Molecular characterization of genetically related co-circulating bovine viral diarrhea virus in cattle and water buffalo within mixed-herd production systems

Interspecies transmission and co-circulation of BVDV among bovines occur frequently, contributing to complex epidemiological dynamics in mixed-herd environments. A cross-sectional study was conducted in mixed bovine herds in the southern region of Bangladesh. A total of 219 blood samples were collected from cattle and water-buffalo across 12 mixed herds. Serum samples were tested for BVDV-specific antibodies using Ab-ELISA, while RT-qPCR on blood to detect seropositivity and active infection, respectively. PCR-positive samples were then subjected to 5′-UTR-based sequencing to identify circulating species and subgenotypes. Biotyping was conducted using the MDBK cell line. At the herd level, the prevalence of BVDV seropositivity and active infection were 75.0% and 66.7%, respectively. At the animal level, seropositivity was 15.9% in cattle and 14.0% in buffalo, while active infection was detected at 9.5% and 7.5%, respectively. Among infected animals,18 (94.7%) were transiently infected (TI), and one calf was persistently infected (PI). Of the 19 isolates, 12 (63.2%) were classified as BVDV-1, representing eight subgenotypes (BVDV-1a, 1b, 1c, 1d, 1j, 1k, 1o, and 1p) detected in both species, indicating co-circulation and high nucleotide identity (93–100%). All BVDV-2 and HoBi-like isolates belonged to subgenotypes BVDV-2a and HoBiPeV-a, respectively. Ten isolates (10/15; 66.7%) were non-cytopathic, and five (5/15; 33.3%) were cytopathic. Stunted growth ( p = 0.036) and a history of clinical diarrhoea ( p = 0.032) were associated with BVDV seropositivity. At the farm level, close proximity between farms ( p = 0.001), larger farm size ( p = 0.034), and introduction of recently purchased animal ( p = 0.034) were significantly associated with seropositivity. The co-circulation of diverse BVDV genotypes at the cattle-water buffalo interface presents challenges for control and eradication in mixed-farming systems. • Simultaneous detection of BVDV antibodies and multiple pestivirus species at the cattle–water buffalo interface indicates ongoing viral persistence. • High nucleotide identity among co-circulating BVDV strains in cattle–water buffalo mixed herds indicate potential interspecies transmission. • Extensive viral genetic diversity detected in mixed production systems, including eight BVDV-1 subgenotypes, BVDV-2a, and HoBiPeV-a. • All infected buffalo were transiently infected (TI), while a persistently infected (PI) calf was detected among cattle population. • Both cytopathic and non-cytopathic biotypes were co-circulating in both bovine species. • Genetic variability and identified risk factors emphasize the urgency of evaluating antigenic compatibility and vaccine efficacy to strengthen preventive measures.