Evolutionary paradigm of distinct viral coding regions of BVDV associated with different nucleotide usage patterns

Due to its high mutation rate, the nucleotide usage variation of bovine viral diarrhea virus (BVDV) is generally considered as one of evolutionary dynamics for evolving distinct coding regions and thus shaping evolutionary pathway of BVDV. Here, we analyzed 168 genetically distinct BVDV strains with verified genotypic classifications to elucidate which selective factor acting on twelve viral coding regions. We employed information entropy, dinucleotide odds ratios, relative synonymous codon usage, the effective number of codons (ENC), and context-dependent codon bias (CDCB) to characterize the genetic features underlying variations in nucleotide usage patterns. Among the twelve viral regions of the BVDV genome, the Capsid, P7, and NS4A regions exhibit stronger biases in overall nucleotide usage patterns than the other regions. Moreover, the nucleotide pair usage in these regions displays a conserved pattern rather than a genotype-specific one. Although certain dinucleotide pairs, such as UpA and CpG, are recognized for their roles in stimulating host immune responses, CpG usage is more strongly suppressed than UpA across all BVDV genomic regions. Compared with dinucleotide usage patterns, synonymous codon usage in these regions has better performance for displaying both genotype-associated evolutionary trends and function-specific coding preferences. Moreover, the overall codon usage bias reflected by ENC in each viral region reflects the interaction of nucleotide usage variability driven by mutational pressure and function-specific patterns shaped by natural selection acts on evolutionary paradigm of BVDV. Additionally, CDCB analysis provides further evidence for the pervasive influence of natural selection in shaping the codon organization of all BVDV genomic regions.