Several influenza A genotypes detected in the same farm, sub-population, and pig

In this collaborative open-access research article from the University of Minnesota, five commercial sow farms were sampled regularly over a year. Sows, gilts, and piglets was sampled with nasal swabs. A little less than 5% of the samples were PCR positive for influenza A. The strains were classified in 7 groups based on their hemagglutinin (a surface protein of the virus) sequences. One additional group was created based on another gene segment.

Complete genome sequencing influenza A Diaz 2017

Several viral groups were detected in the sub-populations of all of the 5 farms, as shown in the figure below. Influenza strains combined segments from several viral groups were detected in three farms. Additionally, several strains were detected in individual animals showing the potential for reassortment and creation of new influenza strains.

Complete genome sequencing influenza A Diaz 2017 group
Influenza viral groups (VG) detected in each farm sub-populations over time (PG:piglets, GL: gilts, NG: new gilts)   *: month during which sampling started.


Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, there is limited information on the genetic diversity of swine IAVs within farrow-to-wean farms, which is where most pigs are born. In this longitudinal study, we sampled 5 farrow-to-wean farms during a year and collected 4,190 individual nasal swabs from three distinct pig subpopulations. 207 (4.9%) samples tested PCR positive for IAV, and 124 IAVs were isolated. We sequenced the complete genome of 123 IAV isolates, and found 31 H1N1, 26 H1N2, 63 H3N2 and 3 mixed IAVs. Based on the IAV hemagglutinin seven different influenza A viral groups (VGs) were identified. Most of the remaining IAV gene segments allowed us to differentiate the same VGs although an additional viral group was identified for gene segment 3 (PA). Moreover, the co-detection of more than one IAV VG was documented at different levels (farm, subpopulation, and individual pigs) highlighting the environment for potential IAV reassortment. Additionally, three out of 5 farms contained IAV isolates (n=5) with gene segments from more than one VG, and 79% of all IAVs sequenced contained a signature mutation (S31N) in the matrix gene that has been associated with resistance to the antiviral amantadine. Within farms, some IAVs were only detected once while others were detected for 283 days. Our results illustrate the maintenance and subsidence of different IAVs within swine farrow-to-wean farms over time, demonstrating that pig subpopulation dynamics is important to better understand the diversity and epidemiology of swine IAVs.

IMPORTANCE At the global scale swine are one of the main reservoir species for influenza A viruses (IAVs), and play a key role on the transmission of IAVs between species. Additionally, the 2009 IAV pandemics highlighted the role of pigs in the emergence of IAVs with pandemic potential. However, limited information is available regarding the diversity and distribution of swine IAVs in farrow-to-wean farms where novel IAVs can emerge. In this study we studied 5 swine farrow-to-wean farms during a year and characterized the genetic diversity of IAVs among three different pig subpopulations commonly housed in this type of farms. Using next generation sequencing technologies, we demonstrated the complex distribution and diversity of IAVs among the pig subpopulations studied. Our results demonstrated the dynamic evolution of IAVs within farrow-to-wean farms, which is crucial to improve health interventions to reduce the risk of transmission between pigs and from pigs to people.

Link to the full open-access article

Science Page: Antibiotic susceptibility in Pasturella multocida and Streptococcus suis isolated at the Minnesota VDL

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.

Antimicrobial resistance has been a preoccupying topic for the past few years. We talked before about what the definition of antibiotic resistance is and how it can be interpreted in two different manners. This week, Dr. Alvarez from the STEMMA lab is reporting the trends in antimicrobial susceptibility observed in strains of Streptococcus suis and Pasteurella multocida isolated at the Minnesota Veterinary Diagnostic Laboratory over the past 10 years. S. suis and P. multocida are common swine pathogens that can cause severe economic losses. Knowing which antibiotics are more likely to be efficient against those bacteria can help in tackling the disease faster.

Key Points:

  • MN-VDL data was analyzed to study antibiotic susceptibility in clinical isolates of Pasteurella multocida and Streptococcus suis from 2006 to 2016.
  • Isolates were highly susceptible to Ampicillin, Ceftiofur, Enrofloxacin and Florfenicol throughout the study period.
  • There were no changes in antibiotic susceptibility against the antibiotics tested routinely across the study period.

The full report can be read here.

Guidelines for the DVM Student Session at the Leman Conference

Veterinary student, did you shadow a swine practitioner this summer or were involved in an interesting clinical case investigation? Did you work on your veterinary skills by designing a differential diagnosis list or working on a treatment plan? Did you investigate a problem by analyzing production records? We want to hear about it!

Call for case description:

The Allen D. Leman Swine Conference is organizing a session for veterinary students to demonstrate their problem-solving skills through the presentation of a case or experience where students challenged their clinical training and problem-solving capabilities necessary for day-to-day practice.
The session will take place on Sunday at the Allen D. Leman Swine Conference, from 1:00−2:45 p.m. at the Saint Paul RiverCentre and will include presentations from 7 veterinary students.

Case description guidelines and instructions:

  • This session primary goal is for students to identify a question they faced when they spent time in the swine industry. The question can relay to production issues (records analysis, performances) or to a clinical case. Some examples of relevant questions can be:
    • How to handle a respiratory case in finishing pigs?
    • What caused mortality observed in this farm?
    • Why did this farm production results drop between February and April?
    • How is the US swine industry different from the Brazilian one?
  • The case description must include the thought process and the steps followed by the student to solve/answer the question.
  • This session will reward students’ creativity: the use of new support material (video files, interviews) is encouraged and will be rewarded. Explain in the case description how you may incorporate this aspect in your presentation.

Submission process:

Submit your one-page case description (one column, font size 11) to Dr. Perle Boyer, by Tuesday, August 15 at midnight and you will be notified by Friday, September 1 whether your presentation has been selected. An optional file can be sent as an appendix to demonstrate creativity.


Students invited to present will receive a $1,000 stipend, free admission to the Leman Swine Conference, and a copy of the Diseases of Swine book (10th edition).

Infection dynamics and genetic variability of Mycoplasma hyopneumoniae in self-replacement gilts

This is a new research paper from the MycoLab under Dr. Maria Pieters’ supervision. In this study, the group looked at the infection dynamics and genetic variability of Mycoplasma hyopneumoniae in self-replacement gilts, in 3 positive herds. Serum samples were taken from the gilts at 150 days of age onward and laryngeal swabs were collected from the gilts and their progeny.

Highlights of this project

  • Genetic variability of M. hyopneumoniae was evaluated using MLVA typing.
  • The highest M. hyopneumoniae prevalence in gilts was detected at 150 days of age.
  • Detection patterns for M.hyopneumoniae were different among farms.
  • Genetic variability was identified within and among farms.


Pieters 2017 infection dynamics Mhyop


The aim of this study was to assess the longitudinal pattern of M. hyopneumoniae detection in self-replacement gilts at various farms and to characterize the genetic diversity among samples. A total of 298 gilts from three M. hyopneumoniae positive farms were selected at 150 days of age (doa). Gilts were tested for M. hyopneumoniae antibodies by ELISA, once in serum at 150 doa and for M. hyopneumoniae detection in laryngeal swabs by real time PCR two or three times. Also, 425 piglets were tested for M. hyopneumoniae detection in laryngeal swabs. A total of 103 samples were characterized by Multiple Locus Variable-number tandem repeats Analysis. Multiple comparison tests were performed and adjusted using Bonferroni correction to compare prevalence of positive gilts by ELISA and real time PCR. Moderate to high prevalence of M. hyopneumoniae in gilts was detected at 150 doa, which decreased over time, and different detection patterns were observed among farms. Dam-to-piglet transmission of M. hyopneumoniae was not detected. The characterization of M. hyopneumoniae showed 17 different variants in all farms, with two identical variants detected in two of the farms. ELISA testing showed high prevalence of seropositive gilts at 150 doa in all farms. Results of this study showed that circulation of M. hyopneumoniae in self-replacement gilts varied among farms, even under similar production and management conditions. In addition, the molecular variability of M. hyopneumoniae detected within farms suggests that in cases of minimal replacement gilt introduction bacterial diversity maybe farm specific.

Access to the full version of the paper

Science Page: Are the farms that broke with PED the same?

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 proud to introduce a new chart in the Morrison’s Swine Health Monitoring Project. This new addition will be able to answer a common question regarding PEDV outbreaks:

Are the farms currently breaking with PEDV the same than the ones which broke in the past?

To interpret the figure, follows these steps.

  • Horizontal axis represents all the farms that borke with PEDV during the season 2016/2017, with each tick representing an individual farm
  • Vertical axis shows the previous seasons with 2016-2017 on top and 2012-2013 at the very bottom.
  • The color of the cell (year : farm) represents the number of outbreaks experienced; darker blue meaning more outbreaks.

Here is the example of this chart presented this week:

Outbreak history of farms that broke during the 2016-2017 season.

Key points:

The farms that break with PEDV do not appear to have a history of PEDV infections in the prior season.

Of the farms that broke during the 2016/17 season, only 5 (6.5%) of them had outbreaks during the previous season and 43 (56.6%) of them had broken at some point since 2013.

Only one farm has had an outbreak every year since the beginning of the epidemic in the US (season 2013/14).

The full report is available.

Dr. Cesar Corzo appointed as new Leman Chair in swine health and productivity

Cesar Corzo
Dr. Cesar Corzo, new Leman Chair

The University of Minnesota, College of Veterinary Medicine is happy to announce that Dr. Cesar Corzo has accepted an appointment to the Allen D. Leman Chair in Swine Health and Productivity effective October 2, 2017. The appointment is considered one of the most prestigious faculty positions in the world involving swine medicine. Corzo was selected following an international search.

Corzo has worked for Pig Improvement Company (PIC) since 2012, most recently as the manager of Latin America Health Assurance and Services Team. The focus of his recent work has been on the emergence of Senecavirus A in Colombia, investigating the likelihood of infection of breeding stock during transit, and strategies for monitoring PRRS and Mycoplasma hyopneumoniae naïve populations of pigs with current serologic tests.

The Leman Chair appointment returns Corzo to the University where he earned his Ph.D. in 2012. He also holds a Master’s from the University of Guelph, and his DVM from La Salle University in Bogota, Colombia. His career also includes a three-year term with Elanco Animal Health.

In his new role, Corzo intends to focus on current industry challenges including personnel turnover and biosecurity compliance, control of endemic bacteria and optimization of antimicrobial usage.Corzo  will play a major role in the Swine Health Monitoring program.

The Leman Chair in Swine Health and Productivity was created in 1995 to honor the career of Allen D. Leman. Those appointed to the chair serve for five years and are expected to significantly influence the swine industry’s adaptation to change. The individual also is expected to act as a catalyst for innovation and change within the University of Minnesota swine faculty.

Science Page: MSHMP Annual Summary

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.

The project runs from July 1st to June 30th so the year 2016-2017 just ended. Below are listed the main point for this year, more details can be found in the full report.

This year the Swine Health Monitoring Project was struck by the sudden and unexpected loss of Bob Morrison in a car accident in Prague. This was a major setback for the group and is a difficult challenge to overcome. However, we received the support of the industry to continue carrying on Bob’s legacy. Since last May the SHMP was renamed after him to Dr. Morrison’s SHMP (MSHMP).

Key points from this week edition:

  1. Monitoring pathogens
    • PRRS incidence (26%) remained stable over the last 2 years.
    • PEDv incidence remained low (7%), at the same level as last year.
    • Seneca Valley virus incidence appears to have a seasonal pattern.
    • Monitoring of VDL atypical CNS cases has been restarted.
  2. Analyzing PRRS virus sequences
    • It appears that there are several characteristic features that would signal emerging PRRSv strains, which may be used for early detection of significant emerging events.
    • Analyzed sequences coming from 3 systems to detect new emerging strains on a monthly basis.
  3. Capturing movement data and incorporating into data management capacity
    • Developed an app to capture truck movement.
    • Tested a first version of the app.
    • A second improved version will be tested shortly.
  4. Expanding enrollment
    • Added 4 production companies.
    • Currently 33 systems with 1,092 sow farms & 2.96 million sows.
    • 161 non participants receive weekly report.