Adaptive Co-evolution between Bovine Viral Diarrhea Virus Envelope Glycoprotein E2 and the Bovine Cellular Receptor CD46

Bovine viral diarrhea virus (BVDV) is a major cattle pathogen whose envelope glycoprotein E2 mediates viral entry by binding the cellular receptor CD46. Adaptive interactions between viral attachment proteins and host receptors are central to viral fitness and virulence, yet direct evidence for co-evolution between BVDV E2 and bovine CD46 has been lacking. In this study, We conducted an integrated evolutionary, cophylogenetic, and structural analysis of 51 BVDV E2 and 17 bovine CD46 gene sequences. The E2 gene was predominantly under purifying selection (114 sites), while positive selection was concentrated in the receptor-binding domain, with 3 pervasive and 25 episodic positively selected sites identified. Cophylogenetic analysis revealed a significant congruence between BVDV E2 and bovine CD46 phylogenies (ParaFitGlobal = 0.0231, P = 0.038). Structural docking of 10 E2 variants with 3 CD46 alleles showed binding free energies ranging from −6.9 to −14.9 kcal/mol, with co-evolutionary E2-CD46 combinations exhibiting stronger binding affinities than non-co-evolutionary pairs (mean −10.62 vs −9.40 kcal/mol).