Identification and Characterization of a Novel BVDV-1b Cluster in Sardinia Through Whole Genome Sequencing

Bovine viral diarrhea (BVD) is a highly infectious disease with a global distribution caused by the bovine viral diarrhea virus (BVDV), primarily affecting cattle. Dairy farms play a central role in the persistence and spread of BVDV in Italy, making control strategies and genetic studies essential to reduce its circulation. This work aimed to identify and characterize the genotype and subgenotype of BVDV infecting cattle in a specific area of Sardinia. Ten BVDV Sardinian strains were isolated and sequenced from the blood of infected cattle collected into EDTA tubes during outbreaks between 2018 and 2024. Then, to characterize the isolates, phylogenetic and variant analyses were performed on the entire collection of BVDV genomes available to date in GenBank. All Sardinian isolates were assigned to the BVDV-1b subgenotype. Except for two divergent strains, the isolates clustered into a distinct monophyletic clade characterized by 61 exclusive variants absent in all other analyzed sequences. These findings point to the existence of a distinct Sardinian genomic signature. Moreover, among these mutations, 19 missenses distributed on genes encoding the E1, E2, Core, NS3, NS4B and NS5A proteins could have a relevant functional impact, given the role these proteins play in the virus life cycle and in interaction with the host.