Porcine circovirus type 2 (PCV2) in Brazil in the past 55 years (1967-2022): evolutionary rates and patterns

Abstract

Porcine circovirus type 2 (PCV2) is a common virus that infects pigs. It exhibits marked genetic variability, which is affected by factors such as vaccination and commercial trade. In this study, a retrospective analysis of PCV2 was performed based on molecular characterization, Bayesian inference, and haplotype networks in tissue samples obtained from Brazilian pig herds from 1967 to 2018. A nested PCR targeting a 225-nucleotide fragment of the PCV2 capsid gene was performed, followed by bidirectional sequencing. Out of 178 samples tested, 39 (21.9%) were positive for PCV2. Phylogenetic analysis showed that strains from this study collected before the introduction of a PCV2 vaccine clustered with genotype 2d reference strains. The mean substitution rate was 1.54 × 10^-3 substitutions per site per year (s/s/y). The haplotype diversity of PCV2 was 0.98, which shows a high mutation rate compatible with the topology found in the haplotype network. Our study shows that most of the Brazilian isolates, including those obtained before the introduction of the PCV2 vaccine, were similar to PCV2d reference strains, suggesting that this genotype was already circulating before the introduction of the vaccine in Brazil. One of the PCV2 sequences was from an isolate from 1967, making it the oldest sequenced isolate from the Americas, and the second oldest worldwide. Phylogenetic analysis and haplotype network analysis indicated a high degree of diversity of PCV2 as well as a high rate of evolution. These results increase our knowledge about the genetic diversity, evolution, and dispersal patterns of PCV2 in Brazil.