Porcine reproductive and respiratory syndrome, influenza A and post-weaning diarrhea are commonly top of mind when producers and veterinarians think about swine diseases. However, enteric diseases continue to be a significant and costly challenge. When investigating causes of diarrhea, veterinary diagnostic laboratories will test samples based on the most common pathogens for each animal’s age category. This list is extensive, including Rotavirus A, B and C, porcine epidemic diarrhea, porcine deltacoronavirus, Cystoisospora suis, beta-hemolytic E. coli, sapovirus, Clostridium perfringens, Lawsonia intracellularis and Brachyspira.
While these panels are helpful, they do not always solve the puzzle. Pathologists frequently face laboratory results showing the detection of several pathogens in the same case, commonly referred to as “co-infections.” When this happens, the microscopic evaluation of intestinal lesions (histopathology) is the most accessible tool to help determine which pathogens are the real culprits behind the clinical signs. This step is important because pigs can harbor some of these microorganisms in their guts without necessarily being affected by them.
Occasionally, even histopathology is not enough to pinpoint a single cause. For instance, several enteric pathogens cause very similar lesions of villus atrophy in the small intestine that may result in diarrhea. Rotavirus (A, B and C), PED, Cystoisospora suis (coccidiosis) and sapovirus all cause damage that can look identical under the microscope. Because of this, a pathologist must combine clinical history, gross and microscopic lesions, and PCR results to attempt to narrow down the most likely cause of the diarrhea.
Since November 2022, porcine sapovirus has been included in the UMN VDL diarrhea workup panel for pigs ranging from 0 to 8 weeks old, and is available to other age categories upon request. This was prompted by the recognition of sapovirus as an emerging swine enteric pathogen. Since the inclusion of sapovirus in routine testing, pathologists noted that a majority of pigs, both with and without diarrhea, seemed to test positive for this agent. However, they also observed that younger pigs (pre-weaning and post-weaning) appeared to have a heavier load of virus in their intestines (indicated by low PCR Ct values). Furthermore, it was observed that pigs with enteric lesions of villus atrophy that were PCR positive for rotaviruses were frequently also positive for sapovirus.
Because the scientific literature on naturally infected pigs is limited, it has been challenging for pathologists to determine exactly when sapovirus should be prioritized on a list of potential causes. To better understand this, we utilized the UMN VDL database to look for epidemiologic information on natural infections.
Our analysis of over 2,500 cases of pigs presenting with diarrhea from late 2022 through 2025 revealed several key findings:
- High prevalence: The overall proportion of positive pigs is around 86%.
- Age matters: Detection is highest in post-weaning pigs, with pigs between 22 and 50 days old being the most frequently affected. In this age group, the virus is detected consistently throughout the year.
- Co-infection trends: The presence of sapovirus is significantly correlated with the presence of rotaviruses A, B, and C.
- The E. coli connection: Importantly, our analysis showed an association between sapovirus and beta-hemolytic Escherichia coli. While E. coli does not cause the same microscopic lesions as sapovirus, it remains one of the most important causes of scours in young pigs.
- No correlation: Cystoisospora suis and PED do not appear to correlate with the presence of sapovirus.
The next step in this project is to utilize another diagnostic platform: duplex chromogenic in situ hybridization (CISH). Unlike standard methods such as immunohistochemistry, CISH detects up to two viruses at once – sapovirus and a rotavirus (A, B, or C) – directly on the same slide. By identifying and observing the distribution of both viruses simultaneously within areas of villus atrophy, we can determine which pathogen is most responsible for the gut damage versus which is simply a secondary finding.
The preliminary findings of this project reinforce the relevance of sapovirus on the enteric diseases of pigs, particularly in the nursery. When facing persistent diarrhea that does not respond to standard interventions, it is important to look at the “whole picture” of the VDL report. Understanding that sapovirus often moves in tandem with rotavirus and E. coli can help us better understand the true cause of enteric challenges on the farm.
This project is being developed with the collaboration and support of Dr. Caitlin Klaeui, Dr. Fabio Vannucci, and the UMN VDL histology lab, whose contributions have been essential to the execution of this research.
This article was written by Maria Clara Viana and Talita Resende of the University of Minnesota Veterinary Diagnostic Laboratory for the National Hog Farmer.