First detection and genomic characterisation of <i>Spinach latent virus</i> in tomato in Canada
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Spinach latent virus (SpLV; genus Ilarvirus, family Bromoviridae) was reported initially from spinach (Bos et al., 1980). However in recent years, reports from New Zealand (Lebas et al., 2007), the United States (Vargas-Asencio et al., 2013), Serbia (Vučurović et al., 2021) and the United Kingdom (Ward et al., 2022) have shown SpLV's ability to also infect tomato, Solanum lycopersicum. On tomato, SpLV causes symptoms including stunted growth, leaf deformation and discolouration, and ringspots on the fruit. In July 2023, the majority of tomato plants (cv. Big Beef) in a Quebec greenhouse (58m2) exhibited several unusual symptoms including blistering, deformation, mosaic, necrosis, zippering and chlorotic ringspots (Figures 1, 2). Diseased tomato samples tested negative by DAS-ELISA for the presence of Alfalfa mosaic virus, Alstroemeria necrotic streak virus, Cucumber mosaic virus, Pepino mosaic virus, Potato virus X, Potato virus Y, Tobacco etch virus, Tomato brown rugose fruit virus, Tomato bushy stunt virus, Tomato chlorotic spot virus, Tomato mosaic virus, Tomato ringspot virus, Tomato spotted wilt virus and Tomato yellow leaf curl virus. dsRNA was extracted from tomato leaves (Javaran et al., 2023; Poursalavati et al., 2023) and cDNA was synthesised using random primers and Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific, USA). The second strand of cDNA was synthesised using RNase H (New England Biolabs, USA), DNA Polymerase I Large (Klenow) Fragment (Promega, USA) and E. coli DNA ligase (New England Biolabs). The resulting cDNA was sequenced on an R9.4.1 flow cell using a direct cDNA Nanopore Sequencing Kit and MinION sequencer (Javaran et al., 2023). A total of 26,530 reads (BioSample: SAMN37658768) were generated from the diseased tomato leaf. Bioinformatic analysis revealed the presence of the three RNA segments of SpLV. No other plant viruses were detected. A total of 159 reads were assigned to SpLV and the genome coverage was nearly complete for two of the three RNA segments, with 78% coverage for RNA1, 94% for RNA2 and 91% for RNA3. This resulted in partial recovery of the genome across all three RNA segments of SpLV. The presence of SpLV was confirmed by RT-PCR on the RNA1 segment using the SpLVRNA1f/ SpLVRNA1r primer pair (Vargas-Asencio et al., 2013). A PCR product of the expected size (744 bp) was obtained from all three samples and the identity was confirmed by Sanger sequencing (GenBank Accession Nos. OR908874-OR908876). Through a detailed phylogenetic analysis of the virus's three distinct RNA segments, the genetic relationships and divergences between global SpLV strains were analysed. SpLV sequences for each RNA segment were retrieved from the GenBank database and phylogenetic analyses for RNA1, RNA2, and RNA3 constructed (Figure 3). These analyses, carried out using the maximum likelihood method with FastTree 2, employed the Generalized Time-Reversible model along with gamma-distributed site-rate heterogeneity. Our findings reveal distinct genetic geographical proximities: the Canadian isolate for RNA1 is closely related to a Serbian isolate, the RNA2 segment is more aligned with isolates from the UK, USA and New Zealand, and the RNA3 segment shows a closer genetic relationship to isolates from the USA. These results underscore the intricate genetic landscape of SpLV and highlight the necessity for ongoing surveillance and research into its evolutionary dynamics. This is the first report of SpLV in tomato in Canada. Due to the rarity of SpLV reports in regions including the USA, its detection in Canada raises further concerns about its spread. The seed-transmissible nature of SpLV makes it crucial to implement rigorous seed testing and preventive measures across Canada to prevent its further spread.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| 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) | 0.000 | 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 it