Evidence map›Paper›PMID 42797765›Full record

ArticleViruses2026

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

Ezekiel Ahn, Insuck Baek, Jishnu Bhatt, Sookyung Oh, Minhyeok Cha, Lalit Kandpal, Seunghyun Lim, Moon S Kim, Sunchung Park, Lyndel W Meinhardt

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Viruses, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Ezekiel AhnSustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0003-4447-4104
Insuck BaekEnvironmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0003-1044-349X
Jishnu BhattSustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0009-0001-3818-8761
Sookyung OhEnvironmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Minhyeok ChaEnvironmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Lalit KandpalEnvironmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Seunghyun LimSustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Moon S KimEnvironmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Sunchung ParkSustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0002-7398-9476
Lyndel W MeinhardtSustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0001-8299-2629

Funding

United States Department of Agriculture In-House Projects Nos. 8042-21220-258-000-D.
6 · The paper itself

Abstract

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

Indexed as

BadnavirusCacaoDNA Barcoding, TaxonomicGenetic VariationGenome, ViralPlant DiseasesOpen Reading FramesPhylogenyalignment-freeBadnavirusCSSVk-mer analysismodular diversityviral genomics

Identifiers

PMID42797765
PMCPMC13612066

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.