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

Bovine viral diarrhea virus (BVDV) is one of the major pathogens hindering the development of the global beef industry. To investigate the epidemic profile and genetic diversity of this virus, a total of 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 results showed that 35 of the 77 bovine samples (45%) were positive for BVDV, with the highest positive rate of 26% (20/77) in Henan province. The 5ʹ-UTR sequences of the viruses from 21 positive samples and the whole-genome sequence from one sample (BVDV-385) were determined and analyzed. The 5ʹ-UTR sequences from this study were 74.7–96.4% identical to those of 23 reference sequences. Phylogenetic analysis based on the 5ʹ-UTR sequences indicated that 20 of the strains belonged to the subtype BVDV-1m, while only one, BVDV-385 from Henan province, belonged to genotype BVDV-3. Analysis of the genome sequence of strain BVDV-385 showed that its E2 protein has a unique amino acid (aa) deletion and ten unique aa substitutions, and its NS5B protein has seven unique aa substitutions. The variations were predicted to affect four potential linear B cell epitopes in the E2 protein and to introduce a potential non-canonical N-glycosylation site (574 NPS) in the NS5B protein. The results of this study contribute to our understanding of the genetic diversity of BVDV in China.