Molecular Characteristics of Bovine Viral Diarrhea Virus Strains Isolated from Persistently Infected Cattle

SIMPLE SUMMARY: Bovine viral diarrhea virus (BVDV) is a pathogen that is widespread throughout the world, causing serious economic losses. Most of the current BVDV infection research focuses on genotyping based on the 5′-UTR sequence, neglecting the molecular characteristics of the whole genome of BVDV strains. Cows infected with non-cytopathic (NCP) BVDV in early pregnancy may give birth to persistently infected (PI) cattle, which are the main sources of virus transmission in the herd. The present study isolated and identified nine BVDV strains from PI cattle in China. The complete genome of the new isolates was sequenced for phylogenetic analysis, recombination analysis and sequence analysis in 5′-UTR, E0 and E2. ABSTRACT: In this study, we reported the isolation, identification, and molecular characteristics of nine BVDV strains that were isolated from the serum of persistently infected cattle. The new strains were designated as BVDV TJ2101, TJ2102, TJ2103, TJ2104, TJ2105, TJ2106, TJ2107, TJ2108 and TJ2109. The TJ2102 and TJ2104 strains were found to be cytopathic BVDV, and the other strains were non-cytopathic BVDV. An alignment and phylogenetic analysis showed that the new isolates share 92.2–96.3% homology with the CP7 strain and, thus, were classified as the BVDV-1b subgenotype. A recombination analysis of the genome sequences showed that the new strains could be recombined by the major parent BVDV-1a NADL strain and the minor parent BVDV-1m SD-15 strain. Some genome variations or unique amino acid mutations were found in 5′-UTR, E0 and E2 of these new isolates. In addition, a potential linear B cell epitopes prediction showed that the potential linear B cell epitope at positions 56–61 is highly variable in BVDV-1b. In conclusion, the present study has identified nine strains of BVDV from persistently infected cattle in China. Further studies on the virulence and pathogenesis of these new strains are recommended.