Molecular characterization of border disease virus strain Aveyron

• This work describes sequencing and analysis of the complete genome of BDV-5 strain Aveyron.
• The genome of BDV Aveyron comprises a unique insertion of 12 nt encoding four additional aa in the C-terminal region of NS2.
• The ncp BDV strain Aveyron significantly differs from other ncp BDV strains in terms of NS2-3 processing and production of significantly higher amounts of NS3.

For the pestivirus border disease virus (BDV) at least seven major genotypes have been described (BDV-1–BDV-7). So far, complete genomic sequences have been reported for four BDV genotypes (BDV-1–BDV-4). In this study we report the entire genomic sequence of the noncytopathogenic (ncp) BDV-5 reference strain Aveyron. The viral genome encompasses 12,284 nucleotides (nt) and contains one large open reading frame (11,700 nt) flanked by a 370 nt long 5′-untranslated region (UTR) and a 214 nt long 3′-UTR. The genome organization as well as the lengths of the viral polyprotein (3899 amino acids) and the 5′-UTR are very similar to the ones of other BDV strains, while the 3′-UTR of BDV Aveyron is considerably shorter when compared to other BDV strains. Comparative analysis of complete coding sequences revealed that BDV Aveyron shares nucleotide sequence identities of 76.9% to 79.0% with the other BDV strains, and less than 72% identity with other pestiviruses. In contrast to other BDV strains, a unique insertion of four amino acids (KAPD) of unknown origin is present in the C-terminal part of the viral autoprotease NS2 encoded by BDV Aveyron. Immunoblot analysis revealed that infection of cells with the ncp BDV strain Aveyron comprising this unique insertion in NS2 resulted in the expression of high amounts of NS3 and thereby showed that BDV Aveyron significantly differs from other ncp BDV strains in terms of NS2-3 processing and production of NS3.