Codon Usage Bias and Host Adaptation of Canine Circovirus Identified from Various Hosts

Canine circovirus (CCV) infection could cause immunosuppression in dogs, predisposing them to secondary complications. The virus also shows notable cross-species transmission potential. To investigate codon usage bias (CUB) and host adaptation, 102 CCV sequences from various hosts, including dogs, wolves, foxes, cats, and badgers, were analyzed. The mean GC% of CCV’s complete coding sequences was 50.31% (σ = 0.47), indicating no significant compositional bias. Furthermore, the replication protein (Rep) gene of CCV exhibited significant overrepresentation of T-ending codons and strongly avoided A-ending codons, whereas the capsid protein (Cap) gene displayed a clear codon bias toward A-ending codons and avoidance of G- or C-ending codons. Effective number of codons, parity rule 2, and neutrality analyses collectively indicated that natural selection acted as the primary evolutionary force governing the codon usage bias of CCV. Correspondence analysis (CoA) and correlation analysis demonstrated that other factors such as nucleotide composition and translational preferences could also affect CCV’s CUB. However, geography and genotype should not be ignored. The host adaptation analysis suggests that foxes are the most suitable hosts for CCV. This study provides a foundation for understanding CCV’s host adaptation mechanisms.