Codon Usage Bias Analysis of Citrus Leaf Blotch Virus

Citrus leaf blotch virus (CLBV) is a positive-sense single-stranded RNA virus belonging to the genus <i>Citrivirus</i> within the family <i>Betaflexiviridae</i>. It infects a broad range of economically significant fruit crops, including citrus, kiwifruit, and apple. Surveys conducted in the field have documented appreciable incidence rates in several hosts, thereby emphasizing its emerging threat to global pomiculture. Comprehensive surveillance of CLBV genetic diversity is indispensable for predicting strain-specific epidemics and designing durable, broadly protective control strategies. Current surveys of CLBV diversity are still gene-fragment-centric, with whole-genome resolution remaining largely untapped. In this study, an analysis of codon usage bias analysis was performed using all available CLBV full-length genomes. The findings revealed that CLBV exhibits low codon usage bias, with natural selection, rather than mutational drift, being the primary driver. Phylogenetic analysis has been demonstrated to categorize isolates according to their host of origin rather than their geographical location. This observation suggests that host adaptation may supersede spatial structure in CLBV evolution and reinforce natural selection as the dominant force shaping its codon usage landscape. From the perspective of the codon adaptation index, <i>Prunus avium</i> is the host that exerts the greatest influence on the formation of its codon usage bias. The present study provides the first genome-wide portrait of CLBV codon usage bias, offering a robust framework for future investigations into its origin and evolutionary dynamics.