Molecular Characterization of Novel Porcine Circovirus 3 (PCV3) in Pig Populations in the North of Vietnam

Abstract

In 2015, a novel circovirus (Porcine circovirus 3, PCV3) was detected for the first time from pigs suffered from porcine dermatitis and nephropathy syndrome and reproductive failure. Since then, PCV3 has been reported in several pig producing countries. This study was carried out in order to investigate the presence and further genetic characterization of PCV3 in the pig populations in northern Vietnam. The screening PCR detected the presence of PCV3 in 6 out of 135 samples (4.44%) which were collected from seven northern provinces in 2011 and 2016-2017. The capsid-coding gene (ORF2, 645 nucleotides in length) was successfully sequenced from 5 out of 6 field strains. Compared to a highly diverse PCV3 strain (GD2016-1, KY421347) 5 Vietnamese PCV3 strains contained 39 point nucleotide mutations and 9 of those were non-synonymous. The Bayesian phylogenetic analysis on the basic of ORF2 revealed that PCV3 evolved at a comparable evolutionary rate of the pathogenic PCV2 (2.284 × 10-3 and 1.440 × 10-3, respectively). Besides, this analysis suggested PCV3 could be separated into PCV3a and PCV3b groups, of which the majority of Vietnamese PCV3 strains belong to PCV3a (sub-cluster a1).