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Background Porcine reproductive and respiratory syndrome virus (PRRSV) is a macrophage-tropic arterivirus with extremely high genetic and pathogenic heterogeneity that causes significant economic losses in the swine industry worldwide. PRRSV can be divided into two species [PRRSV1 (European) and PRRSV2 (North American)] and is usually diagnosed and genetically differentiated into several lineages based on the ORF5 gene, which constitutes only 5% of the whole genome. This study was conducted to achieve nonselective amplification and whole-genome sequencing (WGS) based on a simplified sequence-independent, single-primer amplification (SISPA) technique with next-generation sequencing (NGS), and to genetically characterize Korean PRRSV field isolates at the whole genome level. Methods The SISPA-NGS method coupled with a bioinformatics pipeline was utilized to retrieve full length PRRSV genomes of 19 representative Korean PRRSV strains by de novo assembly. Phylogenetic analysis, analysis of the insertion and deletion (INDEL) pattern of nonstructural protein 2 (NSP2), and recombination analysis were conducted. Results Nineteen complete PRRSV genomes were obtained with a high depth of coverage by the SISPA-NGS method. Korean PRRSV1 belonged to the Korean-specific subtype 1A and vaccine-related subtype 1C lineages, showing no evidence of recombination and divergent genetic heterogeneity with conserved NSP2 deletion patterns. Among Korean PRRSV2 isolates, modified live vaccine (MLV)-related lineage 5 viruses, lineage 1 viruses, and nation-specific Korean lineages (KOR A, B and C) could be identified. The NSP2 deletion pattern of the Korean lineages was consistent with that of the MN-184 strain (lineage 1), which indicates the common ancestor and independent evolution of Korean lineages. Multiple recombination signals were detected from Korean-lineage strains isolated in the 2010s, suggesting natural interlineage recombination between circulating KOR C and MLV strains. Interestingly, the Korean strain GGYC45 was identified as a recombinant KOR C and MLV strain harboring the KOR B ORF5 gene and might be the ancestor of currently circulating KOR B strains. Additionally, two novel lineage 1 recombinants of NADC30-like and NADC34-like viruses were detected. Conclusion Genome-wide analysis of Korean PRRSV isolates retrieved by the SISPA-NGS method and de novo assembly, revealed complex evolution and recombination in the field. Therefore, continuous surveillance of PRRSV at the whole genome level should be conducted, and new vaccine strategies for more efficient control of the virus are needed.

Background Classical porcine parvovirus (PPV1) and novel porcine parvoviruses designated porcine parvovirus 2 through 7 (PPV2-PPV7) are widespread in pig populations. The objective of this study was to investigate the prevalence rates of PPV1-PPV7 in Korea by detecting PPVs in serum, lung and fecal samples and to elucidate the association of PPVs with porcine circovirus type 2 (PCV2) and porcine reproductive and respiratory virus (PRRSV), major pathogens involved in porcine respiratory disease complex (PRDC). A total of 286 serum, 481 lung, and 281 fecal samples collected from 2018 to 2020 were analyzed. Results The results showed that PPVs are widespread in Korea; the highest detection rates were found in lung samples and ranged from 7.9% (PPV1) to 32.6% (PPV2). Regarding age groups, fattening pigs had the highest detection rates of PPVs, ranging from 6.4% (PPV1) to 36.5% (PPV6); this finding suggests the chronic nature of PPV infections and the continual circulation of these viruses. When compared with PCV2- and PRRSV-negative lung samples, PCV2-positive samples with or without PRRSV positivity had significantly higher detection levels of PPV1 and PPV6. In contrast, the prevalence of PPV2 and PPV7 was significantly higher in PRRSV-infected lung samples regardless of PCV2 detection. PPV5 was detected significantly more frequently in samples  with both PCV2 and PRRSV positivity. Conclusions This study could offer a better understanding of the role of PPVs in PCV2 and/or PRRSV infection though further studies are needed to experimentally assess the impact of PPVs in coinfections.

Porcine reproductive and respiratory syndrome (PRRS) is a disease that has inflicted economic losses in the swine industry. The causative agent, porcine reproductive and respiratory syndrome virus (PRRSV), is known to have a high genetic diversity which leads to heterogeneous pathogenicity. To date, the impact of PRRS outbreaks on swine production and the economy of the swine industry in South Korea has been rarely reported. In this study, we compare the reproductive performance in the breeding-farrowing phase and growth performance in the nursery phase, in two 27-week periods, one before and one after a PRRSV1 outbreak on a 650-sow farrow-to-nursery farm caused by a Korean PRRSV1 isolate which was genetically distinct from vaccine strains or other global strains. The reproductive performance of sows and the growth performance of nursery pigs were compared using row data consisting of 1,907 mating records, 1,648 farrowing records, and 17,129 weaning records from 32 breeding batches. The following variables were significantly different between the pre-PRRS outbreak period and the post-PRRS outbreak period: the farrowing rate (−7.1%, p < 0.0001), the abortion rate (+3.9%, p < 0.0001), the return rate (+2.9%, p = 0.0250), weaning to estrus interval days (+1.9 days, p < 0.0001), total piglets born (−1.2 pigs/litter, p < 0.0001), piglets born alive (−2.2 pigs/litter, p < 0.0001), weaned piglets (−2.7 pigs/litter, p < 0.0001), pre-weaning mortality (+7.4%, p < 0.0001), weaning weight (−0.9 kg/pig, p = 0.0015), the mortality rate (+2.8%, p < 0.0001), average daily gain (−69.8 g/d, p < 0.0001), and the feed conversion ratio (+0.26, p = 0.0036). Economic losses for a period of 27 weeks after a PRRS outbreak were calculated at KRW 99,378 (USD 82.8) per mated female for the breeding-farrowing phase, KRW 8,968 (USD 7.5) per pig for the nursery growth phase, and KRW 245,174 (USD 204.3) per sow in the post-outbreak period. In conclusion, the farrow-to-nursery farm in our study suffered extensive production and economic losses as a result of a PRRSV1 outbreak.