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.

As diseases caused by new and emerging viruses continue to be a major threat to humans and animals worldwide the need for new therapeutic options intensifies. A wide variety of viruses including Influenza A virus, Human immunodeficiency virus, Middle East respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus require ion channels for efficient replication. Thus, targeting host ion channels may serve as an effective means to attenuate virus replication and help treat viral diseases. Targeting host ion channels is an attractive therapeutic option because a range of ion channel-blocking compounds already exist for the treatment of other human diseases and some of these possess in vitro and sometimes in vivo antiviral activity. Therefore, identifying the specific ion channels involved in replicative cycles could provide opportunities to repurpose these ion channel inhibitors for treating viral diseases. Furthermore, optimised methodologies for identifying effective ion channel targeting drugs and their mechanisms of action could enable rapid responses to newly emerged viruses. This review discusses the potential of ion channels as suitable drug targets to treat diseases caused by viruses by describing known ion channel targeting drugs including their antiviral activity; by summarising prior research demonstrating the requirement for host ion channels for efficient replication of some viruses; and by hypothesising about the role these drugs might play in our ongoing fight against viral diseases.

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 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.

Bovine betacoronavirus (BoCoV) is a pneumoenteric pathogen of cattle that is closely related to human coronavirus OC43. Vaccines are administered to protect against diseases caused by BoCoV, but knowledge gaps exist with regard to correlates of protection and the effect of immune evasion on driving evolution. In this study, immune epitopes were mapped onto BoCoV structural proteins, including spike and haemagglutinin esterase (HE), and then supported with targeted gene sequencing of Irish clinical isolates and selective pressure analysis. Increased prevalence of diversifying selection and amino acid changes in some mapped immune epitopes suggests that immune escape is selecting for non-synonymous mutations arising in these regions. Selection analysis and sequencing provided increased support for neutralising antibody (nAb) epitopes compared to others, suggesting that nAbs are an important arm of the immune response to BoCoV. Phylogenetic analysis of spike and HE sequences showed that Irish isolates from this study were in the European clade, except for one HE sequence that sat in the Asian/American clade, while the spike gene of this sample was in the European clade. Recombination between a European and an Asian/American isolate would give rise to such a sequence. This study has gathered evidence suggesting that pressure to evade the nAb response is contributing to BoCoV evolution.

The meat processing industry was negatively affected by the COVID‐19 pandemic. The unique conditions in meat processing plants (MPPs) were recognized to have the potential to increase SARS‐CoV‐2 transmission. Should SARS‐CoV‐2 persist for extended periods in these built environments, this may contribute to increased risk of virus transmission. To test this hypothesis, SARS‐CoV‐2 persistence was assessed in conditions reflective of a MPP. Different biotic/abiotic materials were inoculated with SARS‐CoV‐2 and recovery of viable virus measured over time. Findings showed it was possible to recover SARS‐CoV‐2 from beef, pork, and salmon for at least 22 days at −20°C and for at least 12 days at +4°C. SARS‐CoV‐2 recovery from salmon scales and salmon flesh was similar, but viable virus recovered from pork fat was significantly reduced compared to pork meat. In parallel, foods purchased from Irish supermarkets during a COVID‐19 wave were contemporaneously tested for the presence of SARS‐CoV‐2 RNA but none of the samples tested positive by RT‐qPCR. Viable SARS‐CoV‐2 can be inactivated on food or abiotic surfaces by incubation at 56°C or 75°C but fomite transmission during MPP outbreaks cannot be ruled out due to the recovery of SARS‐CoV‐2 from stainless steel and work clothing fabric for up to 10 h under representative conditions. These data support a multilayered approach to reducing the risk of airborne infections such as SARS‐CoV‐2 that should include mitigations such as increased ventilation, mask wearing, and the disinfection of work surfaces to reduce the amount of SARS‐CoV‐2 in the meat processing plant environment.

Shiga toxin-producing Escherichia coli (STEC) poses a significant public health risk due to its zoonotic potential and association with foodborne outbreaks. This study investigates the presence of STEC in faecal samples collected from sheep, focusing on bacteriological methods for isolation and preliminary characterization. Growth on selective agar showed that 90 of 140 faecal samples were positive for STEC. The total average prevalence was 64.3% (95% CI 56.1–71.7%). The highest prevalence was 71.4% (54.9–83.7%), recorded in summertime, while the lowest was 51.4% (35.6–67%) in the autumn. Selected isolates were found to be resistant to commonly used antibiotics, with isolates expressing a resistant phenotype to two, three or more of the tested antibiotics. Based on the Biocheck.UGent system for risk-based assessment of farm biosecurity, the total, internal and exterior average farm biosecurity scores were substantially lower than the world average.