Genetic diversity of ORF 4–6 of type 1 porcine reproductive and respiratory syndrome virus in naturally infected pigs

•Genotype 1 PRRSV strains in Korea have distinct evolution.•The antigenic viral proteins in Korean EU-type PRRSV show unique characteristics at the amino acid level.•The Korean genotype 1 PRRSV strains are presumed to have been affected by individual evolutionary pressure in each ORF. Genotype 1 porcine reproductive and respiratory syndrome virus (PRRSV) has been highly prevalent throughout Korea since the virus was first detected in 2005. However, genetic analyses of genotype 1 PRRSV in Korea have been limited to ORF5 and/or ORF7. In the present study, we determined 10 representative sequence covering ORF4 to ORF6 and each individual ORFs of genotype 1 PRRSV in Korea, and performed molecular analyses. The most variable gene among the individual ORFs of field strains was ORF4, and this gene exhibited only 74.5–87.3% sequence homology compared with strains reported elsewhere. However, the strains showed analogous sequence arrangements with each other. In the phylogenetic analysis, the sequences of Korean field strains formed a distinct cluster with some Austrian and German strains compared to genotype 1 PRRSV strains available in GenBank. In the amino acid analysis, the putative antigenic region of GP4 was highly variable, whereas the predicted epitope regions of ORF5 and ORF6 were relatively conserved. The hydropathy plots of GP4 showed a highly variable pattern in the antigenic region. The non-synonymous and synonymous substitution analysis suggested that ORF4 presumably had more immunogenic pressure compare with the other ORFs. According to these findings, genotype 1 PRRSV in Korea has been diversified and indigenized in Korea, and these strains might have multifarious immunological and genetic properties. This study provides novel insights into genotype 1 PRRSV in a geographically remote area and contributes to the information for further research on the evolution of type 1 PRRSV in the Korean peninsula.