When should PRRS whole-genome sequencing be used?

Genetic variability within porcine reproductive and respiratory syndrome virus (PRRSV) is remarkable, said Albert Rovira, DVM, with the Veterinary Diagnostic Laboratory at the University of Minnesota. He believes there are benefits to using whole-genome sequencing (WGS) in large outbreaks, especially when Orf 5 sequencing doesn’t fully answer important diagnostic questions.

Traditionally, different strains have been identified and differentiated by sequencing the Orf 5 gene of the virus. The method has pros and cons, however, and WGS might provide a more in-depth analysis.

“This sequencing method is currently available at diagnostic laboratories with high precision, good reproducibility and quick turnaround time,” Rovira said during a recent presentation.¹ In addition, Orf 5 sequencing is relatively low cost, and extensive databases are available for sequence comparisons, he explained.

“However, the Orf 5 gene is only 600 nucleotides long, thus representing only 4% of the genome,” Rovira noted. “In some cases, it may be useful to sequence the whole genome of the virus.”

WGS has benefits as well as disadvantages. On the plus side, it provides the ability to analyze virus changes on parts of the genome other than the Orf 5. On the negative side, it is more expensive, less reliable, less sensitive and slower than Orf 5 sequencing, Rovira said.

“All these limitations are being addressed by new advances in next-generation sequencing technology and bioinformatics pipelines,” he said. “WGS is quickly becoming more reliable, easier to interpret, faster and less costly.”

Case in point

Rovira gave several examples of the use of WGS, including one in which multiple abortions were experienced in a sow farm that was positive and stable with vaccination for PRRSV.

“In that case, Orf 5 sequencing suggested a vaccine-like virus, 98% similar to a vaccine that had not been used in that farm for the past 2 years,” he said. “Therefore, the Orf 5 sequencing results did not explain the clinical picture of abortions.”

WGS revealed that the strain apparently causing the abortions was not a vaccine strain, he said. Instead, it was a new strain resulting from several recombination events between two vaccine strains ⸺ one that had been used in the farm in the past and one that was being used at the time of the outbreak.

“It’s possible that the combination of different parts of the genome from two attenuated strains resulted in a virulent recombinant strain,” he added.

WGS has a place

This example, and others provided by Rovira, highlight the benefits of using WGS in certain cases.

“It would be a good practice to run WGS on any major outbreaks observed in a sow herd,” he said. “This will help build a collection of previous PRRSV sequences that will be readily available for comparisons in the future.”

The use of WGS will also help researchers build and maintain a strong database for future outbreak investigations in a specific farm and other potential contact farms, Rovira added.

1 Rovira A. What can we learn from a PRRS whole genome sequence? Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, Minn. Presented at Am Assoc Swine Vet annual meeting, March 2021.