Molecular based detection, genetic characterization and phylogenetic
analysis of porcine circovirus 4 from Korean domestic swine farms
Abstract
Porcine circovirus 4 (PCV4), a novel and unclassified member of the
genus Circovirus, was first reported in China in 2019. Aimed at
providing more evidence about the active circulation of PCV4, this study
screened 335 pooled internal organs and detected the virus (i) at the
rates of 3.28%, (ii) from both clinical healthy and clinical sick pigs
of various age groups, and (iii) in six out of nice provinces of Korea.
The complete genomic sequence of a Korean PCV4 strain (E115) was 1,770
nucleotides in length and had 98.5% to 98.9% identity to three PCV4
strains available at GenBank up to date. Utilizing a set of
bioinformatic programs, it was revealed that the Korean PCV4 strain
contained several genomic features of (i) a palindrome stem-loop
structure with conserved nonanucleotide, (ii) packed overlapping ORFs
oriented in different directions, and (iii) two intergenic regions in
between genes encoding putative replication- associated protein (Rep)
and capsid (Cap) proteins. This study also predicted the presence of
essential elements known so far for the replication of circoviruses, for
example, the origin of DNA replication, endonuclease and helicase
domains of Rep, the nuclear localization signal on the putative Cap
protein. Finally, based on the phylogeny inferred from sequences of the
putative Rep protein, it was suggested that PCV4 belong to genus
Circovirus of family Circoviridae and losely related to three previous
known porcine circoviruses of PCV1, PCV2 and PCV3.