Detection and genotyping of Korean porcine rotaviruses

Abstract

Porcine group A rotavirus (GARV) is considered to be an important animal pathogen due to their economic impact in the swine industry and its potential to cause heterologous infections in humans. This study examined 475 fecal samples from 143 farms located in 6 provinces across South Korea. RT-PCR and nested PCR utilizing primer pairs specific for the GARV VP6 gene detected GARV-positive reactions in 182 (38.3%) diarrheic fecal samples. A total of 98 porcine GARV strains isolated from the GARV-positive feces were analyzed for G and P genotyping. Based on the sequence and phylogenetic analyses, the most predominant combination of G and P genotypes was G5P[7], found in 63 GARV strains (64.3%). The other combinations of G and P genotypes were G8P[7] (16 strains [16.3%]), G9P[7] (7 strains [7.1%]), G9P[23] (2 strains [2.0%]), and G8P[1] (1 strain [1.0%]). The counterparts of G or P genotypes were not determined in three G5, five P[7], and one P[1] strains. Interestingly, phylogenetic analysis indicated that all Korean G9 strains were more closely related to lineage VI porcine and human viruses than to other lineages (I-V) of GARVs and to Korean human G9 strains (lineage III). These results show that porcine GARV infections are common in diarrheic piglets in South Korea. The infecting strains are genetically diverse, and include homologous (G5P[7]), heterologous (G8P[1]), and reassortant (G8P[7]), as well as emerging G9 GARV strains.

Fig. 1

(A) Phylogenetic tree of the complete VP7 genes of the sixty-six G5, seventeen G8, and nine G9 strains of Korean porcine GARVs indicating their genetic relationships with other G genotypes. Black triangles contain rotavirus G5, G8, and G9 strains. (B) A detailed phylogenetic tree of the complete VP7 genes of the nine Korean porcine G9 strains with other known G9 strains indicating their genetic relationships with other known VI lineages of G9 genotype. Reference sequences used in the analysis (A and B) were obtained from the GenBank database (Table 2).

Fig. 1

(A) Phylogenetic tree of the complete VP7 genes of the sixty-six G5, seventeen G8, and nine G9 strains of Korean porcine GARVs indicating their genetic relationships with other G genotypes. Black triangles contain rotavirus G5, G8, and G9 strains. (B) A detailed phylogenetic tree of the complete VP7 genes of the nine Korean porcine G9 strains with other known G9 strains indicating their genetic relationships with other known VI lineages of G9 genotype. Reference sequences used in the analysis (A and B) were obtained from the GenBank database (Table 2).

Fig. 2

Phylogenetic tree of the VP4 gene of the ninety-five porcine rotavirus strains indicating their genetic relationships with other known P genotypes. Reference sequences used in the analysis were obtained from the GenBank database (Table 2).