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.


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.


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.


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.

Influenza epidemiology in breed-to-wean farms and infection dynamics in nursery pigs

Fabian Chamba portrait photoEarlier this year, Dr. Fabian Chamba Pardo successfully defended his PhD under the supervision of Drs. Montse Torremorell and Marie Culhane. The focus of his thesis is influenza epidemiology with an emphasis on sow farms and nurseries. We share with you today a summary of his work.


Influenza is an economically important disease in pigs and a public health threat. Breed-to-wean (BTW) farms play a central role in influenza epidemiology and control because piglets maintain and disseminate influenza A virus (IAV) to other farms. Despite the importance of piglets in influenza epidemiology, there is limited information on IAV infection parameters in piglets, risk factors that impact IAV prevalence in piglets at weaning, and how strategies that are implemented in BTW farms affect IAV infections in weaned pigs.


In this thesis, my goal was to address some of the questions that are central to the transmission and control of influenza in BTW farms, especially infection in piglets ready to wean. The questions addressed are also critical to guide control strategies to mitigate IAV infections in the post weaning period. More specifically, I aimed to: 1) estimate herd-level prevalence and seasonality of influenza in BTW farms, 2) evaluate farm factors associated with IAV infection in piglets at weaning, 3) assess transmission patterns and parameters of influenza in nursery pigs based on IAV prevalence at weaning, and 4) evaluate the impact of maternally-derived antibodies (MDA) at weaning on IAV infection parameters in nursery pigs.

Research Chapter 1

Influenza herd-level prevalence and seasonality in breed-to-wean pig farms in the Midwestern United States

Article published in Frontiers in Veterinary Science:

Results showed that IAV herd-level prevalence in piglets at weaning from Midwestern BTW farms is seasonal with higher infection rates in winter (December) and spring (May) than those in summer and fall. Additionally, influenza seasonality was partially explained by the seasonal variations of outdoor air absolute humidity and temperature. Finally, there was significant genetic diversity of influenza strains circulating in those farms and that, co-circulation of more than one genetically distinct clade over time was very common in the studied farms. This is critical knowledge that may help to identify high risk periods where influenza control measures can be placed. It may also help to create research opportunities on absolute humidity and influenza transmission in pigs and finally, it supports other studies that have shown that genetic diversity and circulation is wide and common and that new vaccines and vaccination strategies should take that into consideration.

Chamba herd level influenza prevalence in the Midwest
Influenza A virus herd-level prevalence in Midwestern US breed-to-wean pig farms.

Research Chapter 2

Breed-to-wean farm factors associated with influenza A virus infection in piglets at weaning

In this chapter, there were 24 farm factors evaluated for their association with influenza at weaning and among those, only IAV sow vaccination and the IAV-negative status of replacement breeding females (gilts) at entry to the herd were significantly associated with less IAV infected piglets at weaning. This is critical information that veterinarians and producers may use to manage IAV levels at weaning. In addition, there was also a lack of significant association with factors such as air filtration and farm density which may be indicative that endemic influenza infections are more important than airborne lateral transmissions between farms. Finally, disease control strategies such as herd closure, early weaning, batch farrowing, gilt isolation and gilt influenza vaccination were not fully evaluated in this study. Hence, more work is needed to further understand how to use these strategies to decrease influenza infections in pigs.

sow vac protocol - Copy
Influenza A virus (IAV) positive mean predicted probabilities over time for breed-to-wean farms with different sow vaccination protocols.

 Research Chapter 3

Influenza A virus transmission patterns and parameters in growing pigs

Results indicate that groups of piglets with different prevalence at weaning had different transmission patterns and parameters after weaning and these patterns were characterized by 1, 2 or no peaks of infection after weaning. Piglets with low prevalence at weaning had less influenza infections in the nursery. This information may help producers and veterinarians to make informed decisions when it comes to use control strategies such as sow vaccination aimed to reduce influenza infections in the nursery.

Figure 1

Research Chapter 4

Effect of maternally-derived antibodies on influenza A virus infection in growing pigs

In my last chapter, I reported that if pigs had high levels of strain-specific maternally-derived antibodies at weaning, IAV infection occurred later and it was of shorter duration after weaning. Piglets with hemagglutination inhibition (HI) titers of 1:40 or higher were less likely to test IAV positive at weaning and during the nursery. These results indicate that strain-specific maternally-derived antibodies generated with sow vaccination pre-farrow significantly reduce influenza infections at weaning and in the nursery.

Figure 1 (1)


Knowledge of influenza seasonality and what factors are significantly associated with influenza in breed-to-wean farms can help producers and veterinarians to better use and allocate influenza control strategies such as sow vaccination. In addition, lower prevalence of influenza at weaning due to high strain-specific maternally-derived antibodies levels may help decrease influenza spread from wean-to-finish farms. Reducing the burden of influenza in growing pigs should decrease influenza-associated economic losses and the generation of novel strains, including strains with pandemic potential. More studies are needed to further elucidate control strategies to limit influenza infections and spread in pigs.

Science Page: Influenza herd-level prevalence and seasonality in Midwestern 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 from Dr. Fabian Chamba regarding influenza herd-level prevalence and seasonality in the Midwest.

Key points:

  • Influenza is endemic and seasonal in piglets from sow farms in the Midwest with higher infections in winter and spring.
  • Influenza seasonality was partially explained by outdoor air absolute humidity and temperature trends.
  • Influenza genetic diversity was high and co-circulation of more than one genetically distinct virus was common.

To study influenza levels over time and its seasonality, monthly testing data of piglets at weaning from 34 sow farms during ~5 years were analyzed.

There were 28% of positive submissions with a median influenza herd-level prevalence of 28%. Genetic diversity was significant with 10 genetically distinct clades of contemporary US swine influenza viruses as shown below. Furthermore, 21% of farms had 3 genetically distinct viruses circulating over time; 18% had 2, 41% had 1 and 20% had no isolates available.

In summary, influenza herd-level prevalence in Midwestern sow farms had a seasonal pattern with higher levels in winter and spring. This is important to better allocate influenza control strategies such as vaccination in sow farms. Influenza seasonality was partially explained by outdoor air absolute humidity and temperature although other factors such as immunity and new introductions may play a role in the observed seasonality.

Read the full story at

The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States

Today, we are sharing a recent publication on swine influenza in the Journal of General Virology. Dr. Marie Culhane from the University of Minnesota collaborated on this study of the genetic diversity of swine viruses in Canada and how it influences the strains found in the US.

The final data set included:

  • 168 genomes from Canadian swine influenza A viruses,
  • 5 genomes from highly under-represented US states (Alabama, Arkansas, Kentucky, Maryland and Montana),
  • 648 genomes from US and Canadian swine influenza A viruses (GenBank).

In total, these data represented 29 US states and 5 Canadian provinces.

Genetic diversity of influenza A viruses

In Canada, H1α viruses were the most frequently identified H1 viruses. In contrast, H1α viruses died out long ago in US herds, and have only been identified sporadically following new viral introductions from Canada. Notably, the two dominant H1 viruses in the United States, H1γ and H1δ-1, were not observed in any Canadian province during 2009–2016. In contrast to H1, H3 viruses are found in both the United States and Canada, with evidence of frequent cross-border transmission.

Sources of viral diversity

The study shows that the source of influenza viruses is aligned with pig movements. Indeed, Iowa and Minnesota receive around 87% of Manitoba swine exports. Therefore, the patterns of swine influenza viruses in those 2 US states correlate with the ones in Manitoba.

Similarly, viral gene patterns found in Illinois, Michigan, Wisconsin, or Ohio are influenced by the ones found in Ontario. Indeed, it only takes 3 hours to transport pigs from Ontario to Michigan. However, North Carolina and Virginia are the largest source of viruses for this region.


Left: Each region is shaded according to the proportion of total ‘Markov jump’ counts from that particular region into the Heartland: red, high proportion of jumps, important source of viruses; light yellow, low proportion of jumps, not an important source of viruses; black, destination. Right: US states are shaded according to the number of live swine imported from Manitoba in 2015 (per 1000 head)


Swine are a key reservoir host for influenza A viruses (IAVs), with the potential to cause global pandemics in humans. Gaps in surveillance in many of the world’s largest swine populations impede our understanding of how novel viruses emerge and expand their spatial range in pigs. Although US swine are intensively sampled, little is known about IAV diversity in Canada’s population of ~12 million pigs. By sequencing 168 viruses from multiple regions of Canada, our study reveals that IAV diversity has been underestimated in Canadian pigs for many years. Critically, a new H1 clade has emerged in Canada (H1α-3), with a two-amino acid deletion at H1 positions 146–147, that experienced rapid growth in Manitoba’s swine herds during 2014–2015. H1α-3 viruses also exhibit a higher capacity to invade US swine herds, resulting in multiple recent introductions of the virus into the US Heartland following large-scale movements of pigs in this direction. From the Heartland, H1α-3 viruses have disseminated onward to both the east and west coasts of the United States, and may become established in Appalachia. These findings demonstrate how long-distance trading of live pigs facilitates the spread of IAVs, increasing viral genetic diversity and complicating pathogen control. The proliferation of novel H1α-3 viruses also highlights the need for expanded surveillance in a Canadian swine population that has long been overlooked, and may have implications for vaccine design.

Flu control: it’s all about the piglet

Our latest collaboration with the National Hog Farmer was written by Drs. Montse Torremorell and Marie Culhane from the University of Minnesota.

Flu never seems to go away in some herds and that is because there are groups of pigs, or subpopulations, that are able to maintain and spread the flu virus.

One of the most important subpopulations that have been identified as sources of virus on a farm is the piglets. Piglets may be infected, but may not show any signs of disease, and as a result, are silent spreaders of flu. Then, at weaning, a small, but significant, percentage of the piglets can be subclinically infected with flu, meaning they appear healthy but are shedding flu at the nursery or wean-to-finish site.

This causes a challenge for producers because even though piglets are born free of flu, they tend to be contaminated by the dam during their second week of like. The peak of flu-positive piglets occurs at weaning when piglets are moved to a nursery where they may be put in contact with naive piglets from another source and therefore become a major source of infection.

We need to understand how piglets become infected in the farrowing room in order to prevent it. Sow vaccination is a tool commonly used to protect piglets via the transmission of antibodies through the colostrum or maternal immunity. It has been shown to decrease the prevalence of flu-positive piglets at weaning but is insufficient to constantly wean negative animals.

“At the University of Minnesota, we have been measuring the impact of piglets on the spread of flu for years. We found, in a study by Allerson of 52 swine breeding herds in the United States, 23 herds (44%) tested IAV RT-PCR positive at least once during a six-month study period. Groups of piglets from those herds also tested positive for flu at weaning about 25% (75 of 305) of the time.

Along those same lines, Chamba and partnering sow farms reported that out of the 34 farms studied for more than five years, all sow farms tested positive for flu at one time or another and the level of flu infection in the groups of weaned pigs ranged from 7% to 57%. More importantly, in this study, approximately 28% (427 of 1,523) of groups of pigs tested positive at weaning. […]

Ultimately, the successful control of on-going flu infections in growing pigs will depend on the sow farm’s ability to wean a negative pig […]”

Click to read the entire article on the National Hog Farmer website.

Science Page: Multiple influenza viruses circulate in growing pigs during epidemic events

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 from Dr. Andres Diaz and the Torremorell lab.

Key points

  • The diversity of influenza A viruses in growing pigs is dynamic
  • Influenza A viruses can replicate as a swarm of viruses that are identical, closely related to each other (>99%), or clearly distinct (H1 vs. H3 subtypes)
  • Influenza A viruses of the same genotype can re-infect pigs within a short period of time.
132 3-week old piglets selected at weaning and placed in a wean-to-finish farm were sampled weekly for 15 weeks (n=2080 samples). Samples were tested by RT-PCR and the complete genome of influenza was obtained from 93 samples using next generation sequencing.
Two epidemic waves of IAV infection were detected with 3 distinct viral groups (VG swarms) found (VG1, VG2 and VG3). An H1 gamma (VG1) dominated the first outbreak, an H3 (VG3) dominated the second outbreak and an H1 beta (VG2) was only recovered when none of the two other viruses dominated.
The complete version of this study can be found online in open-access.

Influenza Herd-Level Prevalence and Seasonality in Breed-to-Wean Pig Farms in the Midwestern United States

The Torremorell lab is continuing to explore swine influenza epidemiology in this recent publication from Dr. Fabian Chamba Pardo in Frontiers in Veterinary Science. After showing that multiple genome constellations of similar and distinct influenza viruses co-circulate in pigs, the group is now presenting new data about influenza herd-level prevalence in the Midwest, and how it is influenced by seasons. Click on the banner below to read the entire research article.

Influenza seasonal prevalence Midwest herds Chamba 2017

60 sow farms from a single Midwestern production system were enrolled in this study. Between one and seven oral fluid samples were collected at each farm weekly and meteorological data (air temperature and relative humidity) was compiled from stations located from the farms.

Swine herd level prevalence Chamba 201728% of submissions had at least one influenza positive result. All farms tested positive at least once during study period. Herd-level prevalence ranged from 7% to 57% as show in the figure above. Prevalence was low in summer, rose during fall, and peaked twice in both early winter (December) and late spring (May). August was the month with the lowest prevalence. Influenza herd-level prevalence was higher when both mean outdoor air temperature and air humidity were lower.

The most common clades identified were H1 delta 1, H1 gamma 1, and clusters H3 IV A  and H3 IV B. Furthermore, 21% of the farms had 3 different influenza genetic clades circulating during the study period and 18% had 2.


Influenza is a costly disease for pig producers and understanding its epidemiology is critical to control it. In this study, we aimed to estimate the herd-level prevalence and seasonality of influenza in breed-to-wean pig farms, evaluate the correlation between influenza herd-level prevalence and meteorological conditions, and characterize influenza genetic diversity over time. A cohort of 34 breed-to-wean farms with monthly influenza status obtained over a 5-year period in piglets prior to wean was selected. A farm was considered positive in a given month if at least one oral fluid tested influenza positive by reverse transcriptase polymerase chain reaction. Influenza seasonality was assessed combining autoregressive integrated moving average (ARIMA) models with trigonometric functions as covariates. Meteorological conditions were gathered from local land-based weather stations, monthly aggregated and correlated with influenza herd-level prevalence. Influenza herd-level prevalence had a median of 28% with a range from 7 to 57% and followed a cyclical pattern with levels increasing during fall, peaking in both early winter (December) and late spring (May), and decreasing in summer. Influenza herd-level prevalence was correlated with mean outdoor air absolute humidity (AH) and temperature. Influenza genetic diversity was substantial over time with influenza isolates belonging to 10 distinct clades from which H1 delta 1 and H1 gamma 1 were the most common. Twenty-one percent of farms had three different clades co-circulating over time, 18% of farms had two clades, and 41% of farms had one clade. In summary, our study showed that influenza had a cyclical pattern explained in part by air AH and temperature changes over time, and highlighted the importance of active surveillance to identify high-risk periods when strategic control measures for influenza could be implemented.