A molecular survey and phylogenetic analysis of porcine circovirus type 3 using oral fluid, faeces and serum

Background: Porcine circovirus type 3 is the most recently discovered porcine circovirus, and an emerging pathogen. In this study the status of its presence on some Slovenian farms is reported. The effectiveness of thevaccine against porcine circovirus type 2 was assessed against porcine circovirus type 3. Group samples of oral fluid, faeces and individual serum samples were taken from six different pig categories andtested for presence of viral DNA, using both real time and conventional PCR. Positive samples were subjected todirect Sanger sequencing. Nucleotide sequences were analyzed and compared to GenBank PCV3 sequences. Results: Positive samples were sent for genome sequencing, which confirmed the presence of virus in all differentpig categories on five farms. A high to moderate correlation of strong statistical significance was found betweenindividual serum samples, oral fluid and faeces. Slovenian PCV3 was found to be distributed in a way similar to thatof other countries. Slovenian PCV3 nt sequences are highly related, sharing more than 99.5% nt identity. On onefarm a commercially available vaccine against porcine circovirus type 2 was used on 3-week-old pigs. It did notaffect the presence of porcine circovirus type 3 in oral fluid or sera of any of the seven age groups of pigs, eachwith two control groups. Conclusions: The results constitute the first discovery of the virus in Slovenia. Genome sequencing has revealed ahigh degree of similarity between Slovenian and GenBank isolates.