{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T05:17:09Z","timestamp":1787807829202,"version":"build-2784847793"},"reference-count":40,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T00:00:00Z","timestamp":1787616000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007917","name":"U.S. Department of Agriculture, Agricultural Research Service","doi-asserted-by":"crossref","award":["8042-21220-258-000-D"],"award-info":[{"award-number":["8042-21220-258-000-D"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"crossref"}]},{"award":["8042-21220-258-000-D"],"award-info":[{"award-number":["8042-21220-258-000-D"]}],"id":[{"id":"https:\/\/ror.org\/01na82s61","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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 \u03c1 \u2248 0.951; permutation p \u2248 0.0002). A three-component mosaic-complexity score summarized low dominant-label purity, barcode entropy normalized by log2(K), and circular switch rate; ORF\u2013mosaic agreement was retained as a separate diagnostic and did not contribute to the ranking. Threshold sensitivity showed that barcode switchpoints were enriched within \u00b1100 and \u00b1200 bp of predicted ORF boundaries, but not within \u00b1400 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.<\/jats:p>","DOI":"10.3390\/v18090932","type":"journal-article","created":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T09:04:30Z","timestamp":1787648670000},"page":"932","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Alignment-Free Genome Geometry and Mosaic Barcodes Characterize Modular Diversity in the Cacao Swollen Shoot Virus Complex"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4447-4104","authenticated-orcid":false,"given":"Ezekiel","family":"Ahn","sequence":"first","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1044-349X","authenticated-orcid":false,"given":"Insuck","family":"Baek","sequence":"additional","affiliation":[{"name":"Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-3818-8761","authenticated-orcid":false,"given":"Jishnu","family":"Bhatt","sequence":"additional","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sookyung","family":"Oh","sequence":"additional","affiliation":[{"name":"Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minhyeok","family":"Cha","sequence":"additional","affiliation":[{"name":"Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lalit","family":"Kandpal","sequence":"additional","affiliation":[{"name":"Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seunghyun","family":"Lim","sequence":"additional","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moon S.","family":"Kim","sequence":"additional","affiliation":[{"name":"Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7398-9476","authenticated-orcid":false,"given":"Sunchung","family":"Park","sequence":"additional","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8299-2629","authenticated-orcid":false,"given":"Lyndel W.","family":"Meinhardt","sequence":"additional","affiliation":[{"name":"Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/s12985-017-0866-6","article-title":"The Proposed New Species, Cacao Red Vein Virus, and Three Previously Recognized Badnavirus Species Are Associated with Cacao Swollen Shoot Disease","volume":"14","author":"Chingandu","year":"2017","journal-title":"Virol. 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