Genomic Characteristics of Bovine Enteric Viruses Beyond Rotavirus: A Systematic Review

Neonatal calf diarrhea exhibits a complex multietiological landscape, yet diagnostic and vaccination paradigms remain historically anchored to Bovine Rotavirus A (BoRVA) and monovalent Bovine Coronavirus (BCoV) infections. The primary objective of this systematic review is to synthesize contemporary genomic evidence to elucidate the evolutionary dynamics, taxonomical diversity, and complex viral coinfection of underreported bovine enteric viruses. In strict adherence to PRISMA 2020 guidelines, we systematically searched Scopus and PubMed for primary genomic studies published between January 2016 and June 2026 and the protocol was pre-registered on OSF Registries on 15 May 2026. The AXIS tool was utilized to appraise the methodological quality of the included studies. Data synthesis involved taxonomical categorization and comparative analysis of clinical morbidity. From an initial 732 records, 70 high-quality studies were included. The review reveals a paradigm shift towards whole-genome sequencing (WGS) and metagenomics (24.3% of studies), uncovering a highly heterogeneous virome driven by Caliciviridae, Picornaviridae, Coronaviridae, and Astroviridae. While BCoV represents 38.6% of the monovalent evidence, multivalent approaches demonstrate that clinical morbidity is significantly amplified by viral co-infections. Notably, evidence from the included literature indicates that tripartite infections (e.g., Bovine Astrovirus + BoRVA + Bovine Kobuvirus) are significantly associated with a higher risk of severe morbidity (OR = 14.82). Furthermore, individual phylodynamic studies report localized instances of rapid mutational dynamics (e.g., in BCoV) and persistent homologous recombination, facilitating structural divergence and immune evasion. The synthesis demonstrates that bovine enteritis is strongly associated with an altered enteric viral-community composition rather than isolated single-pathogen invasions. Future veterinary diagnostics and multivalent vaccine designs must address the genomic plasticity and complex co-detection patterns of the enteric viral consortium.