SHIC Adds New Sapovirus and PRV PCRs to Diagnostic Capabilities

Two new PCR tests have been added to the Swine Health Information Center (SHIC) Diagnostic Assay Catalog. A highly sensitive and specific RT-PCR for detecting porcine sapovirus (SaV) genotype III for neonatal diarrhea investigation and a single-tube triplex real-time PCR (RT-PCR) assay for differential detection of variant strains of pseudorabies virus (PRV), including the Chinese high path strain, gives diagnosticians previously unavailable valuable tools. Each is now available to all veterinary diagnostic labs for use and fits with SHIC’s mission to make sure the US swine industry is prepared for emerging diseases.

The sapovirus PCR project resulted from a refractory case of piglet diarrhea in the lactation phase for more than two years on a farm. Pigs in the case study exhibited a self-limiting diarrhea starting around 10 days of age, but typically lost one to two pounds of expected weaning weight. Researchers use of four independent lines of evidence in this case – metagenomics analysis, real-time RT-PCR, histopathology, and in situ hybridization – confirm that porcine SaV of genogroup III as the cause of the enteritis and diarrhea.

A subsequent prevalence survey of more than 500 samples comparing pigs with clinical diarrhea and clinically healthy pigs suggests that porcine SaV genotype III may play an important role in causing swine enteritis and diarrhea. Study findings provide significant insights for a better understanding of the epidemiology and pathogenicity of porcine SaV.  To the researchers’ knowledge, this is the first evidence SaV likely serves as the sole etiological agent causing enteritis and diarrhea of piglets in the field in the United States. Having effective diagnostics for pathogens on the Swine Viral Disease Matrix and the Swine Bacterial Disease Matrix is key to discovery and detection which is essential for effective management.

The single-tube triplex real-time PCR (RT-PCR) assay for differential detection of variant strains of pseudorabies virus (PRV) is able to differentiate wild-type classical (Bristol) and Chinese variant PRV and the gE-deletion PRV mutant marker vaccines. It could be used as a rapid diagnostic tool for foreign animal disease detection in North America, or for surveillance and in epidemiological studies in countries, like China, where both classical and variant strains of PRV are endemic.

The clinical specificity and sensitivity of the assay was evaluated using whole blood, serum, tissue, and swab samples collected from known negative and experimentally inoculated pigs with either classical (Bristol) or variant (JS-2012 and HeN1) PRV strains. The targeted genomic region of this assay is also deleted in commonly used PRV gE-deleted marker vaccines, and therefore, the triplex assay did not detect viral DNA extracted from two commercial vaccine strains Bartha K-61 and Bucharest. This single-tube triplex assay can be used for routine diagnostics and epidemiological studies for detection and differentiation of classical strains from variant strains of PRV, and as a differentiation of infected and vaccinated animals (DIVA) assay when PRV gE-deletion mutant marker vaccines are used.

As the world deals with the COVID-19 pandemic, SHIC 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. Sundberg at [email protected].