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Article Abstract
This study investigates the codon usage preferences of papillomaviruses across different hosts and examines the evolutionary relationships of key genes (L1, E6, and E7). Complete genome sequences of 86 papillomavirus strains were retrieved from the PaVE database. Phylogenetic trees were constructed using MAFFT and ITOL, and codon usage indices, including RSCU, ENC, CAI, and GC3, were calculated using CodonW. ENC-GC3, Neutrality, and PR2-bias analyses were conducted to explore the factors shaping codon usage patterns. The analyzed genomes were categorized into five groups (Clade1, Clade2, Clade3, Clade4, and Others), exhibiting variations in CAI and ENC values. Phylogenetic analysis revealed three distinct gene clusters. ENC-GC3, Neutrality, and PR2-bias analyses demonstrated that both natural selection and mutation pressure influence codon usage. These findings suggest that codon usage preferences and the evolutionary dynamics of L1, E6, and E7 genes differ across hosts, driven by a combination of selection and mutational forces.
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