Molecular characterization of BCoV infecting vaccinated and non-vaccinated cattle in Thrace district Türkiye and isolation of field strains.

BACKGROUND: Bovine coronavirus (BCoV) causes neonatal calf diarrhea (CD), winter dysentery in young cattle (WD), and respiratory system infections in cattle of all ages worldwide. The aim of this study was the detection, isolation, and investigation of the frequency, and molecular characterization of circulating BCoVs in cattle in the Thrace district of Türkiye. It was also aimed to determine genotypes and variants to include in vaccine and vaccination strategies. METHODS: For this purpose, a total of 47, including 12 integrated and 35 small-scale farms located in the Thrace district bordering European Union, were visited. A total of, 281 samples, consisting of 189 nasal/oropharyngeal and 92 fecal swabs were collected from calves exhibiting diarrhea and respiratory signs. RNA was extracted from samples and SYBR-Green real-time RT-PCR was performed. Phylogenetic and heatmap analyses were made using the sequences obtained from RT-PCR. Virus isolation was performed in HRT-18 cells using trypsin. RESULTS: BCoV RNA was detected in 22.06% (62/281) of swabs collected from calves under 6 months with enteric and/or respiratory signs. Detection rates were 21.69% (41/189) in nasal/oropharyngeal and 22.82% (21/92) in fecal swabs. The virus was identified in 95.7% (45/47) of sampled farms. Statistical analysis showed no significant association between BCoV positivity and the vaccination status of animals. Phylogenetic studies of S1 gene region have indicated that the samples detected in the Thrace district were clustered within the GIb subgroup along with European strains (97.6-100%, nucleotide similarity). These samples also exhibited high nucleotide similarity with HECV-4408 from human CoVs (98.28-99.14%) and DcCoV-HKU23 from other animal CoVs (97.85-99.14%). Despite being collected from distinct regions and years, two field isolates exhibited complete nucleotide identity. BCoV was successfully isolated from both nasal/oropharyngeal and fecal swabs. CONCLUSIONS: This study indicates that BCoV remains a health concern in calves in Türkiye, with isolates clustering in the GIb subgroup alongside European strains. Strengthening biosecurity and regular monitoring should remain priorities; collecting immunologic and field-effectiveness data will help guide the development of regionally updated vaccination strategies. A One Health approach that combines full-genome sequencing with epidemiological studies would help assess zoonotic potential.