Genetic diversity in the capsid protein of Porcine circovirus type 3 in Vietnam from 2018 to 2019

Abstract Porcine circovirus type 3 (PCV3) was first detected in 2016 and has been recorded in many pig-producing countries around the world. PCV3 was quickly reported in Vietnamese pig farms. PCV3 was found in complex cases with multiple clinical syndromes in swine. This study aimed to investigate the genetic diversity among PCV3 strains circulating in Vietnam, which provide novel insights into molecular characteristics and genetic diversity of these PCV3 isolates. A total of 249 samples were collected from swine farms located in eight provinces of Vietnam. We identified 11.65% (29/249) of collected samples with the presence of PCV3. The ORF2 genes of 29 PCV3-positive samples were amplified, purified, and sequenced. Phylogenetic analysis of these strains showed that 23/29 PCV3 strains belong to PCV3b sub-type, while the remaining strains fall into sub-type c and sub-type a (a-1 and a-2). Analysis of the ORF2 genes indicated that the 29 PCV3 strains had high sequence identity (96.90–100% at the genomic level and 96.19–100% at the amino acid level). Fifteen amino acid substitutions were found in the predicted B-cell epitopes in capsid protein of Vietnamese PCV3 strains.