Search Results (431)

Porcine reproductive and respiratory syndrome virus (PRRSV) infection causes significant economic losses in swine production. In May 2021 and March 2023, we detected PRRSV genes in serum samples from two weaned pigs with respiratory disorders on a farm in Japan. Partial gene sequences of these strains closely resembled those of a PRRS vaccine strain. We subsequently isolated two PRRSV field strains, KU-IG21-1 and KU-IG23-1, from the 2021 and 2023 samples, respectively. The KU-IG21-1 strain exhibited more pronounced cytopathic effects and significantly higher replication efficiency in cultured cells compared to both the vaccine and KU-IG23-1 strains. Despite these phenotypic differences, complete genome sequencing revealed high genetic similarity between the field isolates and the vaccine strain, with only 16 and 24 amino acid differences in the KU-IG21-1 and KU-IG23-1 strains, respectively. These findings suggest that the field strains likely emerged through the accumulation of point mutations in the vaccine strain rather than through homologous recombination. Furthermore, we identified three amino acid substitutions that may contribute to the enhanced replication of the KU-IG21-1 strain. This study underscores the potential impact of point mutations on PRRSV phenotypes and provides new insights into the complex evolutionary dynamics of PRRSV. Full article

Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen in pigs and a newly recognized zoonotic coronavirus in humans. Genetic analyses suggest that PDCoV originated from avian deltacoronaviruses, with sparrow deltacoronaviruses (SpDCoVs) being the most closely related. House sparrows (Passer domesticus) frequently visit farms and interact directly with pigs in barns, raising the possibility of interspecies transmission. We hypothesized that PDCoV can be transmitted between pigs and house sparrows. To investigate this, 200 house sparrows near Ohio swine farms were sampled and screened for gammacoronaviruses and deltacoronaviruses using RT-PCR targeting the conserved RNA polymerase region. Deltacoronaviruses and gammacoronaviruses were detected in 18.0% (36/200) and 5.5% (11/200) of fecal samples, respectively. Genomic sequence analysis of representative samples revealed that SpDCoVs are closely related to, but not direct ancestors of, PDCoVs. These SpDCoVs appear to be widespread in the U.S. Midwest and may contribute to PDCoV evolution. Attempts to isolate SpDCoV from these samples in embryonated chicken eggs and four cell lines were unsuccessful. Because coronaviruses frequently cross species barriers to cause epidemics and/or pandemics in humans and livestock, these findings underscore the need for ongoing surveillance of deltacoronaviruses in diverse wild animals, livestock, and humans to safeguard public health. Full article

Porcine Reproductive and Respiratory Syndrome (PRRS) causes significant economic losses in the swine industry. Circular RNAs (circRNAs), a class of stable non-coding RNAs, are increasingly recognized as regulators in immune responses and host–virus interactions. This study investigated the genome-wide circRNA responses in porcine alveolar macrophages (PAMs), key cell targets of PRRSV, following treatment with a modified live virus (MLV) vaccine or two interferon (IFN) subtypes (IFN-α1, IFN-ω5). Using RNA sequencing, we identified over 1000 differentially expressed circRNAs across treatment groups, revealing both conserved and distinct expression profiles. Gene Ontology and KEGG pathway analyses indicated that circRNA-associated genes are significantly enriched in immune-related processes and pathways, including cytokine signaling and antiviral defense. Notably, IFN-ω5 treatment induced a pronounced circRNA response, aligning with its potent antiviral activity. We further explored the regulatory potential of these circRNAs by predicting miRNA binding sites, revealing complex circRNA-miRNA interaction networks. Additionally, we assessed the coding potential of differentially expressed circRNAs by identifying open reading frames (ORFs), internal ribosome entry sites (IRESs), and N6-methyladenosine (m⁶A) modification sites, suggesting a subset may undergo non-canonical translation. These findings provide a comprehensive landscape of circRNA expression in PAMs under different antiviral conditions, highlighting their potential roles as immune regulators and novel players in interferon-mediated antiviral responses, particularly downstream of IFN-ω5. This work contributes to understanding the non-coding RNA landscape in the PRRSV-swine model and suggests circRNAs as potential targets for future antiviral strategies. Full article

Campylobacter spp. are leading causes of bacterial gastroenteritis globally. Swine are recognized as an important reservoir for this pathogen. The emergence of antimicrobial resistance (AMR) and multidrug resistance (MDR) in Campylobacter is a global health concern. Traditional methods for detecting AMR and MDR, such as phenotypic testing or whole-genome sequencing, are resource-intensive and time-consuming. In the present study, we developed and validated a supervised machine learning model to predict MDR status in Campylobacter isolates from swine, using publicly available phenotypic AMR data collected by NARMS from 2013 to 2023. Resistance profiles for seven antimicrobials were used as predictors, and MDR was defined as resistance to at least one agent in three or more antimicrobial classes. The model was trained on 2013–2019 isolates and externally validated using isolates from 2020, 2021, and 2023. Random Forest showed the highest performance (accuracy = 99.87%, Kappa = 0.9962) among five evaluated algorithms, which achieved high balanced accuracy, sensitivity, and specificity in both training and external validation. Our feature importance analysis identified erythromycin, azithromycin, and clindamycin as the most influential predictors of MDR among Campylobacter isolates from swine. Our temporally validated, interpretable model provides a robust, cost-effective tool for predicting MDR in Campylobacter spp. and supports surveillance and early detection in food animal production systems. Full article

This review investigates genetic strategies aimed at improving robustness in pigs to enhance disease resistance and reduce reliance on antibiotics. Robustness refers to a pig’s ability to stay healthy and productive under stressful or challenging conditions. The review outlines current breeding practices focused on key traits such as maternal ability, growth, immune function, and survival, and highlights that these robustness-related traits show measurable heritability, making them suitable for genetic improvement. Special attention is given to resistance against porcine reproductive and respiratory syndrome (PRRS), a major disease in swine. We also evaluate breed-specific differences, environmental influences, and immune response profiles, emphasizing their impact on breeding outcomes. The development of robust pig lines emerges as a sustainable strategy to reduce antibiotic dependence and enhance herd health. A distinctive contribution of this work is the integration of genetic robustness and resilience strategies with antibiotic stewardship objectives. We link genomic selection, advanced phenotyping, and targeted management interventions within a One Health framework to outline actionable, system-level pathways for reducing antimicrobial inputs. To our knowledge, this combined genetic and public health perspective has not been comprehensively addressed previously. Full article

Porcine parvovirus (PPV), a non-envelope single-stranded DNA virus, causes severe reproductive disorders in swine worldwide, characterized by fetal mortality, mummification, and reduced boar fertility. As a highly prevalent pathogen in Chinese swine herds, PPV imposes substantial economic burdens on intensive pig production systems. This review systematically synthesizes recent advances in PPV virology, focusing on genomic evolution of emerging strains (PPV1–PPV8), epidemiological dynamics of emerging strains, molecular pathogenesis, and novel diagnostic tools. Furthermore, we critically evaluate current vaccine strategies, highlighting their limitations in cross-protective efficacy and viral shedding control. By integrating multi-omics insights with immunological profiling, this work delineates actionable pathways for next-generation vaccine design and proposes a roadmap for rational antigen selection. This review consolidates foundational knowledge and establishes a translational bridge between basic virology and prevention and control of porcine parvovirus, addressing critical gaps in porcine reproductive disease management. Full article

Hepatitis E virus (HEV) is an emerging zoonotic pathogen, with swine identified as a major reservoir. Despite the global significance of HEV, epidemiological data regarding its presence in Greek pig farms remain limited. This study investigated the presence of HEV RNA in swine populations across Greece. In 2019, a total of 280 fecal samples from finishing pigs were collected from 28 pig farms in diverse geographic regions. Pooled samples were analyzed by real-time RT-PCR targeting the conserved ORF3 region of the HEV genome (without genotyping). HEV RNA was detected in 42.9% (12/28) of farms, with positive farms identified in five of the six surveyed regions, suggesting widespread viral circulation. These findings confirm, for the first time, the presence of HEV in the Greek swine population, while the observed prevalence aligns with intermediate to high levels reported in other European countries. Considering the zoonotic potential of HEV, especially via occupational exposure or consumption of contaminated pork products, these results highlight the need for continued surveillance and further investigation into potential public health implications. Full article

Pig farms in Southern Nigeria face recurrent threats from enzootic viral infections, yet active surveillance remains limited. This study implemented an active surveillance approach targeting African swine fever virus (ASFV) to assess its circulation across four states. We sampled 40 pig farms and two abattoirs, collecting swine blood and ticks for molecular and serological analysis. Sampling was conducted during both African swine fever (ASF) outbreak (n = 27 pigs) and non-outbreak (n = 204 pigs) periods, resulting in 231 samples tested for ASFV DNA. Additionally, 46 plasma samples from the non-outbreak period were screened for ASFV-specific antibodies. ASFV was detected in all pigs sampled during outbreak periods (27/27; 100%), whereas none of the pigs sampled during non-outbreak periods tested positive (0/204). Of the 27 positives, sequencing generated 7 genomes characterized as genotype II. Serological testing of the 46 plasma samples from non-outbreak pigs revealed no ASFV seropositivity. All tick samples were negative for ASFV DNA. Farm-level risk evaluations revealed widespread biosecurity lapses, suggesting these deficiencies as potential drivers of ASFV circulation. These findings underscore the urgent need to strengthen farm-level biosecurity and demonstrate the pivotal role of active surveillance and genome sequencing in detecting and characterizing ASF outbreaks. Full article

Encephalomyocarditis virus (EMCV) is an important zoonotic pathogen that infects many animals with mild symptoms. However, swine is the most receptive host and causes acute and lethal myocarditis and/or encephalitis, and induces sudden death in piglets. There are currently no approved antivirals against EMCV. In recent years, antiviral therapies based on small interfering RNA (siRNA) have been rapidly developed as effective alternative therapies. In this study, we designed siRNAs targeting highly conserved regions in the EMCV genome coinciding with VP2 and 3C genes. We show that these siRNAs were non-immunostimulatory and significantly inhibited EMCV replication in vitro. The siRNAs were then complexed in liposomes before testing in a lethal EMCV mouse model in vivo. Both prophylactic and therapeutic intravenous delivery of siRNAs ameliorated viral infection in multiple organs and improved animal survival. This is the first demonstration of the use of a liposomal delivery platform to deliver highly conserved anti-EMCV siRNAs for EMCV antiviral therapy in vivo. Full article

Antimicrobial resistance (AMR) in livestock production systems has emerged as a major global health concern, threatening not only animal welfare and agricultural productivity but also food safety and public health. The widespread, and often poorly regulated, use of antimicrobials for growth promotion, prophylaxis, and metaphylaxis has accelerated the emergence and dissemination of resistant bacteria and resistance genes. These elements circulate across interconnected animal, environmental, and human ecosystems, driven by mobile genetic elements and amplified through the food production chain. It is estimated that more than two-thirds of medically important antimicrobials are used in animals, and AMR could cause millions of human deaths annually by mid-century if unchecked. In some livestock systems, multidrug-resistant E. coli prevalence already exceeds half of isolates, particularly in poultry and swine in low- and middle-income countries (LMICs). This narrative review provides a comprehensive overview of the molecular epidemiology, ecological drivers, and One Health implications of AMR in food-producing animals. We highlight key zoonotic and foodborne bacterial pathogens—including Escherichia coli, Salmonella enterica, and Staphylococcus aureus—as well as underappreciated reservoirs in commensal microbiota and livestock environments. Diagnostic platforms spanning phenotypic assays, PCR, MALDI-TOF MS, whole-genome sequencing, and CRISPR-based tools are examined for their roles in AMR detection, surveillance, and resistance gene characterization. We also evaluate current antimicrobial stewardship practices, global and regional surveillance initiatives, and policy frameworks, identifying critical implementation gaps, especially in low- and middle-income countries. Emerging sectors such as aquaculture and insect farming are considered for their potential role as future AMR hotspots. Finally, we outline future directions including real-time genomic surveillance, AI-assisted resistance prediction, and integrated One Health data platforms as essential innovations to combat AMR. Mitigating the threat of AMR in animal agriculture will require coordinated scientific, regulatory, and cross-sectoral responses to ensure the long-term efficacy of antimicrobial agents for both human and veterinary medicine. Full article

Porcine Teschovirus (PTV) is a highly prevalent pathogen within swine populations, primarily associated with encephalitis, diarrhea, pneumonia, and reproductive disorders in pigs, thereby posing a significant threat to the sustainable development of the pig farming industry. In this study, a novel strain of PTV was isolated from the feces of a pig exhibiting symptoms of diarrhea, utilizing PK-15 cell lines. The structural integrity of the viral particles was confirmed via transmission electron microscopy, and the viral growth kinetics and characteristics were evaluated in PK-15 cells. High-throughput sequencing facilitated the acquisition of the complete viral genome, and subsequent phylogenetic analysis and full-genome alignment identified the strain as belonging to the PTV 2 genotype. Further investigation revealed that infection with the PTV-GXLZ2024 strain induces phosphorylation of the eukaryotic translation initiation factor 2α (eIF2α) in PK-15 cells, indicating activation of the unfolded protein response (UPR) through the PERK pathway, with minimal involvement of the IRE1 or ATF6 pathways. Notably, ATF4 protein expression was progressively downregulated throughout the infection, while downstream CHOP protein levels remained unchanged, indicating an incomplete UPR induced by PTV-GXLZ2024. Furthermore, PERK knockdown was found to enhance the replication of PTV-GXLZ2024. This study provides critical insights into the molecular mechanisms underlying PTV pathogenesis and establishes a foundation for future research into its evolutionary dynamics and interactions with host organisms. Full article

Background/Objectives: The African swine fever virus (ASFV) multi-gene family (MGF) 360 proteins play critical roles in immune evasion, replication regulation, and virulence determination. Despite substantial advances in this field, the functional roles of many members within this gene family remain to be fully characterized. Methods: In this study, Transcriptional kinetics analysis indicated that the expression profile of MGF 360-2L was consistent with that of the late marker gene B646L (p72). Transcriptomic profiling identified 13 and 171 differentially expressed genes (DEGs) at 12 and 24 h post-infection (hpi) with ΔMGF 360-2L, respectively. Results: Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that these DEGs were predominantly enriched in Type I interferon (IFN-I) signaling pathways. It is noteworthy that transcriptome analysis further demonstrates that the absence of MGF 360-2L specifically results in the dysregulation of expression of the replication-essential genes E199L and E301R. These findings indicate that MG F360-2L is essential for maintaining the stable expression of these proteins. Conclusions:MGF 360-2L is a late gene that contributes to the precise regulation of viral protein expression and modulates the host immune response during infection. Full article

Accurate genomic prediction of complex phenotypes is crucial for accelerating genetic progress in swine breeding. However, conventional methods like Genomic Best Linear Unbiased Prediction (GBLUP) face limitations in capturing complex non-additive effects that contribute significantly to phenotypic variation, restricting the potential accuracy of phenotype prediction. To address this challenge, we introduce a novel framework based on a self-supervised, pre-trained encoder-only Transformer model. Its core novelty lies in tokenizing SNP sequences into non-overlapping 6-mers (sequences of 6 SNPs), enabling the model to directly learn local haplotype patterns instead of treating SNPs as independent markers. The model first undergoes self-supervised pre-training on the unlabeled version of the same SNP dataset used for subsequent fine-tuning, learning intrinsic genomic representations through a masked 6-mer prediction task. Subsequently, the pre-trained model is fine-tuned on labeled data to predict phenotypic values for specific economic traits. Experimental validation demonstrates that our proposed model consistently outperforms baseline methods, including GBLUP and a Transformer of the same architecture trained from scratch (without pre-training), in prediction accuracy across key economic traits. This outperformance suggests the model’s capacity to capture non-linear genetic signals missed by linear models. This research contributes not only a new, more accurate methodology for genomic phenotype prediction but also validates the potential of self-supervised learning to decipher complex genomic patterns for direct application in breeding programs. Ultimately, this approach offers a powerful new tool to enhance the rate of genetic gain in swine production by enabling more precise selection based on predicted phenotypes. Full article

African swine fever virus (ASFV) and classical swine fever virus (CSFV) are important transboundary animal diseases (TADs) affecting swine. ASFV is a large DNA virus with a genome size of 170–190+ kilobases (kB) belonging to the family Asfarviridae, genus Asfivirus. CSFV is a single-stranded RNA virus with a genome size of approximately 12 kB, belonging to the family Flaviviridae, genus Pestivirus. Outbreaks involving either one of these viruses result in similar disease syndromes and significant economic impacts from: (i) high morbidity and mortality events; (ii) control measures which include culling and quarantine; and (iii) export restrictions of swine and pork products. Current detection methods during an outbreak provide minimal genetic information on the circulating virus strains/genotypes that are important for tracing and vaccine considerations. The increasing availability and reduced cost of next-generation sequencing (NGS) allow for the establishment of NGS protocols for the rapid identification and complete genetic characterization of outbreak strains during an investigation. NGS data provides a better understanding of viral spread and evolution, facilitating the development of novel and effective control measures. In this study, panels of primers spanning the genomes of ASFV and CSFV were independently developed to generate approximately 10 kB and 6 kB amplicons, respectively. The primer panels consisted of 19 primer pairs for ASFV and 2 primer pairs for CSFV, providing whole genome amplification of each pathogen. These primer pools were further optimized for batch pooling and thermocycling conditions, resulting in a total of 5 primer pools/reactions used for ASFV and 2 primer pairs/reactions for CSFV. The ASFV primer panel was tested on viral DNA extracted from blood collected from pigs experimentally infected with ASFV genotype I and genotype II viruses. The CSFV primer panel was tested on 11 different strains of CSFV representing the three known CSFV genotypes, and 21 clinical samples collected from pigs experimentally infected with two different genotype 1 CSF viruses. ASFV and CSFV amplicons from optimized PCR were subsequently sequenced on the Oxford Nanopore MinION platform. The targeted protocols for these viruses resulted in an average coverage greater than 1,000X for ASFV, with 99% of the genome covered, and 10,000X–20,000X for CSFV, with 97% to 99% of the genomes covered. The ASFV targeted whole genome sequencing protocol has been optimized for genotype II ASF viruses that have been responsible for the more recent outbreaks outside of Africa. The CSFV targeted whole genome sequencing protocol has universal applications for the detection of all CSFV genotypes. Protocols developed and evaluated here will be essential complementary tools for early pathogen detection and differentiation, as well as genetic characterization of these high-consequence swine viruses, globally and within the United States, should an outbreak occur. Full article

Swine Inflammation and Necrosis Syndrome (SINS) is a simple and non-invasive animal-based health and welfare indicator that combines the clinical observation of bristle loss, swelling, redness, exudation, necrosis and haemorrhage in various parts of the body. It provides a point-of-care measure with direct intervention capability. Several studies from different countries demonstrate its considerable prevalence, particularly among newborn, suckling and weaned piglets. The syndrome has been demonstrated to be endogenous, as evidenced by clinical, pathohistological, clinical chemical, metabolomic, transcriptomic and genomic analysis. It has been established that the first and fourth weeks of life represent suitable time points for examination. However, longitudinal follow-up of individual animals has hitherto been lacking. In order to address this issue, a total of 1080 complete SINS examinations were conducted on 59 piglets at days 1 to 14, 19, 22, 26 and 41 of life. The findings substantiate the bimodal progression and evince a robust correlation between signs in disparate anatomical regions, including body temperature. Two peaks with significantly increased SINS signs were observed, the first around the fourth day of life and the second around day 26. The majority of indications of SINS in the second peak manifested prior to the initiation of the weaning process. The development of SINS signs in the piglets as a group followed a clear pattern. However, it was not feasible to predict the subsequent course of SINS based on individual animals. It is recommended that SINS, as an animal-based health and welfare indicator, be screened on days three to four and/or in the fourth week of life. It is imperative that the day of life is specified with the greatest possible precision, given the propensity for considerable deviations to occur within a time frame of one to three days, especially during the initial week of life. The implementation of these findings has the potential to make a decisive contribution to improving inventory herd analyses and studies on SINS, thereby improving the welfare and health of piglets. Full article