Genetic Diversity of Porcine Circovirus 2 Subtypes in Wild Boar and Domestic Pigs in Ukraine

Abstract

Porcine circovirus type 2 (PCV2) is responsible for a number of porcine circovirus associated diseases (PCAD) that can severely impact domestic pig herds. For a non-enveloped virus with a small genome (1.7 kb ssDNA), PCV2 is remarkably diverse, with 8 subtypes (a-h). New subtypes of PCV2 can spread through migration of wild boars, which are thought to infect domestic pigs and spread further through the domestic pig trade. Despite a large swine population, the diversity of PCV2 subtypes in Ukraine has been undersampled, with few PCV2 genome sequences reported in the past decade. To gain a deeper understanding of PCV2 subtype diversity in Ukraine, samples of blood serum were collected from wild boars (n = 107) that were hunted in Ukraine during the November-December 2012 hunting season. We found 34/107 (31.8%) prevalence of PCV2 by diagnostic PCR. For domestic pigs, liver samples (n = 16) were collected from a commercial market near Kharkiv in 2019, of which 6/16 (37%) were positive for PCV2. We sequenced the genotyping locus ORF2, a gene encoding the PCV2 viral capsid (Cp), for 11 wild boar and 6 domestic pig samples in Ukraine using an Oxford Nanopore MinION device. Of 17 samples with resolved subtypes, PCV2 subtype b was most common in wild boar (10/11, 91%), while domestic pigs were infected with subtypes b and d. We also detected subtype b/d and b/a co-infections in wild boar and domestic pigs, respectively, and subtype f in a wild boar from Poltava for the first time in Ukraine. Building a maximum likelihood phylogeny, we identified a sublineage of PCV2 subtype b infections in both wild and domestic swine, suggesting a possible epizootic cluster and ecological interaction in northeastern Ukraine.