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.

Science Page: Use of processing fluids for PRRSV diagnostics

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.

Key points

  • Using processing fluids as a diagnostic tool can help us to detect lower PRRS prevalence in the herd.
  • Testicles and tails should be collected in a pail as they are potential spreaders of PRRS in the farrowing room.
  • We should target young parity sows for PRRSV sampling.

Processing fluids PRRS table.gif

What are processing fluids?

In sow farms, piglets get processed during the first week of life. This means that their tails is docked and the males are castrated. The farmer usually collect tails and testicles in a pail to be discarded at a later time.

We propose to use the fluids accumulating at the bottom of the pail to assess the farm PRRSV status.

How did we test those fluids?

The fluids were tested for PRRSV by PCR and the results were compared to the gold standard for this diagnostic: PCR on serum. Sampling was set in a farm that just went through a PRRSV outbreak and 10 litters from various parity sows were selected each week for 8 weeks.

What were the results?

Processing fluids were efficient in detecting PRRSV even if there was only one piglet positive in the litter (determined with the serum samples). Compared to the serum tests, there were 4 false negative samples that were explained by the fact that the virus load in the piglets serums was low and the dilution effect of the processing fluids caused the samples to get negative results. We also found 4 false positive resutls that could be due to cross-contamination of the samples despite the extreme care with which the samples were handled.

Are processing fluids a worthwhile sample?

The agreement between processing fluids and serum results was good and the sensitivity and specificity of the technique was respectively of 83% and 92%. Additionally, this technique requires no further handling of the piglets or use of extra supplies to collect samples and submit them to the laboratory.


Senecavirus A is still with us!

We are continuing our series on Senecavirus A this week with the latest paper written in our rubric for the National Hog Farmer.

Senecavirus is still with us NHF sept 17

More than 230 Senecavirus outbreaks have been confirmed after July 2015 in the United States and this is why it is important:

“The clinical signs in pigs infected with vesicular disease caused by SVA are variable and can range from no outward signs, to nonspecific signs such as decreased appetite or fever, or pigs may develop vesicles, or blisters, on the skin or in the mouth.[..]

While SVA continues to plague U.S. and global pork producers, it is important to be reminded of and understand some basic characteristics and behavior of this virus. SVA causes vesicular lesions affecting the skin, mouth and feet of pigs of all ages and has been associated with increased neonatal mortality which may be accompanied by neonatal diarrhea. If vesicular disease is present, your state animal health official must be notified in order to rule out other foreign animal diseases, such as FMD. The virus can be detected in multiple sample types but there is variability in the amount of time for which each sample type can be used for detection. Finally, SVA is extremely stable and contaminated facilities, transport vehicles and fomites are concerns for possible virus transmission but several disinfectants have been shown to be effective at neutralizing the virus.”

Science Page: Salmonella antimicrobial resistance and emergence of a new serotype S.4,[5],12:i:-

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.

Monitoring antimicrobial resistance is a research topic of utmost importance in the swine industry. Dr. Julio Alvarez at the University of Minnesota is leading some of this effort and this week, his team is presenting the latest results regarding Salmonella antimicrobial resistance in the strains isolated by the University of Minnesota – Veterinary Diagnostic Laboratory between the years 2006 and 2015 and the emergence of a new serotype S.4,[5],12:i:-

Key Points

  • Swine is the reservoir most commonly associated with the S.4,[5],12:i: serotype.
  • The prevalence of S. agona and S. 4,[5],12:i:- in isolates of swine origin recovered from clinical samples received at the Minnesota Veterinary Diagnostic Laboratory (MVDL) in 2006-2015 has increased.
  • In these serotypes an increased proportion of isolates were resistant to ceftiofur and enrofloxacin, compared with other serotypes.
  • The increase in the frequency of isolation of the S.4,[5],12:i:- serotype in humans may be paralleled by a similar increase in swine clinical samples received in the MVDL.

The information synthesized in the figure below is the evolution, over the years, of the percentages of Salmonella isolated at the UMN – VDL, belonging to each of other the following serotypes: typhimurium, agona, derby, typhymurium var5, and 4,5,12:i:-. The increase in the proportion of S.4,5,12:i:- can be seen starting back in 2011-2012.

Salmonella antibiotic resistance

Click here to read the full report about Salmonella serotypes isolated at the UMN – VDL