Detection and characterization of PRRSV-2 viruses with mutations in binding sites of common diagnostic real-time RT-PCR primer and probe sequences

During a field study about porcine reproductive and respiratory syndrome virus (PRRSV) in Danish pig herds, it was discovered that the quantitative real-time RT-PCR (RT-qPCR) assay used in the study was unable to detect PRRSV-2 in two herds (Herds A and B) exhibiting clinical signs consistent with PRRS. Two additional herds (Herd C, identified through clinical suspicion, and Herd D, identified during the field study) showed reduced assay sensitivity. Sequence analysis of viruses from all four herds demonstrated that the reduced sensitivity was caused by mutations within the primer and probe binding sites. Full genome analysis of Danish PRRSV-2 sequences revealed the existence of two phylogenetically separate mutated variants with a high degree of identity to previously identified Danish variants, suggesting that they were not newly introduced but likely arose separately in Denmark.