Emerging and Novel Ovine Viruses: Molecular Diagnostics, Genomic and Metagenomic Surveillance, and One Health Perspectives

Emerging and novel ovine viruses pose increasing threats to animal health, livestock productivity, trade, food security, and public health preparedness. Their emergence is driven by complex interactions among animal movement, mixed-species production systems, wildlife–livestock interfaces, arthropod vectors, environmental changes, and viral evolution. This review critically compares current strategies for identifying major, emerging, re-emerging, zoonotic, and newly recognized ovine viruses, with emphasis on their analytical sensitivity, turnaround time, throughput, operational cost, accessibility, field applicability, validation status, and capacity for novel-virus detection. Conventional diagnostic approaches, including virus isolation, serology, antigen detection, histopathology, and immunohistochemistry, remain essential for confirmation and flock-level surveillance but may be limited by slow turnaround, dependence on specialized facilities, reduced sensitivity at low viral loads, and an inability to identify highly divergent or unknown viruses. Targeted molecular assays, including PCR, RT-PCR, qPCR, multiplex assays, digital PCR, isothermal amplification, and CRISPR-based diagnostics, have improved detection speed and sensitivity but generally require prior knowledge of viral genomic targets. Genomic and metagenomic approaches, including whole-genome sequencing, next-generation sequencing, nanopore sequencing, viral metagenomics, bioinformatics, and phylogenetic analysis, provide broader detection capabilities by enabling characterization of viral diversity, outbreak tracing, co-infection identification, and discovery of previously unrecognized viruses. However, their interpretation remains challenging due to low viral abundance, poor sample quality, host nucleic acid background, contamination, incomplete reference databases, limited computational capacity, and the inability of sequence detection alone to confirm disease causality. Therefore, future ovine virus surveillance requires integration of molecular diagnostics with active, passive, outbreak-based, risk-based, vector, wildlife, and animal-movement surveillance within a One Health framework. Linking genomic information with ecological, epidemiological, and environmental data will be essential for transforming ovine virus surveillance from reactive diagnosis toward proactive preparedness. Advances in standardized sampling, validated field diagnostics, affordable sequencing, curated databases, bioinformatics capacity, and cross-sector data sharing will strengthen early recognition, risk assessment, and preparedness against emerging viral threats in sheep.