Detection, Genotyping and Phylogenetic Characterisation of Porcine Circovirus 2 and Porcine Circovirus 3 in Wild Boar (Sus scrofa) from West Bačka District, Vojvodina, Serbia

Porcine circovirus 2 (PCV2) and porcine circovirus 3 (PCV3) are widespread in domestic pigs and common in wild boar, but Serbian wild boar data come predominantly from the east. Tissue pools from 90 wild boar hunted in West Bačka District, Vojvodina, in 2021 and 2022, collected within national swine fever surveillance, were screened by real-time PCR. PCV2 was detected in 17 animals (18.9%; 95% CI 11.4–28.5) and PCV3 in 12 (13.3%; 95% CI 7.1–22.1), with no co-infection. Four partial PCV2 capsid sequences were obtained, three PCV2b and one PCV2d, all within the diversity already reported from Serbian wild boar and European domestic pigs. Five complete PCV3 genomes differed by no more than 1.46% and met the distance criteria for PCV3-a; at the complete-genome level, the closest reference sequences came mainly from domestic pigs in Serbia and Hungary. Neither of the two PCV3 recombination signals met the acceptance criteria, so no event could be attributed to these sequences; breakpoint analysis of the combined reference-and-study alignment detected topological incongruence at the Cap coding-region boundary, an exploratory finding that does not demonstrate recombination in these genomes. Both viruses circulate in this population, carrying diversity that these data do not separate from that of European domestic pigs.