Mapping evolutionary paradigm of Oropouche virus driven by dinucleotide bias and context-dependent codon bias

Arthropod-borne viruses (arboviruses) pose significant public health threats, and understanding their evolutionary mechanisms can inform molecular diagnostics and vaccine design. Oropouche virus (OROV), a relatively understudied arbovirus, exhibits unique evolutionary dynamics in nucleotide composition. We analyzed 45 OROV strains across genotypes to assess selective pressures shaping nucleoprotein, glycoprotein, and RNA-dependent RNA polymerase (RdRp) evolution. We utilized information entropy, dinucleotide odds ratios, relative synonymous codon usage values, and context-dependent codon bias (CDCB) to elucidate the genetic characteristics associated with mono-, di-, tri-, and tetranucleotide compositions. The extent of overall nucleotide usage bias, dinucleotide bias, and synonymous codon usage bias did not correlate with genotype-specific patterns, but rather exhibited a protein function-dependent pattern across the three proteins. Although dinucleotide bias and synonymous codon usage bias varied within a relatively broad range, the dinucleotide CpG, the over- and under-represented synonymous codons, and CDCB remained strongly influenced by natural selective pressures from both the host and the viral life cycle. Furthermore, the codon usage patterns, as indicated by the effective number of codons, suggest that the OROV nucleoprotein has been subject to stronger selective pressures in its evolutionary paradigm compared to the glycoprotein and RdRp, which appear to be primarily influenced by natural selection and mutation pressure. Additionally, analysis of relative codon deoptimization index (RCDI) and tRNA adaptation index (tAI) revealed suboptimal translational efficiency of OROV coding sequences in human hosts, suggesting limited codon usage adaptation.