Alignment-Free Genome Geometry and Mosaic Barcodes Characterize Modular Diversity in the Cacao Swollen Shoot Virus Complex

Cacao swollen shoot disease (CSSD) remains a major viral threat to cacao production in West Africa and is associated with a genetically diverse complex of badnaviruses. We combined alignment-free whole-genome distances with circular sliding-window mosaic barcodes to characterize global divergence and local compositional modularity across 48 full-length CSSD-associated badnavirus genomes, hereafter termed the cacao swollen shoot virus (CSSV) complex. Whole-genome tetranucleotide cosine distance clusters matched published species assignments exactly (adjusted Rand index = 1.00; normalized mutual information = 1.00; silhouette = 0.703) and were strongly concordant with an alignment-based distance derived from open reading frame 3 (ORF3) proteins (Spearman ρ ≈ 0.951; permutation p ≈ 0.0002). A three-component mosaic-complexity score summarized low dominant-label purity, barcode entropy normalized by log2(K), and circular switch rate; ORF–mosaic agreement was retained as a separate diagnostic and did not contribute to the ranking. Threshold sensitivity showed that barcode switchpoints were enriched within ±100 and ±200 bp of predicted ORF boundaries, but not within ±400 bp. The ten highest-scoring genomes showed slightly higher mean local nucleotide entropy but lower entropy variance and dispersion than the remaining genomes, indicating more uniformly distributed compositional complexity rather than isolated local spikes. These analyses provide a transparent framework for post-sequencing classification, comparison, and prioritization of complete viral genomes. The barcode and score outputs are exploratory summaries and are not direct field diagnostic assays or nucleotide-resolution recombination tests.