Integrated epidemiological and genomic characterization of respiratory bovine coronavirus in U.S. cattle 2020–2025

Bovine coronavirus (BCoV) is an important contributor to the respiratory disease complex in cattle; however, integrated genomic and epidemiological data describing currently circulating respiratory BCoV strains in the United States remain limited. The objective of this study was to monitor respiratory BCoV at the genomic level and analyze its epidemiological patterns over five years, in addition to assess the pathological findings of the currently circulating BCoV in cattle. A total of 4,505 respiratory samples submitted to a diagnostic laboratory between January 2020 and November 2025 were analyzed, of which 693 (15.38%) tested positive for BCoV. Positivity was highest in young calves (0–40 days; 20.0%) and declined significantly with increasing age based on logistic regression analysis. Temporal trend analysis using locally estimated scatterplot smoothing and the Mann–Kendall test showed no significant monotonic change in BCoV detection during the study period. Co-infections were commonly detected between BCoV and other viral respiratory pathogens, while bacterial pathogens predominated in many samples. Lung tissues submitted from bovine respiratory cases were screened by qRT-PCR, and selected samples with high viral loads were subjected to next-generation sequencing. Complete genome sequencing identified four respiratory BCoV isolates (~31 kb), all clustering within genotype GIIb with recent U.S. strains. Comparative genomic analysis revealed amino acid substitutions in structural and non-structural proteins that may influence viral attachment, replication, and tissue tropism. These findings provide updated epidemiological and genomic insights into respiratory BCoV circulating in U.S. cattle. IMPORTANCE This study demonstrates continued detection and genetic evolution of respiratory bovine coronavirus (BCoV) among diagnostic respiratory samples submitted from U.S. cattle, with 15.38% positivity observed among 4,505 submitted samples and a higher proportion of positive submissions from young calves. Whole-genome sequencing of lung-derived isolates revealed consistent clustering within genotype GIIb alongside ongoing molecular diversification, including amino acid substitutions in spike, hemagglutinin-esterase, nucleocapsid, and membrane proteins, and the emergence of a previously unrecognized putative alternative ORF near 4.8-kDa NSP. These findings highlight that respiratory BCoV is continuously evolving at the site of disease. The observed genetic changes provide critical targets to refine diagnostic assays, support updating of vaccine strains, inform antiviral development, and enable more effective, evidence-based management strategies for controlling respiratory BCoV in cattle, requiring potential experimental validation.