence of area spread was not found after evaluating three farm clusters located in two swine dense regions.
  • All barns of a nursery/finishing site should be sampled to define status.
  • Sick pen might not be the best target when sampling for PRRSV in grower pig sites

Background and Objectives

Area spread refers to the transmission of a pathogen (here PRRSV) through small particles in the air as well as through fomites on which the pathogen would have deposited on.

The objective of the study was to determine if the virus detected in a recently infected sow farm was similar to the one detected in neighboring farms (in other words: was local spread a likely source of infection?)

Methods and Results

35 farms were monitored for PRRSV. As soon as a farm broke, all of the neighboring farms were sampled for PRRSV independently of the type of production on site. If a sick pen was present on the farm, effort was made to include it in the sampling. Positive samples were then sequenced to compare to the original virus from the outbreak.

PRRS area spread arruda
Graphical representation of the results of one specific region.

For two of the three area spread assessments performed, no similar sequence to the one obtained from the farm under investigation was found. Also it was not always possible to detect PRRSV in sick pens of the growing pig sites sampled in our study.