Molecular detection and genotyping of bovine viral diarrhea virus in four provinces of China

Bovine viral diarrhea virus (BVDV) has long been one of the major pathogens hindering the development of the global beef industry. In the present study, to further investigate the epidemic profile and genetic diversity of the virus, 77 fecal samples were collected from cattle with diarrhea in Henan, Sichuan, Shandong and Hebei provinces of China during 2023–2024 and screened for the presence of BVDV using reverse transcription-polymerase chain reaction (RT-PCR). The positive samples for BVDV were subjected to the cloning and phylogenetic analysis of the 5ʹ-UTR and whole-genome sequences. The results showed that 35 out of 77 (35/77, 45.45%) bovine diarrhea samples tested positive for BVDV, with the highest proportion rate being observed in Henan province at 57.14% (20/35). Twenty 5ʹ-UTR and one whole-genome sequences of BVDV strains were acquired and analyzed. Phylogenetic analysis of the 5ʹ-UTR sequences indicated that 20 strains belonged to the BVDV-1m subtype, while the BVDV-385 strain from Henan province was clustered within the BVDV-3 genotype, indicating that the BVDV-1m subtype strains were the main strains circulating in China. Further amino acid analysis showed that a unique aa deletion and ten unique aa substitutions were exhibited in the E2 protein of the BVDV-385 strain, while seven unique aa sites in the NS5B protein. Furthermore, linear B cell epitope prediction indicated that four linear B cell potential epitopes were altered in the E2 protein, while predictions of N-glycosylation sites (NGS) revealed an additional glycosylation site (574 NPS) in the NS5B protein. Overall, this study reported the BVDV-3 strain was found in Henan Province, China, and performed a genetic evolutionary analysis of its whole genome sequence, which had important implications for understanding the genetic diversity of ongoing BVDV cases