Detection and genomic characterization of an emerging bovine coronavirus in Southwest China

Bovine coronavirus (BCoV) poses significant economic threats to the cattle industry, yet molecular epidemiological data from Southwest China remain scarce. In this study, we investigated the molecular epidemiology, genomic features, and antigenic characteristics of BCoV circulating in this region. Molecular detection showed that BCoV was frequently detected among clinically affected cattle, with farm-level clinical detection rates exceeding 75% in several major cattle-producing areas. Phylogenetic analysis showed that all identified strains belonged to the GII subclade, among which 11 formed a distinct subclade characterized by purifying selection. The high nucleotide identity (99.5-99.7%) and strict geographic clustering of these strains suggest a likely founder effect. Comparative genomic and structural analyses identified lineage-associated mutations, including substitutions in open reading frame 1ab (W673C, V2780I, M2909L, L4202F, D4642A, L6611M, T6653I, and E6785D), spike protein (D206N and V1288F), and an A43S mutation in the nucleocapsid protein. Computational analyses further suggested that altered spike protein rigidity and reduced O-glycosylation may contribute to altered receptor interaction and potentially influence viral spread. In addition, predicted epitope profiling revealed marked antigenic divergence from the classical Mebus vaccine strain, indicating potential variations in cross-reactive epitope profiles between historical vaccine lineages and currently circulating variants. Furthermore, the identification of the A43S mutation in the nucleocapsid protein also highlights the need to further re-evaluate its potential impact on antigen-based diagnostic performance. Overall, these findings expand current knowledge of BCoV diversity in Southwest China and support continued genomic surveillance, functional validation, and antigenic characterization to guide the development of locally matched vaccines and diagnostic tools.