Science Page: Making epidemiological sense out of large datasets of PRRS sequences

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 epidemiological report regarding a large PRRS sequence dataset from Dr. Igor Paploski in the VanderWaal research group.

Key points:

  • Occurrence of PRRS lineages is not equal in different years, systems or production types
  • Occurrence of specific PRRS lineages is associated with movement of animals
  • Continuous surveillance for PRRS occurrence is important in understanding its determinants and might be able to provide insights that can
    help on its prevention

By utilizing a dataset of 1901 PRRS sequences provided by the Morrison Swine Health Monitoring Project (MSHMP) participants over 3 recent years, the spatiotemporal patterns in the occurrence of different lineages of PRRSV was described and the extent to which the network of pig movement between farms determines the occurrence of PRRS from similar lineages was investigated.

PRRS lineages occurred at different frequencies across geographically overlapping production systems. Preliminary analysis showed that the relative frequency in which specific lineages occur increase while others are decrease over time. The rate at which these changes occur appears to be system-specific. Some lineages were also more common in farms of specific production types (i.e. sow farm or nurseries). As expected, farms that were connected via pig movements were more likely to share the same lineages than expected by chance across all years.

These findings suggest that system-specific characteristics partially drive PRRS occurrence over time and across farms of different production types. Our results also
indicate that animal movement between farms is a driver of PRRS occurrence, strengthening this hypothesis of viral transmission.

Additional research is needed to quantify risks and develop mitigation measures related to animal movement.

Large PRRS sequencing dataset

Use of processing fluids and serum samples to characterize PRRSv dynamics in 3 day-old pigs

This new publication in Veterinary Microbiology describes the best methodology to monitor 3-day-old piglets for PRRS, using both serum and processing fluid samples. The first author of the publication is Dr. Carles Vilalta, member of the Morrison Swine Health Monitoring Program (MSHMP) team.

Key points

  • Processing fluids (PF) constitute a useful sample to detect PRRSV infections at processing.
  • PRRSV can circulate in the farm at a low prevalence, increasing the chances of a re-break.
  • Young parity female litters should be targeted for PRRSV detection.
  • Current practice to bleed 30 pigs could be underestimating PRRSV prevalence in the herd.
  • The decrease in sensitivity at the litter level can be compensated by sampling more litters to detect PRRSV at the herd level.

Methods

The study was conducted in a 6,000 sow farm with a PRRS stable status. Every 3 weeks, serum samples and processing fluids were collected from all piglets in 10 randomly chosen litters. This process was then repeated 8 times, meaning that the farm was monitored for a total of 24 weeks. All samples were tested via PCR. 3 samples with the lowest Ct value were tested by virus isolation and sequencing of the ORF5 gene was performed.

Results

10.6% of the piglets tested positive for PRRSv via serum PCR, representing 29.8% of the litters. The same number of litters tested positive via processing fluid PCR testing.

The percentage of processing fluid positive samples was significantly higher is parity 1 and 2 sows compared to parity 3 and older sows. Additionally, a significant association between parity and probability of detecting a positive pig was observed.

A significant higher proportion of positive serum samples was observed in males compared to females. A similar trend was obtained when comparing positive Ct values by gender with values from males being lower (i.e., higher viral load) than those from females.

ct value processing fluids versus serum samples PRRS
Cycle threshold (Ct) positive (≤35) and suspect (between >35 and 40) value distribution for serum (S, triangle) and processing fluid (P, circle) samples overtime (2, 5, 8, 11, 14, 17, 20 and 23 weeks post outbreak). Horizontal black lines indicate the mean Ct values for each week and sample type

Using a Ct value of 37, processing fluid samples had a Se and Sp of 87% (95% CI: 66%–97%) and 94% (95% CI: 85%–99%), respectively when compared with litter RT-PCR results obtained from individual serum samples. The total agreement between both tests was 92.2% and the positive and negative predictive values were 87% (95% CI: 66%–97%) and 94% (95% CI: 85%–99%), respectively. False negative processing fluids were identified in litters having 2 or less PRRSV positive piglets

The agreement between the PF and serum results was kappa = 0.81 (95% CI: 0.59–1.00). The difference in the proportion of positive samples between both types of sample was not statistically significant (McNemar test, p = 1).

Abstract:

Collection of serum samples of pigs at weaning to monitor for porcine reproductive and respiratory syndrome virus (PRRSV) has become a common practice to determine PRRSV herd infection status. Diagnostic sensitivity of this practice is low in herds undergoing PRRSV elimination once prevalence of infection is near zero. Thus, the goal of this study was to characterize the dynamics of PRRSV infection in 3 day-old pigs overtime using serum and serosanguineous fluids obtained as part of castration and tail docking practices (processing fluids (PF)). Secondary goal was to estimate sensitivity and specificity of PF in the 3 day old population. A 6000 breed-to-wean sow herd was monitored every three weeks for 23 weeks after a PRRSV outbreak by collecting both PF and individual serum samples from all pigs in the selected litters. Out of the 77 litters tested, 23 (29.8%) were identified as positive using the PF and the serum samples, with a Cohen’s kappa statistic of 0.81 (95% CI: 0.59–1) between the results obtained in each sample type. The sensitivity and specificity of the PF relative to the results in serum was 87% (95% CI: 66%–97%) and 94% (95% CI: 85%–99%) respectively. The percentage of PRRSV positive litters decreased over time and litters from gilts were more likely to test positive than those from older sows. Overall, the study demonstrates that PF can be a convenient and reliable specimen to monitor PRRSV infection in breeding herds.

Follow the link to read the entire article.

Science Page: Quarterly review of MSHMP reported PRRSv Restriction Fragment Length Polymorphism (RFLP) patterns

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 from the MSHMP team regarding reported PRRS RFLP patterns.

Keypoints:

  •  Recording PRRSv RFLP and sequences will provide better insights into the epidemiology of the disease at local, state and national level.
  • Building a RFLP database will allow us to assess which factors could be involved or related with the emergence of a new RFLP.
  • The predominant pattern RFLP in this quarterly review is the 1-7-4.

In the first quarter of the 2018/2019 incidence year, 20 breaks affecting 12 production systems were reported. Out of these, 4 occurred in July, 13 in August and 3 in September.

Of those 20 farms, three had a break while still being status 1, one was status 2 in the process of eliminating the disease (not using any immunization protocol at that point), 6 were using field virus as the acclimatization protocol (2fvi), 8 were using vaccine (2vx), one was provisionally negative (status 3) and one broke from a status 4 after being almost 4 years completely negative (see figure below).

RFLP patterns with status at break

The distribution of the breaks is wide and affects different states. Thus, we had 6, 1, 4, 1, 4, 2, 1 and 1 break in the states of IA, IN, MN, MO, NC, NE, OK and PA, respectively. The closest 2 farms that broke were 1.2 miles apart, belonged to the same company and had the break a week from each other (no sequences was provided).

Eight out of the 20 breaks reported were accompanied by the associated RFLP. The predominant (4 out of 8) RFLP pattern since July is 1-7-4. Iowa was the state with the highest number of 1-7-4 cases.

Porcine Circovirus 3: a new episode from At the meeting with… podcast

microphone-2618102_1920Podcasts are a perfect way to get caught up with new swine information! We are presenting you the latest episode from “At The Meeting… Honoring Dr. Bob Morrison” in collaboration with SwineCast.

In this episode of At the Meeting honoring Dr. Bob Morrison, we share a conversation on porcine circovirus 3, or PCV3.

Dr. Montse Torremorell joins Dr. Tom Wetzel and Dr. Gordon Spronk with special guest Dr. Darin Madson, Iowa State University, to talk about porcine circovirus 3 and how it is both similar to, and different from PCV2.

Dr. Madson and the show’s cohosts discuss clinical signs associated with PCV3, including myocarditis, respiratory issues, and reproductive problems, as well as how current research is focused on better understanding the virus, its history, and whether any current PCV vaccines could offer some form of cross-protection.

Listen to the entire episode (17 minutes)

Science Page: Remembering Professor Mike Murtaugh

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 remembering Professor Mike Murtaugh with Cheryl Dvorak.

Michael MurtaughProfessor Michael Murtaugh, PhD, passed away Tuesday September 18 from complications of pancreatic cancer. He was 67.

Mike joined the college in 1985 and spent the entirety of his University of Minnesota career in the Department of Veterinary and Biomedical Sciences. He was a consummate faculty member, excelling in teaching graduate courses and conducting research and
outreach. Mike authored more than 225 peer-reviewed journal articles, was the primary advisor for 30 Master’s and PhD students, and held three U.S. patents. His influence extended throughout the Academic Health Center at the University and throughout the world. At the time of his death, Mike was serving on the editorial boards of more than a dozen academic journals, and had successfully completed nearly 160 sponsored projects as Principal Investigator or Co-Investigator.

Mike was a respected and highly sought after mentor. He always had people coming and going from his office asking for scientific, career, and personal advice. His door was always open and he always stopped what he was doing to help others. He touched many
lives during his career. Besides his numerous graduate student advisees, he also mentored over fifteen veterinary students, thirty-six undergraduate and high school students, twelve post-doctoral researchers, twenty visiting scientists, and numerous others who came to him for advice and support. He cared about everyone not only scientifically, but also personally. He always wanted to do what was in a student’s best interests, even though it may not have been what was in his best interest. His lasting legacy is in the scientific training and education of a generation of swine health specialists and researchers.

Prof. Murtaugh was an international leader in swine immunology, and devoted considerable effort over the past 25 years in battling the Porcine
Reproductive and Respiratory Syndrome virus (PRRSv), a disease that
costs U.S. swine producers alone some $500 million annually. Mike used
molecular biological approaches to first understand the nature of PRRSv
and investigated in detail the immunological response of pigs to this pathogen.

Mike earned the B.S. degree in biology at the University of Notre Dame and
then served as a Peace Corps volunteer in Venezuela. He earned a Ph.D. in entomology at the Ohio State University. The University of Texas Medical School in Houston was his next stop— he spent four years in a post-doctoral position in the Departments of Internal Medicine and Pharmacology— before assuming a faculty position in St. Paul.

He will be remembered for his dry sense of humor and positive outlook on life, character traits that he maintained even as his battle with cancer raged. Mike cared passionately about science and derived some of his greatest personal satisfaction working on the college’s Strategic Plan and the International Conference on One Medicine and One Science (iCOMOS). Mike cared deeply about science informing policy and saw the need for scientists to be more actively involved in communicating about their research.

I am grateful to have known him, and stand in awe of the many contributions he made to our college.

Science Page: Basic Steps for Foreign Animal Disease Preparedness

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 one-page step-by-step reference document for foreign animal disease preparedness, created by the MSHMP team.

Key Points

  • The current African Swine Fever situation in China and Europe makes Foreign Animal Disease preparedness even more crucial.
  • There are steps that can be taken to prepare a site for a Foreign Animal Disease and to improve the probability of continued animal movement.
  • Many producers are already doing these steps in some form and taking the practices to the level of documentation can add benefits when dealing with other diseases such as PRRS and PED.

As African Swine Fever (ASF) has been moving rapidly through China and Europe, the possibility of a Foreign Animal Disease (FAD) event in the United States becomes more of a possibility. In the event of an FAD, state and federal animal health officials will limit movement of animals and animal products to limit disease spread.

Movement permit requirements are decided by regulatory officials from each state’s animal health department, but there are steps producers can take to help them mitigate chances of infection and to increase their likelihood of receiving a movement permit during an FAD. These steps are also outlined on the Secure Pork Supply (SPS) plan website. SPS is a collaboration between USDA APHIS, Pork Checkoff, Iowa State University, and the University of Minnesota.

Basic Steps:

Establishing location and site information:

A site must have a Premises ID Number (PIN) in order to move pigs or pig products. A PIN includes the 911 address and latitude and longitude coordinates of the actual location of the pigs. Having this information allows state and federal animal health officials to determine if a site is within control or quarantine zones based on its location to infected sites. The PIN is also imperative for allowing accurate tracking of pig and supply movement into the farm and identifying any connection to infected sites. It is important to validate that the location information points to the swine location and not an alternative house or building. Additionally, it is good to have information on farm contact such as manager and owner phone numbers and emails, number of animals, and if any other species are present on site.

Proof of biosecurity measures:

secure pork supplyBeing able to demonstrate the biosecurity measures of a production site will greatly improve permitting chances because good biosecurity helps ensure lower infection risk. The SPS supplies a biosecurity self-assessment checklist (http://www.securepork.org/Resources/SPS_Biosecurity_Self-Assessment_Checklist-_-IndoorProduction.pdf) covering the areas that should be included in a biosecurity plan. These areas are staff training, vehicles and equipment, personnel, wildlife and insects, manure management, carcass disposal, animal and semen movement, feed, and establishing protection of the pig herd such as a line of separation, perimeter buffer, disinfection station, and access points, including a map of the site. Being able to track movements in and out of the farm as well as between production sites is highly beneficial. A biosecurity manager should be appointed to write and manage the biosecurity plan.

Disease Monitoring and Epidemiological Information

In the event of an FAD, producers will be asked to provide epidemiological information and confirmation based on monitoring that there is no evidence of infection. Much of the epidemiological information that may be requested overlaps with the SPS biosecurity plan outline, such as knowing movement of equipment, incoming animals, products, and feed, and inter-site movement of personnel. Regular recorded monitoring of the animals allows a producer to provide confirmation that no clinical signs of an FAD have been observed. To make this effective, staff performing the monitoring must know how to identify the diseases and records must be consistent. Additionally, samplescan be stored and used to prove that the herd has been and remains negative. The SPS provides resources in both Spanish and English detailing disease identification for FAD’s, an example questionnaire of epidemiological information that may be requested, and resources for disease monitoring and emergency response.These resources can be found at http://www.securepork.org/pork-producers/disease-monitoring/ and http://www.securepork.org/Resources/SecurePorkSupply-Questionnaire.pdf .

These steps can be labor intensive with no clear immediate return, particularly the development of a biosecurity plan and regular monitoring records. This understandably can make them a low priority as producers deal with many resource decisions and demands on a daily basis.In light of this, it is important to remember that having these steps prepared will be invaluable for maintaining animal movement and continuity of business in the case of an FAD. Many of the steps or questions being used in these tools, like awareness of movement into and out of the farm, regular monitoring for clinical signs, and good biosecurity measures are things producers often do already. These steps simply put them into finalized and recordable forms. The process can also benefit the farm by showing biosecurity gaps and improving monitoring practices and records that are relevant to diseases such as PRRS, PED, and influenza.

Find more info about SPS at: http://www.securepork.org/

The 2018 Allen D. Leman Swine Conference successfully continued its tradition of high-quality content while innovating

The 2018 edition of the Allen D. Leman swine conference held in St. Paul, MN continued to offer a wide range of high-quality, science-driven presentations while innovating on several aspects of its program.

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Megan Bloemer (right) receives the Morrison Swine Innovator Prize from Dr. Perle Boyer (left)

This year marked the second year of the DVM student session at the Leman conference but the first time that a student received the Morrison Swine Innovator Prize. Megan Bloemer, a student from the University of Illinois was truly honored to be the first recipient of this prestigious recognition. Megan received a $7,500 scholarship in addition to participating in an exclusive workshop with the other DVM students-presenters. The quality of the students’ presentations was excellent but the practicality and the innovation with which Megan treated the issue of truck wash biosecurity put her at the top.

Sunday afternoon, the new Beer and Bacon conversation series was launched. The session, during which Dr. Matthew Turner was interviewed by Dr. Marie Culhane, was extremely popular. Seating was limited so do not forget to register early if you would like to attend next year!

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Dr Rebecca Robbins (left), Science in Practice awardee and Dr. Montse Torremorell (right)

We celebrated Dr. Rebecca Robbins for her well-deserved recognition as the Science  in Practice awardee of the year. The reception held in the Science museum in St Paul was sponsored by Boehringer Ingelheim.

 

The spread of African Swine Fever in China and Western Europe prompted us to dedicate two very well-attended sessions on this topic. The first session on Monday afternoon coordinated by Dr. John Deen included a summary of what is known about the disease by Dr. Chris Oura, then a clinical case experienced in Russia by Dr. Gustavo Lopez and a presentation by Patrick Webb on ASF awareness in the industry and beyond. On Tuesday, Dr. Scott Dee presented his latest research on the risk from feed ingredients for the transmission of ASF.

For more information, the University of Minnesota launched two webpages:

The 2018 Allen D. Leman conference continued to propose high quality keynote speakers.
Dr. Brad Freking and Dr. Deb Murray from New Fashion Pork gave the first Morrison lecture and presented their vision of pig farming. They explained how they chose to decrease their antimicrobial usage while reserving the right to treat pigs when needed and why they launched Old Fashion Pork.

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Dr. Maria Pieters presenting

Dr. Maria Pieters reminded us of the issues associated with having a Mycoplasma hyopneumoniae  positive herd and challenged the swine industry to eradicate the diseases that can be eradicated so that we can focus on diseases that are harder to control.

Becca Martin and Randy Spronk gave an update on trade in pigs and the current challenges that we are facing as an exporting nation. Free trade seems to be the best option for our producers in order to maintain the market.

Dr. Michael Rahe presented the Pijoan lecture on behalf of Dr. Michael Murtaugh giving us a overview of the past 30 years dealing with PRRS. Sadly, Dr. Murtaugh passed away that very same day, from his battle with cancer.

As always, we would like to thank all of you for your continuing support. The Allen D. Leman swine conference would not exist without you and we hope to see you next year: September 14-17, 2019.

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