Comparative Genomic and Biological Investigation of NADC30- and NADC34-Like PRRSV Strains Isolated in South Korea

Porcine reproductive and respiratory syndrome virus (PRRSV) is a globally endemic, costly swine arterivirus with wide genetic and antigenic variations, leading to the frequent appearance of novel virulent strains that hampers PRRSV control. Recently, NADC30-like (lineage 1C, L1C) and NADC34-like (lineage 1A, L1A) PRRSV strains were reported to be prevalent in mainland South Korea and became the main epidemic strains persistently attributed to PRRSV outbreaks nationwide, raising great concern in the domestic pork industry. Although the genotypic and pathotypic variability of NADC30- and NADC34-like viruses has been explored in the United States and China, their genomic and biological characteristics have been scarcely studied in South Korea. Here, NADC34-like GNU-2353 and NADC30-like GNU-2377 strains were independently identified from vaccinated swine herds experiencing high piglet mortality. Whole-genome sequencing and phylogenetic analysis revealed that GNU-2353 and GNU-2377 clustered into sublineages L1A (NADC34-like) and L1C (NADC30-like), respectively, sharing high genomic homology with their corresponding lineage-representative strains and harboring the same molecular signatures of continuous 100 and discontinuous 131 amino acid deletions in the nsp2-coding region, respectively. Recombination detection indicated that GNU-2353 and GNU-2377 were recombinants and evolved through natural interlineage recombination between NADC34-like (L1A, major parent) or NADC30-like (L1C, major parent) and RespPRRS modified live virus (MLV)–like (lineage 5, minor parent) strains, respectively. Both viruses displayed homogenous growth kinetics but replicated faster than the prototype VR-2332 in a porcine alveolar macrophage cell line (PAM-KNU). The transcriptional profiles of immune response genes in infected PAM-KNU cells varied between the isolates and VR-2332; particularly, interleukin-10 expression was dramatically upregulated in cells infected with GNU-2353 and GNU-2377. Piglets with GNU-2353 and GNU-2377 infection had high fever; weight loss; increased viremia and nasal shedding; viral distribution in various tissues; thymic atrophy; and apparent macroscopic and microscopic lung lesions, including interstitial pneumonia and viral colonization, compared with control piglets, suggesting that both isolates were virulent to pigs. Remarkably, GNU-2353 caused higher fever, mortality rate (40%) with cyanosis, viremia, and viral shedding within 2 weeks and significantly higher viral loads in several organs than GNU-2377 infection. Thus, NADC34-like GNU-2353 was more pathogenic than NADC30-like GNU-2377. Our findings provide insights into the current epizootic circumstance of NADC30- and NADC34-like PRRSV in South Korea and can aid in tailoring improved control strategies.