The Schroeder’s lab at the University of Minnesota College of Veterinary Medicine recently published a brief report in the journal Pathogens regarding a likely cause of Porcine Reproductive and Respiratory Virus type 2 evolution.

Methods

• Seven strains of PRRSV-2 isolated between 2006 and 2024 were analyzed.
• RNA was extracted and complementary DNA was synthesized.
• Whole-genome sequencing was performed for all seven isolates.
• ORF1-ORF7 were aligned against selected PRRSV genomes and phylogenetic trees were built.
• Lineages for each isolate was determined with ORF5 sequences.
• Lastly, potential recombination events were identified with RDP5 and SIMplot.

Results

• Phylogenetic trees built from full genome or ORF5 sequences were different, suggesting that other regions of the PRRSV genome have different evolutionary history compared to ORF5.
• Three isolates clustered similarly between both trees showing that ORF5 and the rest of the genome had a similar evolution pattern over time.
• The figure below shows the pairwise identity between the analyzed PRRSV strain from MN and two contributing strains (green and gold) on the y axis and the position on the genome on the x axis.

• This figure shows that the part of the genome from ORF1a to ORF3 is similar to strain MZ423535 (green) whereas ORF4-ORF7 are more similar to strain PQ252345 (gold), showing that this PRRSV isolated in 2024 is likely a product of a recombination event.

Abstract

Porcine reproductive and respiratory syndrome virus remains one of the most economically significant pathogens in swine production, with PRRSV-2 being the dominant variant in the United States. While lineage classification has traditionally relied on ORF5 sequencing, recent studies suggest that this single-gene approach may overlook key evolutionary events such as recombination. In this study, we performed whole-genome sequencing and phylogenetic analysis of seven PRRSV-2 isolates collected in the U.S. between 2006 and 2024. Using reference-guided assembly, lineage assignment, and recombination detection with RDP5 and SIMplot, we identified discordant phylogenetic placements between ORF5 and whole genomes in four of the seven isolates. These discordances were explained by multiple recombination events affecting different genomic regions, particularly ORF2-ORF7. In contrast, three isolates showed phylogenetic concordance and no strong evidence of recombination. Our findings demonstrate that recombination plays a significant role in shaping PRRSV-2 evolution and highlight the limitations of ORF5-based lineage classification. Whole-genome surveillance is therefore essential to accurately track viral diversity, detect recombinant strains, and inform control strategies. This work underscores the need for a broader adoption of full-genome analysis in routine PRRSV surveillance and research.