Identical consensus genomes of bovine coronavirus in respiratory and enteric specimens from a single cow and sequence variation after cell culture passage.

Bovine coronavirus (BCoV) causes respiratory and enteric diseases in cattle, but the relationship between viral genetic variation and anatomical distribution remains unclear. We compared BCoV genomes detected in a tracheal swab and diarrheic intestinal content from the same adult cow. The two clinical specimens had identical 31,015-nt consensus genomes. After five passages in HRT-18 cells, the recovered tracheal isolate differed at three consensus-level amino acid positions (HE N104D, S Q179K, and S E965D) and showed marked within-sample heterogeneity. These findings highlight the importance of direct sequencing of clinical specimens because cell-culture passage can alter viral population composition.