Codon usage bias and evolutionary dynamics of porcine Sapelovirus: insights into host adaptation

Porcine sapelovirus (PSV), a member of the Sapelovirus genus within the Picornaviridae family, is a swine pathogen causing respiratory diseases, polioencephalomyelitis, and gastroenteritis. The infection results in economic loss in the swine industry and often co-occurs with bacterial, viral, or fungal infections. Despite its impact, the evolutionary dynamics and adaptation mechanisms of PSV remain poorly understood. This study investigates the evolutionary forces shaping adaptation of the PSV polyprotein gene through codon usage bias and nucleotide composition analysis. A total of 34 polyprotein coding sequences of PSV were retrieved from the NCBI database and analyzed using bioinformatics tools. The nucleotide composition analysis revealed adenine as the most abundant nucleotide, with thymine predominating at the third codon positions. The Guanine-Cytocine (GC) content was balanced overall, with variations in GC content at the third codon position values suggesting mutational pressure. Relative synonymous codon usage analysis identified overrepresented and underrepresented codons, highlighting host-specific selection pressures. The Effective number of codons and neutrality plots indicated that natural selection predominantly influences codon usage bias in PSV, while mutational pressure contributes less. Chargaff's second parity rule analysis confirmed deviations influenced by these forces, while dinucleotide abundance analysis provided insights into codon usage trends. The codon adaptation index (CAI = 0.584) suggested moderate adaptation of PSV to its natural host, Sus scrofa domesticus, reflecting evolutionary constraints on translational efficiency. Correspondence analysis highlighted factors driving viral evolution. These findings contribute to our understanding of PSV molecular evolution, supporting the development of antiviral strategies, vaccines, and diagnostic for disease control.