Phylogenetic characterization of circulating bovine viral diarrhea virus subgenotypes 1b and 1l in cattle from the Mediterranean region of Türkiye

Bovine viral diarrhea virus (BVDV), a member of the genus Pestivirus within the family Flaviviridae , is a globally significant pathogen affecting livestock health and productivity. The genus includes Pestivirus bovis (BVDV-1), Pestivirus tauri (BVDV-2), Pestivirus ovis (BDV), and Pestivirus suis (CSFV), all capable of infecting multiple host species, including cattle, sheep, goats, and wild ruminants. In cattle, BVDV infection ranges from subclinical to severe respiratory, gastrointestinal, and reproductive disorders. Infection during early gestation may result in immunotolerant, persistently infected (PI) calves that shed virus throughout life, serving as reservoirs for transmission. BVDV-1 (Pestivirus A) and BVDV-2 (Pestivirus B) are the principal genetic species, while HoBi-like viruses represent emerging pestiviruses. BVDV-1 is genetically diverse, comprising at least 24 subgenotypes (1a–1x), with 1b being the most prevalent globally. In Türkiye, BVDV is endemic, with multiple BVDV-1 subtypes, BVDV-2, and HoBi-like viruses reported. Notably, subgenotype 1l has recently emerged as a predominant lineage in certain regions. To investigate circulating pestiviruses in the Mediterranean region of Türkiye, 444 serum samples were collected from unvaccinated cattle exhibiting compatible clinical signs in Burdur province during 2021–2022. Screening by conventional RT-PCR targeting the conserved 5′ untranslated region (5′-UTR) identified 83 of 444 samples (18.7%; 95% CI: 15.3–22.6%) as pestivirus-positive. Pestivirus detection rates differed significantly across clinical categories ( p = 0.011), with cattle presenting reproductive disorders (22.9%) and growth retardation (22.7%) showing higher positivity. Five representative isolates were successfully propagated in MDBK cells, confirmed by direct immunofluorescence assay, and subsequently characterized by phylogenetic analysis. All five isolates belonged to BVDV-1, clustering within subgenotypes 1b (n = 2) and the endemic lineage 1l (n = 3). These findings confirm the circulation of BVDV-1 subgenotypes 1b and 1l in southern Türkiye and highlight the value of continued molecular surveillance and targeted removal of persistently infected animals to support regional control programs.