Evolutionary paradigm of distinct viral coding regions of BVDV associated with different nucleotide usage patterns | BMC Veterinary Research

Analysis of Nucleotide Usage Bias in BVDV

Recent research has identified significant discrepancies in nucleotide usage bias across the viral coding sequences of Bovine Viral Diarrhea Virus (BVDV). The study found that pyrimidine content (U + C) is notably lower than purine content (A + G) within the open reading frame (ORF) of BVDV, with variations observed among its three genotypes. Specifically, coding regions such as Capsid, E1, E2, and NS5B displayed different usage biases for mononucleotides, with p-values < 0.001. Analysis of the first, second, and third codon positions also revealed significant biases, particularly in regions like Npro and Capsid. The study concluded that synonymous substitutions play a crucial role in the evolution of BVDV.

Additionally, evidence of strong suppression of certain nucleotide pairs, particularly CpG dinucleotides, was observed across all viral regions. The dinucleotide usage patterns varied considerably between genotypes, indicating a level of genotype-specific differentiation. Synonymous codon usage analysis further illustrated inconsistencies and polarization in usages across various viral regions, hinting at underlying selective pressures that influence evolutionary dynamics.

Implications for Future Research

• Why it matters: Understanding nucleotide usage bias may provide insights into viral evolution and inform strategies for vaccine development.
• The latest: Ongoing analysis focuses on the correlation between codon usage patterns and immune responses in host species.