Search Results (291)

(1) Background: Bovine viral diarrhea virus (BVDV) is an economically important pathogen affecting cattle worldwide. The genetic diversity of BVDV-2 in buffalo remains poorly understood. This study aimed to elucidate the genomic and antigenic features of GX24, the first BVDV-2b isolate identified from dairy buffalo in China. (2) Methods: The virus was isolated from a rectal swab through three blind passages in MDBK cells and identified through immunofluorescence and RT-PCR. The near-complete genome was sequenced using the Illumina platform and subjected to phylogenetic and recombination analysis. B-cell epitopes and glycosylation sites were predicted using BepiPred-3.0, Epitope1D, DiscoTope-3.0, NetNGlyc-1.0, and NetO-Glyc-4.0. (3) Results: The 12,267-nt GX24 genome (GenBank: PX682047) was classified as BVDV-2b. Recombination analysis detected a putative recombination signal within the NS5A gene involving Chinese BVDV-2b and Italian BVDV-2a strains. Integrative analyses predicted conserved linear and conformational epitope clusters in the N- and C-terminal regions of the E2 protein. Spatial analysis indicated that several epitope residues may be masked by glycan shielding. (4) Conclusions: This study provides the first genomic evidence of a BVDV-2b isolate from dairy buffalo in China, suggesting that BVDV-2b may be present in this population. The putative recombination signal and antigenic characteristics offer valuable insights for the development of diagnostics and vaccine design in the future. Full article

Introduction: The Kumamoto sub-breed of Japanese Brown cattle is a small population facing increasing inbreeding and declining effective population size driven by the intensive use of a limited number of elite sires. Methods: We analyzed 811 Japanese Brown cows genotyped using a 30K SNP array, retaining 19,745 SNPs after quality control. We calculated and compared ten genomic inbreeding estimators, including SNP-by-SNP and segment-based measures. Population structure was first assessed by rearing region using principal component analysis (PCA) and was then evaluated using ADMIXTURE-based clustering and distance-based hierarchical clustering, from which representative subsets were retained under predefined filtering criteria and further examined using PCA and neighbor-joining (NJ) tree analyses. Finally, we calculated the contribution of each ADMIXTURE group to total gene and allelic diversity, and integrated these two measures into a final conservation index after Z-score standardization. Results: ROH- and HBD-based estimators showed high concordance, whereas allele-frequency-dependent SNP-by-SNP estimators exhibited distinct distributions. Rearing region did not explain the main genetic structure. Instead, four representative ADMIXTURE-based groups, supported by independently identified family groups, captured the major genetic structure associated with paternal backgrounds. ADMIXTURE group 2 made the largest contribution to both gene and allelic diversity, and showed lowest genomic inbreeding. Conclusions: These findings suggest that ROH- and HBD-based estimators may serve as valuable indicators of genomic inbreeding in the Kumamoto sub-breed of Japanese Brown cattle; paternal background has played an important role in shaping the current genomic structure; and ADMIXTURE group 2, mainly associated with the Haru-yama-to/-sakae sire background, may provide a valuable breeding resource for limiting future inbreeding accumulation and maintaining genetic diversity. Full article

Accurate cattle pose estimation is important for precision livestock farming because body landmarks can provide quantitative visual inputs for potential health monitoring, behavior analysis, lameness assessment, and welfare evaluation. This study focuses on keypoint-localization performance and provides a foundation for future task-specific studies of these downstream outcomes. However, real farm images commonly contain inter-cattle occlusion, cluttered backgrounds, small anatomical landmarks, and visually similar animals, which limit the reliability of existing one-stage pose estimators. This study proposes LEC-Pose, a hierarchical locality refinement framework for occlusion-robust cattle pose estimation. Built on YOLOv8-Pose, LEC-Pose first predicts cattle boxes and auxiliary coarse keypoints, then extracts instance-level ROI features to recover local anatomical evidence. A lightweight refinement network directly predicts the final keypoints from heatmaps and offsets on enhanced ROI features. The detected boxes guide the ROI pathway, while the initial keypoints remain auxiliary outputs. During training, an instance-level contrastive loss regularizes a compact global ROI descriptor. During inference, pair construction and contrastive-loss computation are removed, while descriptor fusion remains in the prediction path. Across three runs on CattleEyeView, LEC-Pose reaches 39.47 ± 0.33 mAP@50:95, compared with 33.91 ± 0.28 for YOLOv8-Pose, while running at 111.6 FPS versus 138.2 FPS for YOLOv8-Pose, corresponding to a 19.2% throughput reduction on the evaluated RTX 4090. On NWAFU-Cattle, it obtains 76.08 ± 0.36 and 80.03 ± 0.38 mAP@50:95 under the 50%/50% and 80%/20% protocols, respectively; the former is comparable to FSMC-Pose, whereas the latter is the highest mean among the three repeated principal models. An end-to-end zero-shot evaluation on three external cattle datasets, second-dataset occlusion analysis, detailed module combinations, and descriptor diagnostics further assess the framework within their stated protocols. These results suggest that LEC-Pose can serve as a pose-estimation component for future automated cattle monitoring, and future task-specific studies can connect these keypoints to health, behavior, and welfare outcomes. Full article

Background: Salmonellosis is a major global public health concern, commonly caused by serovars such as Salmonella enterica serovar Typhimurium and Salmonella enterica serovar Enteritidis. Rare serovars, however, may represent underrecognized links between environmental reservoirs and human infection. Salmonella enterica serovar Haifa is a sporadic serotype primarily associated with livestock and environmental sources and has previously been reported in Indian poultry but not in human clinical cases to date. Case Presentation: A 70-year-old male with a history of type 2 diabetes, presented with acute watery diarrhea and dehydration. One week prior to symptom onset, the patient reported direct contact with cattle and poultry in a rural setting. Laboratory investigations revealed leucopenia and elevated procalcitonin (3.73 ng/mL). Stool culture yielded non-lactose fermenting colonies on MacConkey agar and H₂S-producing colonies on Hektoen enteric agar. The isolate was identified via VITEK 2 and confirmed as Salmonella enterica serovar Haifa by the National Institute for Research in Bacterial Infections (NIRBI). Antimicrobial susceptibility testing (AST) revealed that the isolate showed resistance to ampicillin, ceftriaxone, and ciprofloxacin. The patient was successfully treated with a three-day course of intravenous Azithromycin (1 g) and achieved rapid clinical recovery. Conclusions: To the best of our knowledge, this case represents the first reported human infection caused by S. Haifa in India. The finding highlights the potential zoonotic risk of rare non-typhoidal Salmonella serovars and emphasizes the importance of surveillance, routine serotyping, and antimicrobial resistance monitoring within a One Health framework. Full article

Background/Objectives: The domestic yak (Bos grunniens) is a livestock species of major relevance in high-altitude environments and an important model for studying adaptation and reproductive isolation within Bovini. Despite its close phylogenetic relationship with cattle (Bos taurus), yak × cattle hybrids show a marked sex-biased fertility pattern, with fertile females and generally sterile F1 males, suggesting that subtle chromosomal or genomic differences may underlie post-zygotic reproductive barriers. In this study, we performed a cytogenetic characterization of eight adult yak bulls imported and reared in Central Italy using conventional and molecular cytogenetic approaches. Results: GTG-, RBG-, RBA- and CBA-banding confirmed the yak diploid number as 2n = 60 and the fundamental number as NF = 62, with banding patterns highly comparable to the standardized cattle karyotype. CBA-banding showed an X chromosome lacking evident constitutive heterochromatin and a Y chromosome with distal C-positive blocks. Chromosome instability was low, with 3.75% abnormal metaphases, mainly represented by chromatid and iso-chromatid breaks, while the mean sister chromatid exchange (SCE) rate was 5.19 ± 2.14 per cell. Sequential Ag-NOR/RBA staining localized nucleolar organizer regions (NORs) at the telomeres of autosomes 2, 3, 4, 11 and 25, as in cattle. Zoo-FISH using bovine chromosome paints for X, Y, 5 and 15 showed complete hybridization to the corresponding yak chromosomes, and BAC-FISH mapped the Y-linked ZFY and SRY genes to positions homologous to those reported in cattle. A comparative bioinformatics analysis of available yak genome assemblies confirmed the overall genome-wide correspondence with cattle, while revealing chromosome orientation issues and small local inconsistencies that may be relevant for comparative mapping and probe design. Conclusions: Overall, at the resolution tested, these findings support broad macrostructural conservation of yak and cattle karyotypes and provide cytogenetic reference data for yak populations reared outside of their traditional range. The persistence of F1 male sterility despite this large-scale chromosomal conservation suggests that fine-scale sex chromosome differences, particularly involving pseudoautosomal regions, recombination boundaries, or heterochromatin organization, may deserve targeted investigation. Full article

Background: Foot-and-mouth disease (FMD) is a highly contagious viral disease causing substantial economic losses in livestock. Conventional intramuscular (IM) vaccination is widely used for FMD control but may be associated with transient reductions in milk production. This study evaluated whether intradermal (ID) vaccination could induce comparable immune responses and protection while minimizing potential impacts on productivity. Methods: In cattle, the immunogenicity of an experimental bivalent ID vaccine was compared with that of a commercially available IM vaccine by measuring antibody responses for up to 140 days post-vaccination (dpv). Milk production was monitored for 7 dpv in a separate cohort of lactating cattle. Protective efficacy was evaluated in goats following ID vaccination and challenge with a 2025 Republic of Korea serotype O field isolate (O/ME-SA/Ind-2001). Results: ID vaccination induced humoral immune responses comparable to those elicited by IM vaccination throughout the 140-day observation period. Although no statistically significant difference in milk production was observed, the ID group showed a smaller numerical reduction in milk yield. Following viral challenge, ID-vaccinated goats developed rapid neutralizing antibody responses, exhibited no clinical signs, and showed lower viral RNA levels than unvaccinated controls. Conclusions: Intradermal vaccination induced long-lasting immune responses comparable to conventional IM vaccination, was associated with a smaller numerical reduction in milk yield, and protected goats against challenge with a contemporary FMDV field isolate. These findings provide preliminary evidence supporting the potential of ID vaccination as an alternative strategy for FMD control in ruminants and warrant further comparative studies with conventional IM vaccination. Full article

Achieving accurate cattle detection in complex barn environments is a critical technical challenge for smart livestock farming. Cattle exhibit highly similar appearances, severe occlusion, and significant multi-scale variations, making it difficult for existing detection methods to balance accuracy with model efficiency. This paper proposes a lightweight cattle detection model, DMFRNet, with YOLO11 as the baseline. To address these challenges, DMFRNet introduces three targeted improvements. First, C3K2-DIMB is designed to enhance multi-scale feature extraction by adaptively reweighting multi-branch depthwise convolution features, thereby improving the representation of cattle with different body sizes, poses, and viewing distances. Second, SimAM is embedded after the SPPF layer to refine high-level semantic features without introducing additional parameters, which improves feature discrimination under occlusion, low contrast, and complex backgrounds. Third, LSCDH replaces the original decoupled detection head to reduce parameter redundancy through cross-scale shared convolution while preserving multi-scale prediction capability. These designs jointly address the key challenges of multi-scale cattle appearance, occlusion, and lightweight model construction in complex barn scenes. Experimental results on the combined CBVD-5 and Dairy Cow dataset demonstrate that DMFRNet achieves a Precision of 93.49%, F1 of 89.84%, mAP50 of 93.85%, and mAP50–95 of 61.74%, with only 2.16 M parameters, 5.10 GFLOPs, and a model size of 4.5 MB. Comparative experiments demonstrate that DMFRNet provides a favorable accuracy–efficiency trade-off for lightweight dairy cow detection. Full article

Background/Objectives: Bovine respiratory disease (BRD) remains a major concern in cattle research, and the long-term effects of vaccination on health and immune responses are not well defined. This study compared gene expression in vaccinated (VAX) and unvaccinated (NOVAX) preweaned calves and subsequent BRD development during backgrounding. Methods: Whole blood was collected at four timepoints (TIME; T1-4; median age 107, 114, 183, and 230, respectively) from 73 bull calves enrolled in a blinded randomized controlled trial; VAX calves received a commercial attenuated multivalent viral vaccine at T1 and T3. Results: Whole-blood transcriptomics was used to quantify mRNA, identifying 5364 differentially expressed genes (DEGs) for TIME, 84 DEGs for vaccination (VAX), and 129 for BRD status using both glmmSeq and QLF testing (glmmSeq only DEGs: 11,068 TIME, 358 VAX, and 9241 BRD). VAX calves at T3 were clustered uniquely with the enrichment of pathways related to the cellular response to stress, neutrophil degranulation, and antigen processing and presentation compared to NOVAX cattle and VAX at other timepoints. Interferon pathways, natural killer cell responses, and neutrophil activity were generally absent across all timepoints, while antigen presentation pathways were persistently enriched. Regardless of vaccination or future BRD diagnosis, immunological development over time was indicated by DEGs related to adaptive immunity, lymphocyte development, and inflammatory resolution. At T4, cattle diagnosed with BRD during backgrounding had differential gene expression related to oxygen transport, hemoglobin function, and metabolic processes compared to cattle that remained healthy. Conclusions: This study provides insights into the possible genomic mechanisms underlying vaccine responses and preclinical BRD susceptibility in preweaned beef cattle. Full article

Background/objectives: The emergence of highly pathogenic avian influenza A (H5N1) virus infections in dairy cattle in the United States revealed a novel mammalian host and a potential transmission pathway involving raw milk and dairy production systems. Sustained circulation of H5N1 in dairy herds is of concern because ongoing viral adaptation in mammals may increase the risk of efficient mammalian transmission and subsequent zoonotic spread. In response to this emerging threat, we developed a chimpanzee adenovirus (ChAd)-vectored vaccine expressing the haemagglutinin 5 antigen (H5HA) from the dairy cattle isolate A/dairy cattle/Texas. Methods: Lactating dairy cows were vaccinated by either intramuscular (N = 3) or intranasal administration (N = 3). H5HA clade 2.3.4.4b antibodies in cow’s milk and sera were evaluated by ELISA. Hemagglutination and neutralisation capacity were also evaluated. Results: IgG and IgA H5HA-specific antibodies were detected in serum and milk from parenterally vaccinated animals, demonstrating the induction of a systemic immune response. The neutralising antibody responses elicited were only detected in serum of cows vaccinated via the intramuscular route. Conclusions: These preliminary findings support the feasibility of ChAd-vectored vaccination as a strategy to induce humoral immunity in cattle against emerging H5N1 influenza A viruses. Cross-reactive antibody responses against both A/dairy cattle/Texas/24-008749_001/2024 and A/Ibis/Egypt/RLQP-229S/2022 support the capacity of the vaccine to recognise antigenically related H5N1 clade 2.3.4.4b viruses circulating in mammalian and avian reservoirs. Further studies of vaccine efficacy and the immunological mechanism of protection should now be undertaken with the aim of reducing viral transmission and milk-associated shedding in dairy herds. Full article

Background/Objectives: Zoonotic tuberculosis (TB) remains a persistent public health challenge worldwide. It is particularly common in settings with close human–livestock–environment interactions. In Tanzania, progress toward TB control is increasingly threatened by multidrug-resistant tuberculosis (MDR-TB), yet genomic data from regions characterized by pastoralist and mining activities remain scarce. This study employed whole-genome sequencing (WGS) to characterize M. tuberculosis complex (MTBC) strains circulating among human and cattle populations in the Manyara region of northern Tanzania, with a focus on resistance-associated mutations and phylogenetic relationships. Methods: This cross-sectional study was conducted between September 2024 and February 2025. A total of 178 presumptive human TB cases provided sputum samples. From cattle, 161 samples were collected (110 milk samples and 51 lymph node aspirates), with each animal contributing only one type of sample. Specimen were analyzed using GeneXpert MTB/RIF, Lowenstein–Jensen culture, and WGS. Phylogenetic reconstruction was performed using SNP-based methods and IQ-TREE2 version 2.2.0. Results: Among human participants, 14 (7.8%) sputum samples were GeneXpert positive and were confirmed as members of MTBC by LJ culture. In cattle, one (0.62%) lymph node aspirate was positive for MTBC. Significant predictors of MTBC positivity included previous TB history, weight loss, and occupation involving mining and cattle keeping. WGS of five human isolates identified Lineages 1, 3, and 4. One isolate (Sample 98) harbored mutations associated with XDR-TB. Conclusions: WGS revealed M. tuberculosis Lineages 1, 3 and 4 circulating in the Manyara region, with diverse genetic mutations conferring with resistance to first- and second-line anti-TB drugs. These findings highlight the importance of integrated genomic surveillance to monitor drug resistance patterns in Tanzania and similar settings across human and animal populations. Full article

Methane (CH₄) emissions from dairy cattle contribute substantially to agricultural greenhouse gas production and are influenced by genetic, physiological, environmental and management-related factors. The present study investigated CH₄-related traits and genotype–system interactions in Holstein Friesian (HF) dairy cows using repeated laser methane detector (LMD)-based measurements. A total of 134 cows from one research herd reflecting a commercial production system were repeatedly recorded for CH₄ traits (739 observations per trait) between 2020 and 2024 and linked with milk performance test-day data, behavioral observations, environmental measurements and genomic breeding values. CH₄ traits were derived separately for respiration- and eructation-related emissions. Generalized linear mixed models revealed significant effects of wind speed, rumination behavior, interaction behavior and days in milk on several CH₄ traits. Across lactation, respiration-related CH₄ traits slightly decreased, whereas eructation-related traits increased toward later lactation stages. Correlations between CH₄-related breeding values and production traits were generally low to moderately negative, ranging from −0.24 to 0.08, indicating that selection for reduced CH₄ emissions may be achievable without major unfavorable effects on milk production traits. To evaluate the complex relationships among CH₄ emissions, production, behavior, environment, diet and genetic background, a structural equation model (SEM) was applied. Environmental conditions, particularly temperature and humidity, showed the strongest positive association with CH₄ emissions, while eructation-related CH₄ traits contributed more strongly to the latent CH₄ construct than respiration-related traits. Behavioral activity, especially rumination, indicated relevant associations with CH₄ expressions. The SEM further suggested that CH₄ emissions are shaped by interconnected environmental, physiological and genetic pathways rather than by a single dominant factor. Overall, the results highlight the importance of environmental sensitivity and longitudinal biological variation in CH₄ phenotypes under commercial dairy production conditions. Repeated on-farm CH₄ measurements, particularly eructation-associated traits, may provide valuable indicator traits for future genomic breeding and management strategies to reduce the environmental footprint of dairy cattle production. Full article

Clostridium perfringens type A causes neonatal clostridial enteritis, hemorrhagic enteritis, and sudden death syndrome in cattle. This study examined a fatal outbreak at a fattening farm housing 58 adult yaks in Southwest China, with an incidence of 22.41% (13/58) and a 100% case fatality rate. Histopathology of deceased yaks showed widespread multi-organ hemorrhage and severe hemorrhagic enteritis. A specific PCR assay amplified the alpha-toxin gene of Clostridium perfringens, while no other pathogens were detected. Clostridium perfringens was isolated from small intestinal contents using TSC agar, designated strain CQ1, and identified as type A through toxinotyping. Whole-genome sequencing revealed that strain CQ1 carries the core alpha-toxin gene along with key accessory virulence determinants (pfoA, colA, and cloSI). Phylogenomic analysis based on core single-nucleotide polymorphisms revealed that strain CQ1 is clustered into a distinct, independent evolutionary lineage with an existing historical yak isolate and a canine-origin isolate. Intraperitoneal challenge in mice confirmed its extreme lethality, causing 100% mortality within 36 h with severe intestinal necrosis. These findings provide fundamental genetic resources for understanding the virulence mechanisms and genetic background of this pathogen and offer critical insights for preventing and controlling clostridial diseases in high-altitude yak farming. Full article

Background: The major histocompatibility complex (MHC) is a well-known gene complex that plays a fundamental role in immune recognition; however, its influence on reproductive processes in cattle is not yet fully established, particularly regarding how it modulates the female response to the embryo. Therefore, this study aimed to investigate the relationship between MHC genes and reproductive processes in cattle and to identify potential molecular targets involved in these mechanisms. Methods: Data from four studies identified through a systematic review were integrated. MHC genes associated with reproduction were identified, neighboring genomic regions were explored to detect candidate genes and transcription factors, and biological process networks were constructed using differentially expressed genes associated with cattle. Results: The integrated analysis led to the identification of six MHC genes associated with reproduction, along with 54 candidate genes from genome-wide association studies and 46 from transcriptomic studies located in neighboring regions. Among these, BoLA-DQB and BoLA-DQA5 stood out in all analyses, while the transcription factors FOXA1, FOXO3, ELF5, and STAT3 appeared across the different datasets. These genes and factors may represent potential targets for future functional validations and could be explored using genome editing technologies to better understand their roles in reproductive processes. The identified biological pathways were related to embryonic development and reproductive organ formation, providing a preliminary foundation for future investigations. Conclusions: This work integrates currently available evidence and highlights potential molecular targets that can be explored in cattle breeding and reproductive biology, associating MHC genes with these roles and advancing innovative perspectives in the field of molecular genetics. Full article

Cross-view re-identification of Hanwoo cattle remains challenging: weak texture provides only limited identity cues, and large pose and viewpoint changes easily distort these cues, causing severe feature dispersion. As a result, samples from the same individual may be scattered in the feature space, whereas visually similar individuals can form ambiguous local neighborhoods. To address this problem, we propose a framework that explicitly improves identity compactness for weakly textured cattle ReID. Specifically, Pose- and Text-Conditioned Inpainting Diffusion (PTID) is trained to generate pose-diverse yet identity-consistent samples and, during inference, aggregates their features with the original input feature to approximate a compact identity center and reduce pose-induced feature dispersion. Dual-Adaptive Viewpoint-Aware Feature Centralization (DVFC) further refines retrieval features by adaptively exploiting viewpoint consistency and neighborhood reliability, thereby suppressing unreliable neighbor mixing under large cross-view variation. We also construct a Hanwoo ReID dataset containing 37 identities and 12,480 images collected from three farm environments with substantial variations in pose, illumination, occlusion, and background conditions. Extensive experiments on multiple strong baselines under both closed-set and open-set settings demonstrate consistent improvements, with gains of up to 40.8 points in mAP and 26.1 points in Rank-1 accuracy. These findings demonstrate that explicitly improving identity compactness through identity-consistent generation and viewpoint-aware feature centralization is a promising solution for the robust re-identification of weakly textured cattle. Full article

Mycoplasma bovis (M. bovis) is a major pathogen in cattle, primarily responsible for bovine respiratory disease complex (BRDC). Characterized by high infectivity and morbidity, M. bovis spreads rapidly within herds and is challenging to control and eradicate, underscoring the need for early and accurate diagnosis. To address this, we developed a competitive enzyme-linked immunosorbent assay (cELISA) for detecting M. bovis-specific antibodies in bovine sera. The assay uses recombinant MbovP579 protein (1 μg/mL) as the coating antigen and an HRP-conjugated 1A2 monoclonal antibody against MbovP579 (mAb, 0.35 μg/mL) as the competitor. With a cut-off value of 40.69% (percentage inhibition, PI), the cELISA demonstrated apparent sensitivity (90%; 95% CI: 78.64–95.65%) and specificity (96.15%; 95% CI: 90.53–98.49%) using the known background positive and negative sera. In addition, it yielded 100% positivity (9/9) against sera collected from 21 days post-immunization. The assay showed no cross-reactivity with other Mycoplasma species or two common bovine bacterial pathogens, confirming its high specificity. The intra- and inter-assay coefficients of variation (CVs) were below 10%. In clinical evaluations, this cELISA generated a 55.57% positivity rate for field samples (n = 1069) and exhibited 90.46% overall agreement (967/1069; 95% CI: 88.54–92.15%) with the commercial indirect ELISA kit, demonstrating strong diagnostic consistency. Discrepant specimens were further analyzed by a metabolic inhibition test (MIT), which suggested improved specificity, although further validation is required of this cELISA. Full article