Molecular detection of bovine coronavirus in the environment of a naturally infected dairy cattle herd

Bovine coronavirus (BCoV) causes neonatal diarrhea and respiratory diseases in cattle. Detection of BCoV on surfaces and fomites in dairy facilities is rarely reported. We examined the presence of BCoV on various surfaces of a dairy farm with previous BCoV-positive cattle. A total of 61 samples were collected, including 37 samples of surfaces and fomites from the housing of suckling calves, weaned calves, heifers, and lactating cows. Fecal samples (n = 13) and nasal secretions (n = 11) were collected from calves and cows. Molecular identification of BCoV was performed using semi-nested RT-PCR. Amplicons of BCoV genes N and S1 from three positive samples (environment, diarrheic feces, and nasal secretions) were selected for nucleotide (nt) sequencing analysis. BCoV RNA was detected in 27% (10/37) of environmental samples, including wooden surfaces, concrete and tiles, plastic feed troughs, drinkers, and calf bottles. Furthermore, BCoV RNA was amplified in 46.1% of fecal and 36.4% of nasal secretion samples. Analysis of the N gene revealed 100% nt similarity between strains from different sources, while the S1 gene showed 99.7 to 99.8% similarity. The same BCoV strain was detected in cattle and on the evaluated surfaces. These strains were ancestrally different from the prototype strains but clustered with other Brazilian field strains. In conclusion, BCoV is present in cattle and on different surfaces within the environment of the evaluated dairy cattle farm. Biosecurity measures, such as cleaning and disinfection, are crucial to mitigate infection risk, especially for calves.