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: Detecting influenza virus with a portable device

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.

We are presenting today the work done in Dr. Cheeran’s lab on the detection of influenza virus in farms. The objective of their research project is to develop a portable diagnostic platform that is capable of performing on-site testing of influenza viruses in swine with minimum sample handling and laboratory skill requirements.

The device is using giant magnetoresistance (GMR) technology. In a nutshell, if influenza viruses are present in the sample, they will bind to sensors, cause a disruption in resistance, and create an electric signal in the device that will be able to wirelessly transmit the result to a smartphone or computer.

Key points from this week edition:

  • Portable, hand held device for detection of influenza A virus (IAV) based on giant magnetoresistance (GMR) biosensor has been developed.
  • Although in its developmental stage, if successful this test has the potential for rapid on-site testing of influenza viruses in swine.

The first sensitivity tests of the device look very promising!

Air samples successful in detecting on-farm PRRSV, PEDV, and high-path avian influenza virus

Reducing the likelihood of a piglet reservoir when dealing with influenza in swine herds

Drs. White, Torremorell and Craft from the University of Minnesota recently published an article in Preventative Veterinary Medicine regarding practices that can decrease the likelihood of creating an endemic piglet reservoir in the case of an infection by swine influenza. Indeed, a stochastic model was developed considering that the pigs were in one of the following categories: Susceptible, Exposed,  Infectious, Recovered, or Vaccinated. Loss of immunity over time and differences between naturally infected and vaccinated animals were taken into account. Several scenarios were evaluated regarding their impact on piglet prevalence: timing of gilt introductions, gilt separation, gilt vaccination upon arrival, early weaning, and sow vaccination strategies.

In this model, homologous mass vaccination and early weaning were the most efficacious interventions. By combining frequent homologous mass vaccination, early weaning, gilt separation, gilt vaccination and longer periods between gilt introductions reduced endemic prevalence overall by 51% relative to the null scenario and the endemic prevalence in piglets by 74%.


Abstract: Recent modelling and empirical work on influenza A virus (IAV) suggests that piglets play an important role as an endemic reservoir. The objective of this study is to test intervention strategies aimed at reducing the incidence of IAV in piglets and ideally, preventing piglets from becoming exposed in the first place. These interventions include biosecurity measures, vaccination, and management options that swine producers may employ individually or jointly to control IAV in their herds. We have developed a stochastic Susceptible-Exposed-Infectious-Recovered-Vaccinated (SEIRV) model that reflects the spatial organization of a standard breeding herd and accounts for the different production classes of pigs therein. Notably, this model allows for loss of immunity for vaccinated and recovered animals, and for vaccinated animals to have different latency and infectious periods from unvaccinated animals as suggested by the literature. The interventions tested include: (1) varied timing of gilt introductions to the breeding herd, (2) gilt separation (no indirect transmission to or from the gilt development unit), (3) gilt vaccination upon arrival to the farm, (4) early weaning, and (5) vaccination strategies of sows with different timing (mass and pre-farrow) and efficacy (homologous vs. heterologous). We conducted a Latin Hypercube Sampling and Partial Rank Correlation Coefficient (LHS-PRCC) analysis combined with random forest analysis to assess the relative importance of each epidemiological parameter in determining epidemic outcomes. In concert, mass vaccination, early weaning of piglets (removal 0–7 days after birth), gilt separation, gilt vaccination, and longer periods between introductions of gilts (6 months) were the most effective at reducing prevalence. Endemic prevalence overall was reduced by 51% relative to the null case; endemic prevalence in piglets was reduced by 74%; and IAV was eliminated completely from the herd in 23% of all simulations. Importantly, elimination of IAV was most likely to occur within the first few days of an epidemic. The latency period, infectious period, duration of immunity, and transmission rate for piglets with maternal immunity had the highest correlation with three separate measures of IAV prevalence; therefore, these are parameters that warrant increased attention for obtaining empirical estimates. Our findings support other studies suggesting that piglets play a key role in maintaining IAV in breeding herds. We recommend biosecurity measures in combination with targeted homologous vaccination or vaccines that provide wider cross-protective immunity to prevent incursions of virus to the farm and subsequent establishment of an infected piglet reservoir.

Link to the full article

Which air sampler to detect swine airborne viruses?

This is the question that Drs. Carmen Alonso, Sagar Goyal, Peter Davies, and Montse Torremorell from the College of Veterinary Medicine studied in collaboration with Drs. Bernard Olson and Peter Raynor from the College of Science and Engineering and the School of Public Health respectively,  in the following paper published in Aerosol Science and Technology this past month.

In this study, the team form the University of Minnesota compared the capacity of two different air samplers to detect PRRSv and SIV in an experimental setting. The challenge to detect viral aerosol is to find a technique capable of capturing small amount of virus in a large amount of air. This experiment found that the particle size, the media used for collection as well as the extraction technique (passive or active) all had a significant effect on the detection of the viruses.


Abstract: Detection and quantification of dilute viral aerosols, as encountered outside animal housing facilities, requires methods that are able to detect small numbers of viruses in large volumes of air. This study compared the performance of two size-differentiating cascade impactors; an Andersen 8-stage (ACI; 28.3 L/min) and a high volume Tisch (TCI; 1,133 L/min) to assess sampling efficiency for detecting porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV). Samples of particles sorted by aerodynamic diameter were analyzed by quantitative polymerase chain reaction (qPCR) and collection efficiency was assessed by particle size. Collection media (minimum essential medium [MEM] and beef extract [BE]), elution technique (active versus passive), and sampling times (10, 20, and 30 min) were variables assessed for the TCI sampler. Extraction efficiency was 35% higher with BE as compared to that of MEM (p = 0.0007); active extraction technique was 19% more efficient than the passive technique (p = 0.03); time of sampling did not significantly affect the amount of virus recovered. The ACI sampler was more efficient in detecting both viruses from small and medium sized airborne particles (≤3 μm) as compared to the TCI sampler (p < 0.001). The latter sampler, however, was more efficient at IAV detection from large airborne particles (>3 μm) (p = 0.0025) indicating the potential of this sampler in detecting the presence of small amounts of viruses in aerosols under field conditions.

Link to the full article

Airborne transmission of highly pathogenic avian influenza during the 2015 outbreak in the Midwest

In 2015, the Midwestern part of the United States was the theater of an outbreak of a highly pathogenic strain of avian influenza. Drs. Torremorell, Alonso and Davies from the University of Minnesota were involved during the epidemic and just published in Avian Diseases and their findings concerning the airborne transmission of the virus were just published in Avian Diseases.

The study showed that the air exhausted from an infected poultry facility was a source of contamination for the environment but also a risk of transmission for Highly Pathogenic Avian Influenza (HPAI) that needs to be seriously taken into consideration. Indeed, live and infectious virus was found at a distance up to 70m (76.5 yards) from the farm facilities.


Abstract: We investigated the plausibility of aerosol transmission of H5N2 highly pathogenic avian influenza (HPAI) virus during the 2015 spring outbreaks that occurred in the U.S. midwest. Air samples were collected inside and outside of infected turkey and layer facilities. Samples were tested to assess HPAI virus concentration (RNA copies/m3 of air), virus viability, and virus distribution by particle size. HPAI virus RNA was detected inside and up to 1000 m from infected facilities. HPAI virus was isolated from air samples collected inside, immediately outside, up to 70 m from infected facilities, and in aerosol particles larger than 2.1 lm. Direct exposure to exhausted aerosols proved to be a significant source of environmental contamination. These findings demonstrate HPAI virus aerosolization from infected flocks, and that both the transport of infectious aerosolized particles and the deposition of particles on surfaces around infected premises represent a potential risk for the spread of HPAI.

Link to the full text

Effect of electrostatic particle ionization technology on swine airborne pathogens

Dr. Alonso who just graduated from her PhD at the University of Minnesota, published in collaboration with Drs. Davies, Morrison and Torremorell an article evaluating the electrostatic particle ionization (EPI) technology as a technique to reduce  particle load in the air. The results showed that EPI was the most efficient when the system was close to the particle source and when the particle size was between 3.3 and 9 μm no matter what swine pathogen was evaluated. This technique could be promising in decreasing the risk of disease transmission between swine facilities.

Alonso ionization technology 2016

Abstract Influenza A virus (IAV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and Staphylococcus aureus are important swine pathogens capable of being transmitted via aerosols. The electrostatic particle ionization system (EPI) consists of a conductive line that emits negative ions that charge particles electrically resulting in the settling of airborne particles onto surface s and potentially decreasing the risk of pathogen dissemination. The objectives of this study were to determine the effect of the EPI system on the quantity and viability of IAV, PRRSV, PEDV and S. aureus in experimentally generated aerosols and in aerosols generated by infected animals. Efficiency at removing airborne particles was evaluated as a function of particle size (ranging from 0.4 to 10 μm), distance from the source of ions (1, 2 and 3 m) and relative air humidity (RH 30 vs. 70 %). Aerosols were sampled with the EPI system ‘‘off’ and ‘on.’ Removal efficiency was significantly greater for all pathogens when the EPI line was the closest to the source of aerosols. There was a greater reduction for larger particles ranging between 3.3 and 9 μm, which varied by pathogen. Overall airborne pathogen reduction ranged between 0.5 and 1.9 logs. Viable pathogens were detected with the EPI system ‘‘on,’ but there was a trend to reducing the quantity of viable PRRSV and IAV. There was not a significant effect on the pathogens removal efficiency based on the RH conditions tested. In summary, distance to the source of ions, type of pathogen and particle size influenced the removal efficiency of the EPI system. The reduction in inf ectious agents in the air by the EPI technology could potentially decrease the microbial exposure for pigs and people in confinement livestock facilities.

Link to the full article