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.

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.

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