Isolation and Genomic Characteristics of the First Bovine Viral Diarrhea Virus Subgenotype 2b Isolate from Buffalo in Guangxi Province, China

Abstract

(1) Background: Bovine viral diarrhea virus (BVDV) is an economically important pathogen affecting cattle worldwide. The genetic diversity of BVDV-2 in buffalo remains poorly understood. This study aimed to elucidate the genomic and antigenic features of GX24, the first BVDV-2b isolate identified from dairy buffalo in China. (2) Methods: The virus was isolated from a rectal swab through three blind passages in MDBK cells and identified through immunofluorescence and RT-PCR. The near-complete genome was sequenced using the Illumina platform and subjected to phylogenetic and recombination analysis. B-cell epitopes and glycosylation sites were predicted using BepiPred-3.0, Epitope1D, DiscoTope-3.0, NetNGlyc-1.0, and NetO-Glyc-4.0. (3) Results: The 12,267-nt GX24 genome (GenBank: PX682047) was classified as BVDV-2b. Recombination analysis detected a putative recombination signal within the NS5A gene involving Chinese BVDV-2b and Italian BVDV-2a strains. Integrative analyses predicted conserved linear and conformational epitope clusters in the N- and C-terminal regions of the E2 protein. Spatial analysis indicated that several epitope residues may be masked by glycan shielding. (4) Conclusions: This study provides the first genomic evidence of a BVDV-2b isolate from dairy buffalo in China, suggesting that BVDV-2b may be present in this population. The putative recombination signal and antigenic characteristics offer valuable insights for the development of diagnostics and vaccine design in the future.