Mapping evolutionary paradigm of bovine viral diarrhea virus <i>Npro</i> associated with different organizations of nucleotide

The non-structural protein (Npro) of bovine viral diarrhea virus (BVDV) is a crucial virulence factor that impairs the host's antiviral immune response and facilitates virus production. This study establishes a foundation for understanding how different selective pressures influence the formation of nucleotide pairs, synonymous codon, and context-dependent codon bias (CDCB) in BVDV <i>Npro</i>. BVDV genotype 1 exhibits a greater number of subgenotypes compared to other genotypes, yet its overall nucleotide usage bias in <i>Npro</i> is stronger. Within <i>Npro</i>, certain dinucleotides, specifically CpG and UpA, are notably suppressed, while UpG is selected with high frequency across all genotypes. The BVDV <i>Npro</i> region exhibits a pronounced bias in synonymous codon usage and possesses a genetic capacity to distinguish between genotypes. Unlike the patterns of mononucleotide and synonymous codon usage associated with BVDV genotyping, nucleotide pair usage and CDCB show significant variability due to the high mutation rate in the Npro coding sequence. Despite this variation, both nucleotide architectures demonstrate a unique evolutionary paradigm that goes beyond genotype-specific models. Aside from nucleotide composition constraints imposed by the high mutation rate in the viral genome, natural selective pressures arising from translational selection and host immune response also significantly influence the formation of various nucleotide architectures in the BVDV <i>Npro</i>. By analyzing the genetic characterizations associated with the different nucleotide architectures in the <i>Npro</i>, the diverse repertoire of nucleotide pairs, synonymous codons and CDCB may provide BVDV mutants with ample opportunities for direct adaptation and exaptation, thereby overcoming the robust immune defenses of the host.