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Recombinants Are the Key Drivers of Recent PRRSV-2 Evolution
Clarissa Pellegrini Ferreira1, Lucina Galina-Pantoja2, Mark Wagner3
1Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1365, Gortner Ave, Falcon Heights, MN 55108, USA.
Pathogens (Basel, Switzerland)
|August 28, 2025
Summary
Whole-genome sequencing reveals recombination significantly impacts Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) evolution in the U.S. Relying solely on ORF5 sequencing can misclassify PRRSV-2 strains, emphasizing the need for full-genome analysis in surveillance.
Area of Science:
- Veterinary Virology
- Molecular Epidemiology
- Swine Disease Research
Background:
- Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economic threat to global swine production.
- PRRSV-2 is the predominant variant in the United States, traditionally classified using ORF5 gene sequencing.
- ORF5 sequencing may fail to detect crucial evolutionary mechanisms like recombination in PRRSV-2.
Purpose of the Study:
- To investigate the role of recombination in the evolution of U.S. PRRSV-2 isolates.
- To compare phylogenetic classifications based on whole-genome sequencing versus ORF5 sequencing.
- To assess the limitations of ORF5-based lineage assignment for PRRSV-2.
Main Methods:
- Whole-genome sequencing of seven U.S. PRRSV-2 isolates (2006-2024).
- Phylogenetic analysis using reference-guided assembly.
- Recombination detection using RDP5 and SIMplot software.
Main Results:
- Four out of seven PRRSV-2 isolates showed discordant phylogenetic placements between whole genomes and ORF5 sequences.
- Discordances were attributed to multiple recombination events, particularly in ORF2-ORF7.
- Three isolates exhibited phylogenetic concordance with no significant evidence of recombination.
Conclusions:
- Recombination is a significant driver of PRRSV-2 evolution, impacting viral diversity.
- ORF5-based lineage classification is insufficient for accurately characterizing PRRSV-2 strains.
- Whole-genome sequencing and surveillance are critical for precise viral tracking and effective control strategies.
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