Whole-Genome Sequencing Reveals the Evolutionary Characterization of Bovine Coronavirus

Abstract

Bovine coronavirus (BCoV) is endemic worldwide, causing gastrointestinal and respiratory diseases in cattle, making it a topic of significant interest. The present study investigated the prevalence and evolutionary characterization of BCoV identified in Yunnan, China. The results indicated that the overall seroprevalence was 21.75% (65/285), with a higher rate (25.56%) in diarrhea samples than in healthy samples (15.24%). Meanwhile, PCR was used to detect BCoV pathogens in 616 fecal samples. The overall BCoVs positive rate in Yunnan was 28.73% (177/616), with diarrhea samples showing a higher rate (37.46%) compared to healthy samples (20.50%). The whole genomes of three BCoV strain were successfully amplified, namely, BCoV/YN1LC/2023, BCoV/YNZT/2023, and BCoV/YNLP/2023. These identified strains showed high homology to strains derived from calf diarrhea and respiratory samples than to the classical and vaccine strains. Sequence analyses revealed that seven consistent amino acid mutations in the S protein of three BCoV identified strains, including M¹¹/T, K¹¹⁵/D, N¹⁴⁶/I, D¹⁴⁸/G, L¹⁵⁴/F, N⁴⁹⁹/S, and N⁵⁰⁹/H. Additionally, mutations L⁵/P, N⁴⁹/T, and L³⁹²/I were observed in the HE protein, and mutations L⁵³/Q, M³⁸⁶/T, M³⁸⁷/I, S⁴²³/I, and Y⁴⁴¹/F were found in the N protein. Identified as a recombinant strain, the BCoV/YNLP/2023 displays a unique mutation S⁵⁰¹/F in the S protein, D⁶⁶/G in the HE protein, and the ²⁰⁶SRA²⁰⁸ deletion in the N protein. Phylogenetic analysis suggested that the identified strains could be the predominant strains in Yunnan Province or even in Southwest China, demonstrating geographic clustering. These data highlight BCoV’s high prevalence and evolutionary characterization in Yunnan, China, providing valuable information for the effective prevention and control of BCoV in the future.