Genetic diversity, codon usage, and evolutionary dynamics of bovine parainfluenza virus type-3

Bovine respiratory disease syndrome, primarily caused by bovine parainfluenza virus type-3 (BPIV-3), is characterized by a high incidence in calves. However, despite its significant clinical importance, the codon usage patterns and evolutionary dynamics of BPIV-3 hosts remain elusive. Hence, this study aimed to systematically analyze the codon usage bias of the BPIV-3 structural protein gene HN, and the roles of mutational pressure and natural selection in its evolution were evaluated. Herein, analysis of indicators such as effective codon number (ENC), relative synonymous codon usage, and codon adaptation index revealed a low codon bias for BPIV-3, with codon preferences showing significant differences from the host. Notably, ENC-GC content at the third codon spot analysis indicated that natural selection dominated codon usage. Additionally, phylogenetic analysis divided BPIV-3 into three main genotypes (namely a, b, and c), with genotype C exhibiting a higher codon adaptability to the host. Altogether, these findings reveal the host-BPIV-3 evolutionary interaction mechanisms, providing a theoretical basis for vaccine design and epidemiological surveillance.