Genetic variability of PRRS virus in Austria: consequences for molecular diagnostics and viral quantification.

Porcine reproductive and respiratory syndrome virus is a virus with a relatively high level of sequence variation, especially between the European and the American-type strains. This high degree of sequence variations will influence the accuracy of results obtained by molecular diagnostic methods, especially if mutations are located in the primer or probe binding regions of PCR or real-time PCR based assays. In order to provide the basis for the development of an accurate, region-tailored assay we have analysed samples obtained from several Austrian pig herds using a series of RT-PCR assays. Subsequent sequencing of the PCR products from ORF5 and phylogenetic analysis revealed the occurrence of both the European and the American-type of porcine reproductive and respiratory syndrome virus in Austria. Since vaccination with the American-type vaccine is not authorized in Austria the import of vaccinated animals is the most likely explanation for the occurrence of these strains. The study highlights the importance of a detailed study on the sequence variations occurring in the region of interest before the development of a reliable PCR-based assay.