Genomic insights into host-associated variants and transmission features of a ToBRFV isolate from Mexico
Bibliographic record
Abstract
Tomato brown rugose fruit virus (ToBRFV) poses a global threat to tomato and pepper production due to its high transmissibility and adaptability. Understanding its genomic features and transmission mechanisms is critical for effective disease management. We characterized the genome and biological properties of a ToBRFV isolate from Mexico. Comparative genomic analyses were conducted using 100 global genomes, with particular focus on single nucleotide variants (SNVs) and their distribution across different host species. Phylogenetic analysis and experimental bioassays, including seed transmission tests, were also performed. Phylogenetic analysis revealed genetic proximity between the Mexican isolate and strains from Mexico, USA, Canada, Israel, and China, indicating shared transmission routes. Genomic comparisons confirmed general sequence stability, but SNVs were found in the 126-kDa replicase, particularly within the methyltransferase domain. These SNVs exhibited host-associated patterns, with conserved profiles in tomato and unique substitutions in Capsicum annum, Solanum nigrum, and Citrullus lanatus. Bioassays demonstrated susceptibility in additional solanaceous hosts, and seed transmission assays in Nicotiana rustica indicated reduced germination and low-frequency viral detection in seedlings. The study highlights the genomic conservation and host-specific variation in ToBRFV, suggesting that the methyltransferase domain may undergo differential evolutionary pressures. The findings provide valuable insights for improving risk assessment, seed health testing, and biosecurity measures.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".