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. 2020 Apr 15;16(1):113.
doi: 10.1186/s12917-020-02329-z.

PCR-based detection and genetic characterization of porcine parvoviruses in South Korea in 2018

Hee-Chun Chung  1 , Van-Giap Nguyen  2 , Thi-My-Le Huynh  2 , Yong-Ho Park  3 , Kun-Taek Park  4 , Bong-Kyun Park  5
Affiliations

PCR-based detection and genetic characterization of porcine parvoviruses in South Korea in 2018

Hee-Chun Chung et al. BMC Vet Res. .

Abstract

Background: with the advantage of sequencing technology, many novel porcine parvoviruses (PPV) rather than PPV1 has been reported. This study ultilized specific PCR- based method and gene- based analysis to study the presence and genetic diversity of porcine parvoviruses in South Korea in 2018.

Results: The present study was conducted in 2018 and found PPV1 and PPV7 in nine out of 151 field samples (organs and semen) by the PCR method. Among these, the complete genome sequences of five strains (N2, N91, N108, N133, and N141) were recovered. Phylogenic analysis revealed that the strains N2, N91, and N108 belong to the PPV1 genotype, while N133 and N141 belong to PPV7 genotype. The PPV7 strains collected in this study had deletion mutations in the VP2 gene but differed from that of PPV7 strains collected in 2017. Among the PPV1 strains, the amino acid variations in the B cell epitopes of the VP2 protein were observed between three Korean PPV1 field strains (N2, N91, and N108) and the reference PPV1 strains. Those substitutions resulted in six out of 12 predicted epitopes having significant differences in antigenic index compared to the other PPV1 strains.

Conclusions: This study confirmed the presence of different genotypes of porcine parvoviruses in South Korea. The PPVs circulating in South Korea were phylogenetically classified as PPV1 and PPV7 genotypes. Three Korean PPV1 strains collected in 2018 were predicted to have antigenic alteration in VP2 compared to several reference strains of PPV1.

Keywords: Detection; Genetic characterization; Porcine parvoviruses; South Korea.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Maximum likelihood phylogenetic trees of porcine parvoviruses in the relationships with eight genera of subfamily Parvovirinae. The phylogenetic trees were inferred based on alignment of NS1 protein and were midpoint rooted. Given for the main internal nodes were the associated boostrap support values. The positions of Korean porcine parvoviruses in the phylogeny were indicated by arrows. The scale under each tree measures changes in the unit of the number of amino acid substitutions per site
Fig. 2
Fig. 2
A comparison of the nucleotide sequences of Korean PPV7 strains. Panel a showed the sequence similarity between the two PPV7 strains (N133 and N141) collected in this study and six strains collected in 2017. The genomic region of VP2 gene that exhibits a drop of sequence similarity was indicated by a dashed line. The nucleotide comparison in panel b shows that the two PPV7 strains collected in 2018 had genetic deletion but were distinct from the six PPV7 strains sampled in 2017
Fig. 3
Fig. 3
Branch rate heterogeneity observed in maximum clade credibility trees of PPV1- PPV7 genotypes based on genomic sequences. The trees were inferred from the data best-fit model of molecular clock (random local clock- RLC) and coalescent tree prior (Bayesian skyline plot- BSP; coalescent constant population- Const.; coalescent exponential population- Expo.). Branches are colored by inferred local clock rates (blue = slow, red = fast). Dots indicates the positions of Korean PPV strains in the phylogenetic tree. The time-scale (year) of evolutionary changes represented in the tree is indicated by the scale bar
Fig. 4
Fig. 4
Estimated nucleotide substitution rates of complete genomes for each PPV1- PPV7 genotype. The genome-wide rates were inferred from the best-fit molecular clock and coalescent tree prior models. Error bars indicate 95% highest posterior density (HPD) interval. The vertical red line delimit rates less than one order of magnitude of 1 × 10− 3 subsitutions/ site/ year
Fig. 5
Fig. 5
Comparison of the genetic distance between the seven PPV genotypes based on the complete genome. The frequency of each p-distance is shown as a column and the genetic distance of the virus in each country is indicated by arrows
Fig. 6
Fig. 6
Amino acid alignment of the VP2 protein of PPV1. Twelve predicted B cell linear epitopes on the VP2 protein are shaded in gray. Three identified experimental linear B cell epitopes are marked as boxes. The amino acid substitutions that correspond to tissue tropism and attenuation are indicated by solid arrows
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