To date, three naturally occurring  porcine epidemic diarrhea virus (PEDV) strains have been identified in the U.S.: the original PEDV, the PEDV with changes in the spike gene (INDEL), and the PEDV strain (S2aa-del) reported in a recent article in the Centers for Disease Control and Prevention's (CDC) Emerging Infectious Diseases Journal.

The University of Minnesota Veterinary Diagnostic Laboratory (UMVDL) has tested clinical samples from thousands of case-patients to determine the presence of PEDV by real-time reverse transcription PCR. Some of the PEDV-positive samples from case-patients were selected for PEDV spike gene sequencing per veterinarian’s request, whereas other samples were selected for complete genome sequencing to fulfill a grant objective. When PEDV was first detected in the United States, the University of Minnesota Veterinary Diagnostic Laboratory was only sequencing the PEDV spike gene segment to clarify the phylogenetic relationship between PEDV strains.

In February 2014, after the identification and analysis of PEDV variant-INDEL strains, UMVDL decided to sequence the complete PEDV genome by using next generation sequencing to clarify the phylogenetic relationship of the U.S. PEDV strains.

The American Association of Swine Veterinarians (AASV) notes that the role of genetic changes in the U.S. PEDV strains to clinical disease has yet to be reported. The clinical presentation of diarrhea in this case was reported as equally or more severe than such presentation in cases caused by the prototype PEDV Colorado/2013. Other factors such as concurrent infections and the rate of group exposure, which is rapid in most PEDV cases affecting neonatal piglets, may influence the clinical presentation.

UMVDL says documenting PEDV variation is vital to understanding the natural evolution of the virus and possibly identifying portions of the genome associated with different clinical disease features. Animal studies are required to define the effects of these mutations on clinical disease, pathogenesis, immunity; these studies will be conducted in the future with the S2aa-del strain. A consistent model to properly evaluate these differences is required to control PEDV infection. The most compelling need is to understand how exposure by sows to different PEDV strains correlates with protection of piglets from clinical disease. Whether the PEDV S2aa-del strain will circulate in the North American swine population is not known.

The project was conducted by Douglas Marthaler, Laura Bruner, James Collins, and Kurt Rossow. Read more in the article, "Third Strain of Porcine Epidemic Diarrhea Virus, United States," in the CDC's Emerging Infectious Diseases, Vol. 20, No. 12, December 2014.