SHIC/AASV Webinar Addresses Undiagnosed Respiratory Disease Pursuit and Sampling

Undiagnosed Respiratory Disease: How to Sample for Success and What’s New, a webinar presented by SHIC and AASV, included viewpoints of the practitioner, diagnostician, and pathologists all seeking answers to ongoing respiratory issues. Diagnoses of porcine astrovirus 4 and porcine hemagglutinating encephalomyelitis virus resulted from the pursuit of a diagnosis when more common viruses were ruled out. While unlimited resources for testing and diagnosis would be ideal for identifying root causes of respiratory issues not identified as common viruses, it is unrealistic per the participants in the webinar. However, knowing unresolved respiratory issues could be PAstV4 or porcine hemagglutinating encephalomyelitis virus expand the scope of diagnostic possibilities.

Dr. Evan Koep, Pipestone Veterinary Services, shared an overview of the challenge of endemic influenza on the farm, the system’s push for higher health, and desire to identify the cause of ongoing coughing. With a goal of eliminating influenza in sow herds within the Pipestone system, they hope to achieve a result of improved health and improved client satisfaction.

After two years, their influenza elimination program has a roughly 70% elimination success rate. Despite this success, some farms continue to have piglets coughing. This non-productive cough, at 20% to 60% prevalence, resembles influenza yet is confirmed not to be IAV via udder wipes, nasal swabs, and lung tissue testing.

Dr. Koep sought a definitive diagnosis, with tests for IAV, PPIV, PHEV, PRCV, MHR, and other bacteria requested. He also submitted fixed and fresh lung, trachea, heart, spleen, liver, kidney and tonsil tissues. While these tests were all PCR negative for viruses, histopathology said, “Lesions in the trachea and upper airways are suggestive of an epitheliotropic virus.”

From this point, next generation sequencing on lung samples with lesions was the next step with porcine astrovirus 4 found and confirmed by follow-up PCR on past cases. PAstV4, an uncommon virus, is not well known nor is its association with the respiratory tract.

Dr. Hause shared there are five genotypes of porcine astrovirus. Historically, they are associated with gastroenteric disease though in 2015, PAstV4 was detected in multiple respiratory samples submitted for metagenomic sequencing at the Kansas State VDL. Genome sequencing identified a novel AstV in the PAstV4 lineage in those cases.

Testing at KSVDL compared Ct values for positive samples between nasal and fecal material. There were significantly lower Ct values (higher levels of PAstV4 genetic material) in nasal swabs. It suggests positive tests are indicative of a respiratory tropism. Dr. Hause’s presentation summary revealed astrovirus infections are common in pigs and extraintestinal infection in pigs includes the respiratory system.

Dr. Derscheid reviewed trachea physiology. While a non-collapsible passageway for air, the trachea includes cartilage rings and mucosal lining, regulating both temperature and humidity. The trachea protects and cleans columnar epithelium, goblet cells, and mucociliary apparatus. Dr. Derschied shared typical respiratory tissue VDL submissions and provided guidance for sampling the trachea for study.

In presenting a case history, Dr. Derschied shared initial results of testing which indicated typical respiratory issues, including IAV. When the producer submitted additional tissues due to ongoing coughing, including notes on negative IAV, porcine parainfluenza virus 1, and porcine respiratory coronavirus results, further tests were initiated, including NGS, PCR, and in situ hybridization. These results indicated tracheitis with and without bronchitis, not just for PAstV4. Porcine hemagglutinating encephalomyelitis virus and Mycoplasma hyopneumoniae causing persistent cilia damage were other viruses identified.

Dr. Derscheid said, “We don’t see what we don’t look for,” and recommended examination of the trachea, submitting fixed trachea and/or leaving a portion attached to fresh lung. And, she emphasized communication.

In a retrospective evaluation of bronchitis and tracheitis of unknown etiology, Dr. Rahe began with a case observation. The clinical report was of coughing in three-week-old pigs with multifocal to coalescing atelectasis, all of which are classic findings for influenza. However, the case was influenza PCR negative. The diagnostic code was respiratory – bronchitis, viral – non-specified. PAstV4 was identified via NGS.

Dr. Rahe then addressed the question, “How many cases of non-specific tracheitis/bronchitis are caused by non-influenza viral infections?” The review did identify some cases of PAstV4 associated tracheitis/bronchitis. Those tend to be limited to the trachea and bronchi but do not seem to extend into bronchioles, perhaps due to a lack of receptors. Cts over 25 in these cases were negative via RNA scope.

SHIC and AASV present webinars on topics of industry interest. ISU Swine Medicine Education Center conducts the webinars; previous webinars can be accessed here:

SHIC, launched by the National Pork Board in 2015 solely with Pork Checkoff funding, continues to focus efforts on prevention, preparedness, and response to novel and emerging swine disease for the benefit of US swine health. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. SHIC is funded by America’s pork producers to fulfill its mission to protect and enhance the health of the US swine herd. For more information, visit or contact Dr. Paul Sundberg at [email protected].