Viral metagenomic next-generation sequencing (vmNGS) has transformed our capacity for the untargeted detection and characterisation of (re)emerging zoonotic viruses, surpassing the limitations of traditional targeted diagnostics. In this review, we critically evaluate the current landscape of vmNGS, highlighting its integration within the One Health paradigm and its application to the surveillance and discovery of (re)emerging viruses at the human–animal–environment interface. We provide a detailed overview of vmNGS workflows including sample selection, nucleic acid extraction, host depletion, virus enrichment, sequencing platforms, and bioinformatic pipelines, all tailored to maximise sensitivity and specificity for diverse sample types. Through selected case studies, including SARS-CoV-2, mpox, Zika virus, and a novel henipavirus, we illustrate the impact of vmNGS in outbreak detection, genomic surveillance, molecular epidemiology, and the development of diagnostics and vaccines. The review further examines the relative strengths and limitations of vmNGS in both passive and active surveillance, addressing barriers such as cost, infrastructure requirements, and the need for interdisciplinary collaboration. By integrating molecular, ecological, and public health perspectives, vmNGS stands as a central tool for early warning, comprehensive monitoring, and informed intervention against (re)emerging viral threats, underscoring its critical role in global pandemic preparedness and zoonotic disease control.

Ovine pulmonary adenocarcinoma (OPA), caused by Jaagsiekte sheep retrovirus (JSRV), is characterised by the development of invariably fatal lung tumours primarily in adult sheep. High infection rates and disease prevalence can develop during initial infection of flocks, leading to on-farm economic losses and animal welfare issues in sheep with advanced disease. The disease has been reported in Ireland and is notifiable, but the presence of JSRV has never been confirmed using molecular methods in this country. Additionally, due to the difficulties in ante-mortem diagnosis (especially of latently-infected animals, or those in the very early stages of disease), accurate information regarding national prevalence and distribution is unavailable. This study aimed to confirm the presence of JSRV in Ireland and to obtain estimates regarding prevalence and distribution by means of an abattoir survey utilising gross examination, histopathology, JSRV-specific reverse transcriptase polymerase chain reaction (RT-PCR) and SU protein specific immunohistochemistry (IHC) to examine the lungs of adult sheep. Lungs from 1911 adult sheep were examined macroscopically in the abattoir and 369 were removed for further testing due to the presence of gross lesions of any kind. All 369 were subject to histopathology and RT-PCR, and 46 to IHC. Thirty-one lungs (31/1911, 1.6%) were positive for JSRV by RT-PCR and/or IHC but only ten cases of OPA were confirmed (10/1911, 0.5%) Four lung tumours not associated with JSRV were also identified. JSRV-positive sheep tended to cluster within the same flocks, and JSRV-positive sheep were identified in the counties of Donegal, Kerry, Kilkenny, Offaly, Tipperary, Waterford and Wicklow. The presence of JSRV has been confirmed in the Republic of Ireland for the first time using molecular methods (PCR) and IHC. In addition, an estimate of OPA prevalence in sheep at slaughter and information regarding distribution of JSRV infection has been obtained. The prevalence estimate appears similar to that of the United Kingdom (UK). Results also indicate that the virus has a diverse geographical distribution throughout Ireland. These data highlights the need for further research to establish national control and monitoring strategies.

Bovine respiratory disease (BRD) remains among the leading causes of death of cattle internationally. The objective of this study was to identify risk factors associated with exposure to BRD pathogens during the peri-weaning period (day (d)-14 to d 14 relative to weaning at 0) in dairy bull calves using serological responses to these pathogens as surrogate markers of exposure. Clinically normal Holstein-Friesian and Jersey breed bull calves (n = 72) were group housed in 4 pens using a factorial design with calves of different breeds and planes of nutrition in each pen. Intrinsic, management and clinical data were collected during the pre-weaning (d − 56 to d − 14) period. Calves were gradually weaned over 14 days (d − 14 to d 0). Serological analysis for antibodies against key BRD pathogens (BRSV, BPI3V, BHV-1, BHV-4, BCoV, BVDV and H. somni) was undertaken at d − 14 and d 14. Linear regression models (for BVDV, BPI3V, BHV-1, BHV-4, BCoV and H. somni) and a single mixed effect random variable model (for BRSV) were used to identify risk factors for changes in antibody levels to these pathogens. BRSV was the only pathogen which demonstrated clustering by pen. Jersey calves experienced significantly lower changes in BVDV S/P than Holstein-Friesian calves. Animals with a high maximum respiratory score (≥8) recorded significant increases in H. somni S/P during the peri-weaning period when compared to those with respiratory scores of ≤3. Haptoglobin levels of between 1.32 and 1.60 mg/ml at d − 14 were significantly associated with decreases in BHV-1 S/N during the peri-weaning period. Higher BVDV S/P ratios at d − 14 were significantly correlated with increased changes in serological responses to BHV-4 over the peri-weaning period. Haptoglobin may have potential as a predictor of exposure to BHV-1. BRSV would appear to play a more significant role at the ‘group’ rather than ‘individual animal’ level. The significant associations between the pre-weaning levels of antibodies to certain BRD pathogens and changes in the levels of antibodies to the various pathogens during the peri-weaning period may reflect a cohort of possibly genetically linked ‘better responders’ among the study population.

Clostridium difficile is a recognised cause of typhlocolitis and diarrhoea in neonatal pigs but has never been confirmed in association with pathology and disease in Irish pigs. Four neonatal piglets, with a history of diarrhoea were referred to the Central Veterinary Research Laboratory, Backweston for necropsy. They were from a fully integrated, commercial pig farm with approximately 1000 sows. Three piglets had acute, superficial, erosive and suppurative typhlocolitis and the other had mild suppurative mesocolitis. Clostridium difficile (C. difficile) toxins A/B were detected using ELISA in the colonic contents from each piglet. C. difficile isolates from two of the piglets were PCR-ribotyped as 078 and an isolate from a third pig was ribotyped as 110. This is the first report confirming C. difficile in association with typhlocolitis in Irish pigs.

Mammary tumors of all types are rare in herbivores, and there is a particular paucity of reports in sheep. The present report describes a case of mammary carcinoma in a 6-year-old uniparous ewe. The tumor was present for at least 18 months, during which time the ewe remained clinically well. At postmortem examination, the mass was found to be multilobulated with occasional cysts. Histologically, the lobules consisted of tubules lined by cuboidal to low columnar epithelium with loss of polarity and moderate anisokaryosis within a moderately extensive fibrous stroma. It was classified as a low-grade carcinoma. The histologic classification and lack of evidence of invasion correlated well with the slow clinical progression.