Background: Porcine reproductive and respiratory syndrome virus (PRRSV) has caused huge economic losses in the global swine industry. Frequent genetic variations in this virus cause difficulties in controlling and accurately diagnosing PRRSV.Methods: In this study, we investigated the genetic characteristics of PRRSV-1 and PRRSV-2 circulating in Korea from January 2018 to September 2021 and evaluated three one-step real-time reverse transcription polymerase chain reaction (RT-PCR) assays.Results: A total of 129 lung samples were collected, consisting of 47 samples for PRRSV-1, 62 samples for PRRSV-2, and 20 PRRSV-negative samples. Nucleotide sequence analysis of open reading frames (ORFs) 5, ORF6, and ORF7 genes from PRRSV samples showed that PRRSV-1 belonged to subgroup A (43/47, 91.49%) and subgroup C (4/47, 8.51%), whereas PRRSV-2 was classified as lineage 1 (25/62, 40.32%), Korean lineage (Kor) C (13/62, 20.97%), Kor B (10/62, 16.13%), lineage 5 (9/62, 14.52%), and Kor A (5/62, 8.06%). Amino acid sequence analysis showed that the neutralizing epitope and T cell epitope of PRRSV-1, and the decoy epitope region and hypervariable regions of PRRSV-2 had evolved under positive selection pressure. In particular, the key amino acid substitutions were found at positions 102 and 104 of glycoprotein 5 (GP5) in some PRRSV-2, and at positions 10 and 70 of membrane protein (M) in most PRRSV-2. In addition, one-step real-time RT-PCR assays, comprising two commercial tests and one test recommended by the World Organization for Animal Health (OIE), were evaluated.Conclusion: The results revealed that two of the real-time RT-PCR assays had high sensitivities and specificities, whereas the real-time RT-PCR assay of the OIE had low sensitivity due to mismatches between nucleotides of Korean PRRSVs and forward primers. In this study, we genetically characterized recent PRRSV occurrences and evaluated three one-step real-time RT-PCR assays used in Korea.

Feline panleukopenia virus (FPV), a member of the species Protoparvovirus carnivoran1, is one of the most fatal pathogens of domestic and wild carnivores. The virus endemically infects domestic carnivores worldwide and its cross-species transmission threatens endangered wild carnivores, including Siberian tigers. In this study, a fatal FPV infection in endangered Siberian tigers was investigated to trace the origin of the virus and elucidate the reason behind FPV’s infection of the vaccinated tigers. Our genetic characterization and phylogenetic analysis revealed that the virus detected in the infected tigers, designated as the KTPV-2305 strain, was closely related to FPV strains circulating in Korean cats, suggesting that it might have been transmitted from stray cats wandering around the zoo. Compared with the prototype FPV reference strains, the KTPV-2305 strain carried three distinct amino acid (aa) mutations in the VP2 protein sequence (I101T, I232V, and L562V) in this study. These three mutations are commonly found in most global FPV strains, including Korean strains, indicating that these mutations are common evolutionary characteristics of currently circulating global FPVs. The reason why the vaccinated tigers were infected with FPV was most likely the insufficient protective immunity of the affected tigress or vaccine failure triggered by the interference of maternal-derived antibodies in the affected tiger cubs. These findings suggest that improved vaccination guidelines are urgently needed to save the lives of wild carnivores from this fatal virus.

This study was conducted to examine the in vitro activity of antimicrobials against Campylobacter spp. isolates from chicken and human sources and the genetic interrelation among them. During 2004–2008, a total of 173 Campylobacter spp. isolated from chicken meats (60 domestic and 62 imported chicken meats) and humans (n = 51) were tested for susceptibility to nine antimicrobials. Of 173 isolates, 140 (80.9%) showed multidrug resistance (MDR) against three to eight antimicrobials. The most frequent pattern type was MDR to four antimicrobials: ciprofloxacin, nalidixic acid, ampicillin, and tetracycline. Over 52.6% (91/173) of the isolates tested were resistant to these four antibiotics simultaneously. Especially, two and five isolates originated from Korea and Brazil showed resistance against all antibiotics tested, except for florfenicol. Further, 95% (57/60) of the isolates originated from domestic chicken showed resistance to ciprofloxacin, the antimicrobial agent of choice for treatment of human campylobacteriosis. Genotypic characterization of all Campylobacter isolates performed by pulsed-field gel electrophoresis yielded 74 types among the 173 isolates. Isolates sharing the same or similar genetic clusters were detected in different countries at different times. The pulsed-field gel electrophoresis patterns of chicken-related isolates were closely related to those of isolates from humans with gastroenteritidis. The results of this study suggest that MDR Campylobacter spp. are widespread and that Campylobacter with similar genotypes are circulating both in humans and in chicken meat in Korea.

Rapid and specific detection of foot‐and‐mouth disease virus (FMDV) is a key factor for promoting prompt control of FMD outbreaks. In this study, a real‐time reverse transcription loop‐mediated isothermal amplification (RRT‐LAMP) assay with high sensitivity, rapidity and reliability was developed using a targeted gene‐specific assimilating probe for real‐time detection of seven FMDV serotypes. Positive assay signals were generated within 15 min for the lowest concentration of a standard RNA sample at 62°C; this was substantially faster than that achieved by the OIE (World Organisation for Animal Health)‐recommended real‐time quantitative reverse transcription polymerase chain reaction (qRT‐PCR) assay. The new assay specifically amplified the 3D gene of all seven FMDV serotypes and did not amplify other viral nucleic acids. The detection limit of the assay was 10² copies/µl which is comparable to that achieved by qRT‐PCR. Furthermore, using clinical samples, the results of the RRT‐LAMP assay were largely in agreement with those from the qRT‐PCR assay with a kappa value (95% confidence interval [CI]) of 0.94 (0.86–1.02). The established RRT‐LAMP assay that features assimilating probes is an advanced molecular diagnostic tool that is easily applicable to a wide range of circumstances and has high potential for use as an on‐site diagnostic assay for rapid, specific, and reliable detection of FMDVs in clinical samples.

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important pathogens in the swine industry worldwide. In Korea, Fostera PRRS commercial modified live virus (MLV) vaccines have been used since 2014 to control the PRRSV infection. In this study, two PRRSV-2 strains (20D160-1 and 21R2-63-1) were successfully isolated, and their complete genomic sequences were determined. Genetic analysis showed that the two isolates have recombination events between the P129-like strain derived from the Fostera PRRS MLV vaccine and the strain of lineage 1. The 20D160-1 indicated that partial ORF2 to partial ORF4 of the minor parental KNU-1902-like strain, which belongs to Korean lineage C (Kor C) of lineage 1, was inserted into the major parental P129-like strain. The 21R2-63-1 revealed that partial ORF1b of the P129-like strain was inserted into the backbone of the NADC30-like strain. This study is the first to report natural recombinant strains between Fostera PRRS MLV-like strain and the field strain in Korea. These results may have significant implications for MLV evolution and the understanding of PRRSV genetic diversity, while highlighting the need for continuous surveillance of PRRSV.

Novel swine orthopneumovirus (SOV) infections have been identified in pigs in the USA and some European countries but not in Asian countries, including South Korea, to date. The current study reports the first SOV infections in four domestic pig farms located in four provinces across South Korea. The detection rate of SOV in oral fluid samples using qRT-PCR was 4.4% (14/389), indicating the presence of the virus in pigs at commercial farms in Korea. Two complete genome sequences and one glycoprotein (G) gene sequence were obtained from SOV-positive samples. The complete genome analysis of KSOV-2201 and KSOV-2202 strains showed 98.2 and 95.4% homologies with a previously reported SOV, and the phylogenetic tree exhibited a high correlation with a previously reported SOV strain from the US and a canine pneumovirus (CPnV) strain from China. Based on the genetic analysis of the viral G gene, the murine pneumonia virus (MPV)-like orthopneumoviruses (MLOVs) were divided into two genogroups (G1 and G2). Seventeen CPnVs and two feline pneumoviruses were grouped into G1, while the Korean SOV strains identified in this study were grouped into G2 along with one SOV and two CPnVs. These results will contribute to expanding our understanding of the geographical distribution and genetic characteristics of the novel SOV in the global pig population.