Molecular epidemiology and genetic characterization of PCV2 and PCV3 circulating in domestic pigs and wild boars in central-southern regions of Italy

Porcine circoviruses (PCVs) are significant pathogens impacting swine health globally. In Italy, both viruses have been reported to circulate significantly in commercial and rural farms as well as in wild boar populations. However, most information to date originates from studies conducted in Northern Italy, where the majority of pig production is concentrated, while limited data are available from Central Italian regions. This study aimed to address the knowledge gap regarding PCV epidemiology in Central Southern Italy, an area characterized, mainly, by small-scale family, traditional pig farming systems. Between March 2020 and March 2024, 362 samples were collected and tested using real-time PCR. Positive samples were further characterized by next generation sequencing (NGS) and phylogenetic analysis. The 47.1% ( 95% CI 95% CI: 40.9-53.38%) of the samples were positive for PCV2, with a higher prevalence in wild boars (62.07%; 95% CI 95% CI: 52.19–70.91%) compared to domestic pigs (34.97%; 95% CI: 27.19–43.38%). For PCV3, 38% ( 95% CI: 28.48–48.25%), of the tested animals were positive, with wild boars again showing a higher prevalence (45.16%; 95% CI: 32.48–58.32%).) compared to domestic pigs (26.32%; 95% CI: 13.40–43.10%). Phylogenetic analysis revealed significant genetic variability and confirmed the dominance of the PCV2d genotype. Comparison with other Italian strains highlighted extensive regional circulation and connections between wild and domestic populations. Sequences of this study frequently clustered with strains from the densely pig-populated areas of Northern Italy, supporting multiple long-range introduction events likely mediated by domestic pig trade. The study underscores the importance of continuous monitoring of PCVs to manage their impact on developing pig farming systems and mitigate potential biosecurity risks associated with interactions between wild and domestic animal populations.