Genetic Diversity of Porcine Circovirus Types 2 and 3 in Wild Boar in Italy

Abstract

Porcine circovirus (PCV) infection is associated with relevant economic impact to the pig industry. To date, four species of PCV (PCV1 to 4) have been identified but only PCV2 has been associated firmly with disease in pigs. The objective of this study was to assess the prevalence of PCV2 and PCV3 in the wild boar population in Basilicata region, Southern Italy, since this region is characterized by large forested and rural areas and the anthropic pressure is lower than in other Italian regions. Liver samples from 82 hunted wild boar were collected in 2021 from 3 different hunting districts. Sixty (73%, 95%CI: 63-82) samples tested positive for PCVs by quantitative PCR. In detail, 22 (27%, 95%CI: 18-37) were positive for PCV2, 58 (71%, 95%CI: 60-79) for PCV3, and 20 (24.4%, 95%CI 16-35) for both PCV2 and PCV3. On genome sequencing, different types and sub-types of PCV2 and PCV3 were identified, remarking a genetic diversity and hinting to a global circulation for the identified PCV strains. Overall, the high prevalence suggests that PCV2 and PCV3 infections are endemic in the wild boar population, posing risks for semi-intensive and free-range pig farming, typical of this region, due to contact with PCV-infected wild boar.

Keywords: Circoviridae; Southern Italy; porcine circoviruses; swine diseases; viral diseases; wild boar.

Figure 1

Map of Basilicata region showing distribution of semi-intensive and free-range pig farms (A) and intensive pig farms (B). Distribution of collected samples (C) and of PCV2-positive, PCV3- positive and PCV-2/PCV3-co-infected wild boar in different hunting districts (Ambiti territoriali di Caccia, ATC) (D). The choropleth map (C,D) shows the wild boar density per ATC, computed as the mean of wild boar harvested from 2015/2016 to 2019/2020 hunting season.

Figure 2

Full-genome-based unrooted phylogenetic tree Porcine circovirus 2 strains identified in this study and reference strains recovered in the GenBank database. The Maximum Likelihood method and Tamura-Nei model (four parameters) with a gamma distribution and invariable sites were used for the phylogeny. A total of 1000 bootstrap replicates were used to estimate the robustness of the individual nodes on the phylogenetic tree. Bootstrap values greater than 70% were indicated. Black arrows indicate strains detected in this study. Numbers of nucleotide substitutions are indicated by the scale bar.

Figure 3

Full-genome-based unrooted phylogenetic tree Porcine circovirus 3 strains identified in this study and reference strains recovered in the GenBank database. The Maximum Likelihood method and Tamura-Nei model (four parameters) with a gamma distribution and invariable sites were used for the phylogeny. A total of 1000 bootstrap replicates were used to estimate the robustness of the individual nodes on the phylogenetic tree. Bootstrap values greater than 70% were indicated. Black arrows indicate strains detected in this study. Numbers of nucleotide substitutions are indicated by the scale bar.