Background and aims: Runting-stunting syndrome (RSS) in chickens, also known as malabsorption syndrome, which is characterized by mild to severe enteritis and diagnosed through typical histopathologic examination as well as clinical signs, results in considerable economic losses. Despite the many studies carried out over decades to determine the etiologic agents of RSS involved in the disease, several outbreaks remained without the elucidation of, potentially multiple, etiologies involved. Methods: We performed comparative analysis of viral metagenomes from four chicken flocks affected with RSS using next-generation sequencing. Primers for the detection of chicken enteric viruses were designed from the sequencing data obtained with metagenomics. Multiplex reverse transcription–polymerase chain reaction (PCR) and PCR were performed to detect a variety of etiological agents previously described in natural cases of RSS. Results: The most abundant viral families identified in this study were Astroviridae, Picornaviridae, Parvoviridae, Caliciviridae, Reoviridae and Picobirnaviridae. Chicken astrovirus sequences were present in all four samples, suggesting an association between chicken astrovirus and RSS and chicken astrovirus as a candidate pathogen responsible for RSS. Picobirnavirus and the newly identified chapparvovirus were found in chickens in the Republic of Korea for the first time, and the genetic diversity of enteric viruses and viral communities was showed. Conclusions: Chicken astrovirus was consistently detected in broilers affected with RSS and the result of this study may contribute to knowledge of enteric diseases and viruses in chickens.

Infectious bursal disease (IBD), caused by IBD virus (IBDV), threatens the health of the poultry industry. Recently, a subtype of genogroup (G) 2 IBDV named G2d has brought a new threat to the poultry industry. To determine the current status of IBDV prevalence in South Korea, active IBDV surveillance on 167 randomly selected broiler farms in South Korea from August 2020 to July 2021 was conducted. The bursas of Fabricius from five chickens from each farm were independently pooled and screened for IBDV using virus-specific RT-PCR. As a result, 86 farms were found to be infected with the G2d variant, 13 farms with G2b, and 2 farms with G3. Current prevalence estimation of IBDV infection in South Korea was determined as 17.8% at the animal level using pooled sampling methods. G2d IBDV was predominant compared to other genogroups, with a potentially high-risk G2d infection area in southwestern South Korea. The impact of IBDV infection on poultry productivity or Escherichia coli infection susceptibility was also confirmed. A comparative pathogenicity test indicated that G2d IBDV caused severe and persistent damage to infected chickens compared with G2b. This study highlights the importance of implementation of regular surveillance programs and poses challenges for the comprehensive prevention of IBDV infections.

Objectives: Selecting and managing suitable seed strains according to standard principles is a critical factor in manufacturing high-quality biological products. In this study, we determined the complete genomes of live animal vaccine bacterial strains used in South Korea and comprehensively analyzed their gene annotations. This detailed genomic analysis provides a robust foundation for identifying and verifying whether manufacturers utilize the same seed strains at the strain level. Furthermore, these data serve as a valuable reference to ensure consistent mass production and reliable quality control of biological products. Data description: Complete genome sequencing and annotation were performed on five bacterial strains ( Erysipelothrix rhusiopathiae NL-11, Clostridium chauvoei B, Bordetella bronchiseptica 12-147-AFQ2, Bordetella bronchiseptica S-55, and Mycoplasmoides gallisepticum str. F) obtained directly from live attenuated vaccines. A hybrid genome assembly approach combining Illumina short reads (NovaSeq 6000) and Oxford Nanopore long reads (MinION Mk1B) was used to obtain complete, high-quality, gap-free, and well-annotated genome sequences. The genome sizes of E. rhusiopathiae NL-11, C. chauvoei B, B. bronchiseptica 12-147-AFQ2, B. bronchiseptica S-55, and M. gallisepticum str. F were 1.78, 2.40, 5.34, 5.34, and 0.95 Mb, respectively.

Vaccination against Newcastle disease (ND) is the most effective means of controlling the disease, and these vaccines are commercialized only after their safety and effectiveness have been verified through tests that comply with Korean Standards of National Lot Release for Veterinary Biologics. This study investigated whether a relatively convenient and safe serological test can be used in place of the challenge test using highly virulent ND virus. Hemagglutination inhibition (HI) assay and enzyme-linked immunosorbent assay (ELISA) were considered positive of log2 2 or more and cutoff value of 200 or more, respectively, in both live and inactivated vaccines. However, when the antibody levels of the live and inactivated vaccines induced using the Ulster 2C, KBNP-C4152R2L, and K148/08 strains were compared, the antibody titers for inactivated vaccines were significantly higher than those for live vaccines in both the HI assay and ELISA. A strong positive correlation was observed between HI and ELISA antibody titers. The live vaccines corresponded to a survival rates of ≥ 80% and the inactivated vaccines corresponded to 100% survival rates. This study confirmed that standard efficacy tests can serve as serological tests, and can replace the challenge test and that the vaccine approval process can be improved.

Objectives: Production of high-quality biological products depends on the careful selection and consistent management of seed strains. In this study, we generated complete genome sequences of bacterial strains employed in inactivated animal vaccines in South Korea and comprehensively examined their gene annotations. The genome data thus obtained provide a solid basis for confirming, at the strain level, whether manufacturers are using the same seed strains over time. In addition, these data offer a useful reference resource to support stable large-scale production and quality control of biological products. Data description: The complete genomes of eleven bacterial strains employed for inactivated vaccine production were generated and annotated. A hybrid assembly workflow combining Illumina short reads (NovaSeq 6000) with Oxford Nanopore long reads (MinION) produced high-quality, gap-free genomes for all strains, with genome sizes ranging from 2.28 Mb to 5.35 Mb. The strains comprised Pasteurella multocida (D, 3A, A), Actinobacillus pleuropneumoniae (2 and 5), Glaesserella parasuis 4, Mannheimia haemolytica KO, Avibacterium paragallinarum C, and three Escherichia coli strains (F41, YC21-F17, K99S). All assemblies exhibited high completeness (>99%) and minimal contamination (<1%), ensuring reliable downstream genomic characterization.

Background: Genetic stability of live-attenuated infectious laryngotracheitis virus (ILTV) vaccines is essential for consistent efficacy and safety; however, marker-based assessments targeting partial genes are often insufficient given the virus’s large, structurally complex genome. The ILTV genome contains long internal inverted repeats (IRs) that can give rise to genomic isomers, complicating short-read assembly and accurate resolution of genome structure. Methods: To overcome these limitations, we used a hybrid whole-genome sequencing (WGS) strategy, combining Oxford Nanopore Technologies (ONT) long reads to improve assembly contiguity with Illumina short reads for high-accuracy polishing at the single-nucleotide level. Using this approach, we generated complete de novo genome assemblies for the commercial Serva and Salsbury #146 vaccine strains. Results: The assemblies showed high sequence concordance with targeted regions validated by Sanger sequencing. Whole-genome analysis further enabled detection and independent validation of a structural inversion in the unique short (US) region of the Salsbury strain, consistent with herpesvirus genome isomerization. To enable phylogenetic inference despite structural variability, we performed a pangenome-based analysis to define a conserved core-genome dataset that robustly resolved vaccine-associated lineages, separating Serva- and Salsbury-derived strains. Conclusions: Collectively, these findings show that a hybrid WGS workflow can generate high-confidence genome assemblies for the specific commercial ILTV vaccine vials analyzed and can support QC-relevant detection of major structural variations. Because this study is cross-sectional (two strains; single lot/vial per strain), it cannot distinguish potential biological lot-to-lot variation from methodological differences, and a comprehensive genetic stability evaluation will require applying this workflow across defined passage levels and/or multiple production lots.