A constellation of strains co-circulate in pigs during influenza epidemics

This recent publication in Nature comes from the Torremorell’s lab and aims at answering the question of the number of strains circulating in pigs during an influenza outbreak and how genetically different they may be. The full article is available in open access, click on the banner below to access it.

Constellation influenza banner Torremorell

To answer the question of multiple strains of influenza in pigs, the group followed a cohort of 132 pigs placed in a 2,200-head a wean-to-finish barn, endemic for influenza. All the pigs originated from the same sow farm . The history of past influenza episodes did not include any information regarding the strain of viruses circulating in the barn. Nasal swabs were collected for each individual pig and were tested in the laboratory by PCR.

Results from this study showed that:

  • Only 2 pigs out of 132 tested negative every week during the entire duration of the study.
  • Around 88% of the pigs tested positive for influenza more than once.
  • 20.5% of pigs were positive for influenza at weaning.
  • Weekly influenza prevalence ranged between 0% and 65%.
  • 3 different viral groups were identified VG1, VG2, and VG3.
  • Groups belonged to the swine H1-gamma, H1-beta and H3-cluster-IV influenza A respectively. (Here is a review of the H1 genetic clades and one of the H3 genotype patterns)

The figure below shows the genetic make up of the influenza strains isolated each week, the viral group each genetic segment belonged to and the number of times this specific combination was found.

For example, the second line can be interpreted as: during week one, one sample in which 10 sequences were recovered, had influenza virus with segments 1, 2, 3, 4, 5, and 7 belonging to the Viral Group 1 (H1 gamma) and segments 6 and 8 were from Viral groups 1 and 3.

Influenza constellation Torremorell

In conclusion, this study shows that influenza infections in pigs after weaning and under field conditions are complex. The influenza virus genome is diverse and changes rapidly. Prolonged persistence of influenza viruses in pigs could be the result of multiple influenza epidemic events that take place repeatedly over time or the re-infection with influenza viruses that are closely related to each other.


Swine play a key role in the ecology and transmission of influenza A viruses (IAVs) between species. However, the epidemiology and diversity of swine IAVs is not completely understood. In this cohort study, we sampled on a weekly basis 132 3-week old pigs for 15 weeks. We found two overlapping epidemic events of infection in which most pigs (98.4%) tested PCR positive for IAVs. The prevalence rate of infection ranged between 0 and 86% per week and the incidence density ranged between 0 and 71 cases per 100 pigs-week. Three distinct influenza viral groups (VGs) replicating as a “swarm” of viruses were identified (swine H1-gamma, H1-beta, and H3-cluster-IV IAVs) and co-circulated at different proportions over time suggesting differential allele fitness. Furthermore, using deep genome sequencing 13 distinct viral genome constellations were differentiated. Moreover, 78% of the pigs had recurrent infections with IAVs closely related to each other or IAVs clearly distinct. Our results demonstrated the molecular complexity of swine IAVs during natural infection of pigs in which novel strains of IAVs with zoonotic and pandemic potential can emerge. These are key findings to design better health interventions to reduce the transmission of swine IAVs and minimize the public health risk.

Longitudinal study of Senecavirus shedding and viremia in sows and piglets

How long do sows and piglets shed Senecavirus A after a clinical outbreak? How long is the viremia? Those are the questions answered in this case study of a Senecavirus A outbreak in one US farm.

Objective and Methods

Senecavirus A is a challenge for producers and veterinarians because of its clinical similarity to Food and Mouth Disease (FMD). In this study, 34 sows and 30 individual piglets from 15 different litters were sampled at day 1 post-outbreak and later at 1, 2, 3, 4, 6, and 9 weeks post-outbreak (PO). Serum, and tonsil, rectal, and vesicular swabs were collected for all of the pigs included in the study. The objective of the study was to explore the viremia and shedding patterns in those infected animals. All samples were submitted to the University of Minnesota, Veterinary Diagnostic Laboratory to be tested by PCR.

longitudinal study of senecavirus figures Tousignant 2017.gif
Percentage of serum (a), tonsil swabs (b), and rectal swabs (c) positive for Senecavirus A. Clinical outbreak happened in sow farm 1 (S1) and piglets from sow farm 2 (S2) were mixed with piglets from S1 at weaning.



Vesicular lesions were seen in sows only for 2 weeks and had the highest amount of virus. In sows, the detection of Senecavirus A in tonsil and rectal swabs was greater than 90% at 0 week PO and remained as high as 50% through 5 weeks PO. Generally, viremia was detected up to 1 week PO in sows but it is important to note that viremia was not detected in 11 out of 34 (32%) of the sows at any point during the study. Viremia was detected in 18 out of 30 (60%) and 19 out of 30 (63%) in the suckling piglets from site 1. Similar to sows, viremia was not detected in 9 out of 30 (30%) of the site 1 piglets enrolled in the study.

The detection of Senecavirus A in sows tonsil swabs peaked 1 week PO (94% positive) whereas it peaked at day 1 PO for piglets (83% positive). The detection of virus shedding decreased over time in sows and piglets, and a single sow and piglet tested positive at 9 weeks PO.

The peak of Senecavirus A detection from rectal swabs in sows (91%) occurred at day 1 PO and continued to steadily decrease and was not detected at 9 weeks PO. In site 1 piglets, the detection of SVA peaked at 1 week PO (90% positive). 64% of the rectal swabs were positive at 4 weeks PO in site 1 piglets. At 6 weeks PO, the detection of Senecavirus A was same for both site 1 and 2 piglets (11%); however, a single piglet from site 1 was still shedding SVA at 9 weeks PO.


The study assessed the shedding pattern of SVA in sows and piglets during an outbreak on a farm in the US and investigated the spread of SVA between pigs during the post weaning period. Vesicular lesions were seen in sows only for 2 weeks and had the highest amount of virus. In sows, the detection of SVA in tonsil and rectal swabs was greater than 90% at 0 week PO and remained as high as 50% through 5 weeks PO, these sample types should be collected and submitted, in addition to vesicular lesion swabs and fluid (if present), as part of FAD investigations for the detection of SVA.


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longitudinal study of senecavirus Tousignant 2017


Background: The study highlights the shedding pattern of Senecavirus A (SVA) during an outbreak of vesicular disease in a sow farm from the South-central Minnesota, USA. In this study, 34 individual, mixed parity sows with clinical signs of vesicular lesions and 30 individual piglets from 15 individual litters from sows with vesicular lesions were conveniently selected for individual, longitudinal sampling. Serum, tonsil, rectal, and vesicular swabs were collected on day 1 post outbreak, and then again at 1, 2, 3, 4, 6, and 9 weeks post outbreak. Samples were tested at the University of Minnesota Veterinary Diagnostic Laboratory for SVA via Real Time Polymerase Chain Reaction (RT-PCR)
Results: In sows, vesicular lesions had the highest concentration of SVA, but had the shortest duration of detection lasting only 2 weeks. Viremia was detected for 1 week post outbreak, and quickly declined thereafter. SVA was detected at approximately the same frequency for both tonsil and rectal swabs with the highest percentage of SVA positive samples detected in the first 6 weeks post outbreak. In suckling piglets, viremia quickly declined 1 week post outbreak and was prevalent in low levels during the first week after weaning (4 weeks post outbreak) and was also detected in piglets that were co-mingled from a SVA negative sow farm. Similar to sows, SVA detection on rectal and tonsil swabs in piglets lasted approximately 6 weeks post outbreak.
Conclusion: The study illustrates the variation of SVA shedding patterns in different sample types over a 9 week period in sows and piglets, and suggests the potential for viral spread between piglets at weaning.

How much floor space does a pregnant sow need in a group-housing system with electronic sow feeders?

Sows housed in groups at the UMN facility in Morris

The University of Minnesota – Morris owns a swine research facility which provides an excellent set up to study the behavior of sows housed in groups. In the past few years, swine producers have committed to change the conditions in which the sows are housed in farms and to keep them in groups where they can interact with each other instead of housing them individually. Putting sows in group reminded us that pigs need a hierarchy and that they will compete and fight to establish it. Because space allowance can impact sows behavior we wondered what the optimum floor space is.

Read the entire report on floor space allowance for sows by Dr. Yuzhi Li

Determining floor space allowance for gestating sows can be controversial because more floor space allowance means low output per square footage of the barn and will potentially reduce profitability for producers. On the other hand, floor space allowance less than sow requirement can compromise sow welfare and performance. To answer the question in the title of this article, we conducted a two-year project (titled ‘Determining the Minimal Floor Space Allowance for Gestating Sows Kept in Pens with Electronic Sow Feeders’). The project was partially sponsored by the National Pork Board, and the research team includes Yuzhi Li and Lee Johnston from the WCROC in Morris, and Sam Baidoo from the SCROC (Southern Research and Outreach Center) in Waseca.[…]


M.hyopneumoniae: knowledge gaps for improved disease control

Enzootic pneumoniae is a chronic respiratory disease caused by Mycoplasma hyopneumoniae in pigs. It has been present in the industry for decades and causes significant economic losses. Yet, control methods like vaccination have not been able to contain the disease. Why is that? What information are we missing to design more effective control methods? This is the goal of the review paper co-authored by Dr. Maria Pieters from the University of Minnesota.

Focusing on various aspects of the disease like epidemiology, pathogenicity, diagnostics, and control measures, this publication regroups all the knowledge we currently have of Mycoplasma hyopneumoniae and identifies what we need to investigate to improve disease control.

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Update on Mhyopneumoniae infections in pig Pieters 2017


Mycoplasma hyopneumoniae (M. hyopneumoniae) is the primary pathogen of enzootic pneumonia, a chronic respiratory disease in pigs. Infections occur worldwide and cause major economic losses to the pig industry. The present paper reviews the current knowledge on M. hyopneumoniae infections, with emphasis on identification and analysis of knowledge gaps for optimizing control of the disease. Close contact between infected and susceptible pigs is the main route of M. hyopneumoniae transmission. Management and housing conditions predisposing for infection or disease are known, but further research is needed to better understand M. hyopneumoniae transmission patterns in modern pig production systems, and to assess the importance of the breeding population for downstream disease control. The organism is primarily found on the mucosal surface of the trachea, bronchi and bronchioles. Different adhesins and lipoproteins are involved in the adherence process. However, a clear picture of the virulence and pathogenicity of M. hyopneumoniae is still missing. The role of glycerol metabolism, myoinositol metabolism and the Mycoplasma Ig binding protein—Mycoplasma Ig protease system should be further investigated for their contribution to virulence. The destruction of the mucociliary apparatus, together with modulating the immune response, enhances the susceptibility of infected pigs to secondary pathogens. Clinical signs and severity of lesions depend on different factors, such as management, environmental conditions and likely also M. hyopneumoniae strain. The potential impact of strain variability on disease severity is not well defined. Diagnostics could be improved by developing tests that may detect virulent strains, by improving sampling in live animals and by designing ELISAs allowing discrimination between infected and vaccinated pigs. The currently available vaccines are often cost-efficient, but the ongoing research on developing new vaccines that confer protective immunity and reduce transmission should be continued, as well as optimization of protocols to eliminate M. hyopneumoniae from pig herds.

What are the acclimation practices for Mycoplasma hyopneumoniae accross the EU?

This new publication in the Porcine Health Management journal is the result of a collaboration between the University of Barcelona in Spain, PIC (Pig improvement Company) and the MycoLab at the University of Minnesota.

321 farms were surveyed across Europe and Russia regarding their practices for gilt acclimation especially in the context of Mycoplasma hyopneumoniae. The farms are spread over 18 countries and this is reflected in the strong variation of the measures taken to acclimate the incoming gilt population.

Among the questions asked, the type of farm as well as the size of the herd were recorded. Regarding the gilts, the researchers took into account receiving schedule as well as origin and age in addition to the acclimation measures.

In the table below, you can see the summary of  the measures taken to acclimate the gilts to Mycoplasma hyopneumoniae. The vast majority of the herds (77%) used vaccination either as a single intervention or coupled with exposure to sows about to be culled.  Another popular option (22.4%) was no intervention at all.

Acclimation methods for Mycoplasma hyopneumoniae across the EU
Number of farms (%)according to the methods used for replacement gilt acclimation in terms of M. hyopneumoniae

Click on the table above to see the full open-access publication.


Gilts are considered to play a key role in Mycoplasma hyopneumoniae (M.hyopneumoniae) transmission and control. An effective gilt acclimation program should ideally reduce M. hyopneumoniae shedding at first farrowing, decreasing pre-weaning colonization prevalence and potential respiratory problems in fatteners. However, information on gilt acclimation practices is scarce in Europe. The aim of this study was to identify current acclimation strategies for M. hyopneumoniae in Europe using a questionnaire designed to assess 15 questions focused on gilt replacement status,
acclimation strategies and methods used to ascertain its effect. A total of 321 questionnaires (representing 321 farms) were voluntarily completed by 108 veterinarians (from 18 European countries). From these farms, 280 out of 321 (87.2%) were aware of the health status of gilts on arrival. From these 280 farms, 161 (57.5%) introduced M. hyopneumoniae positive replacements. In addition, 249 out of 321 (77.6%) farms applied an acclimation process using different strategies, being M. hyopneumoniae vaccination (145 out of 249, 58.2%) and the combination of vaccine and
exposure to sows selected for slaughter (53 out of 249, 21.3%) the most commonly used. Notwithstanding, only 53 out of 224 (23.6%) farms, knowing the M. hyopneumoniae initial status and performing acclimation strategies against it, verified the effect of the acclimation by ELISA (22 out of 53, 41.5%), PCR (4 out of 53, 7.5%) or both (27 out of 53, 50.9%). This study showed that three fourths of the farms represented in this European survey have M. hyopneumoniae acclimation strategies for gilts, and one fifth of them verify to some extent the effect of the process. Taking into account that the assessment of acclimation efficacy could help in optimizing replacement gilt introduction into the breeding herd, it seems these practices for M. hyopneumoniae are still poorly developed in Europe.

Link to the full open-access publication

Bioaerosol sampling for airborne virus surveillance in swine facilities

Bioaerosol sampling refers to the methods by which one is able to collect the particles of biological origin (microbial, animal, or plant) in the air. This is useful information in swine production because many economically important pathogens can be transmitted by air from one farm to the next. 73 scientific reports were included in this review published in the journal Frontiers in Veterinary Science. The information regarding the presence of viruses in the air around swine settings is limited but their findings has been compiled in the figure below. Overall, bioaerosol sampling could be a promising way to conduct non-invasive viral surveillance among swine farms.

Viruses detected in radisuses around farms
Influenza A, PRRSV, PEDV detection downwind from farms with infected source populations


Modern swine production facilities typically house dense populations of pigs and may harbor a variety of potentially zoonotic viruses that can pass from one pig generation to another and periodically infect human caretakers. Bioaerosol sampling is a common technique that has been used to conduct microbial risk assessments in swine production, and other similar settings, for a number of years. However, much of this work seems to have been focused on the detection of non-viral microbial agents (i.e., bacteria, fungi, endotoxins, etc.), and efforts to detect viral aerosols in pig farms seem sparse. Data generated by such studies would be particularly useful for assessments of virus transmission and ecology. Here, we summarize the results of a literature review conducted to identify published articles related to bioaerosol generation and detection within swine production facilities, with a focus on airborne viruses. We identified 73 scientific reports, published between 1991 and 2017, which were included in this review. Of these, 19 (26.7%) used sampling methodology for the detection of viruses. Our findings show that bioaerosol sampling methodologies in swine production settings have predominately focused on the detection of bacteria and fungi, with no apparent standardization between different approaches. Information, specifically regarding virus aerosol burden in swine production settings, appears to be limited. However, the number of viral aerosol studies has markedly increased in the past 5 years. With the advent of new sampling technologies and improved diagnostics, viral bioaerosol sampling could be a promising way to conduct non-invasive viral surveillance among swine farms.

Link to the full article

Translating big data into smart data for veterinary epidemiology: the MSHMP perspective

Big data can be defined as the daunting accumulation of abundant and diverse information. While recording data is the first step to measure progress or quickly identify an issue, the large amount of information collected can make it difficult to analyze.

At the University of Minnesota, one of the main projects using big data is the Morrison’s Swine Health Monitoring Program. This ongoing project collects veterinary reports and diagnostic results from numerous swine producers on a daily basis. The compiled information is then analyzed, interpreted and reported back as smart data to the participants every week. Smart data is commonly defined as a piece of information useful enough to make educated decisions.


Data pipeline utilized by the Morrison Swine Health Monitoring Project.jpg
Data pipeline used by the Morrison Swine Health Monitoring project for generating near real-time insight about the incidence of PRRSV


The increasing availability and complexity of data has led to new opportunities and challenges in veterinary epidemiology around how to translate abundant, diverse, and rapidly growing “big” data into meaningful insights for animal health. Big data analytics are used to understand health risks and minimize the impact of adverse animal health issues through identifying high-risk populations, combining data or processes acting at multiple scales through epidemiological modeling approaches, and harnessing high velocity data to monitor animal health trends and detect emerging health threats. The advent of big data requires the incorporation of new skills into veterinary epidemiology training, including, for example, machine learning and coding, to prepare a new generation of scientists and practitioners to engage with big data. Establishing pipelines to analyze big data in near real-time is the next step for progressing from simply having “big data” to create “smart data,” with the objective of improving understanding of health risks, effectiveness of management and policy decisions, and ultimately preventing or at least minimizing the impact of adverse animal health issues.

Review the full article