Genetic and Phylogenetic Analysis of Porcine Circovirus Type 2 on Jeju Island, South Korea, 2019–2020

Abstract

Porcine circovirus type 2 (PCV2) is the most ubiquitous viral pathogen of pigs and has persistently affected the global swine industry. Since first being identified in South Korea in 1999, the virus has undergone considerable genetic diversity and genotype shifts during the past two decades. These events have contributed to the co-existence of genotypes PCV2a, PCV2b, and PCV2d in Korean pig populations, which may promote viral recombination. The genotypic and phylogenetic characteristics of PCV2 strains circulating in pig herds on Jeju Island from 2019 to 2020 were the focus of this study. Genotype-specific PCR indicated that PCV2d is the dominant viral genotype and that co-infections with PCV2d and PCV2a (75%) or PCV2a and PCV2b (25%) are common in provincial pig herds. The whole-genome sequences of 11 PCV2 strains, including three PCV2a, two PCV2b, and six PCV2d, were determined. A genomic comparison showed that all viruses had the highest nucleotide identity with their corresponding genotypic reference strain. Notably, genetic and phylogenetic analyses revealed that one PCV2d strain, KNU-1931, exhibited nucleotide variation at the ORF1 gene when compared to other PCV2d strains but shared high similarity to that of PCV2b strains. Comprehensive recombination analysis demonstrated that KNU-1931 originated from natural recombination within ORF1 between PCV2b (the minor parent) and PCV2d (the major parent) strains. Our findings provide evidence regarding the frequency of genetic recombination between two different PCV2 genotypes circulating in the domestic field, illustrating the importance of continuous inter-genotypic recombination for viral fitness under the concomitance of multiple genotypes