In May 2018 samples of tomato (Solanum lycopersicon cvs. Camargue, Delisher, Piccolo and Summer Sun) were submitted to Fera Science Ltd, from a production glasshouse in the southeast of England. The plants had originated from The Netherlands. The sample was sent following the appearance of virus-like symptoms appearing throughout the crop, in two separate glasshouses. The grower informed the lab of the suspicion of Tomato chlorosis virus (ToCV; genus Crinivirus) on their premises following testing by a third-party commercial laboratory (unknown identity). Observed symptoms included mottle, necrosis and distortion of the leaves. These symptoms are not typical for ToCV and may be due to mixed infections with other viruses. Large numbers of whitefly (Trialeurodes vaporariorum), known to be a vector of ToCV, had also been detected in the crop.
Four leaf samples were tested by ELISA for ToCV (antisera from DSMZ, Germany) and for pospiviroids by real time PCR (Botermans et al., 2013). The samples tested positive for ToCV and all were negative for pospiviroids. Seven further samples were submitted from the crop to determine presence of ongoing infection; these were tested by real time PCR for ToCV (European and Mediterranean Plant Protection Organization, 2013) and one further sample tested positive. A pooled sample of the ELISA and real time PCR-positives was tested by high throughput sequencing using a MiSeq sequencer (Illumina, UK) following the protocol described in Fowkes et al. (2021). Over half the genome of ToCV was detected (GenBank Accession Numbers PP116316 and PP116317 for ToCV RNA 1 and RNA 2, respectively), as well as Pepino mosaic virus (PP116314) and Southern tomato virus (PP116315). The partial genome of ToCV had 97 and 98% identity to genomes of ToCV isolates KJ200304.1 and KY810787.1 (Spanish isolate). BBMap () was used to calculate the average coverage (x2.1) and mapped reads (151). Overall, there were 2,050,104 reads in the sample, therefore the percentage of reads in the sample that mapped to ToCV was 0.007%. Sequencing data has been submitted to the NCBI short read archive, BioProject PRJNA1061138.
Symptomatic plants were removed but the crop was allowed to continue until the end of the cropping cycle, when all the plants were removed, and the glasshouse disinfected. ToCV has been detected in many tomato growing regions of the world, however, this is the first report of ToCV in the UK. Eradication was declared in June 2020 after testing of the new tomato crop was negative.
ACKNOWLEDGEMENTS
This work was funded under the Defra-Fera Long Term Service Agreement
References
Botermans, M., van de Vossenberg, B.T.L.H., Verhoeven, J.T.J., Roenhorst, J.W., Hooftman, M., Dekter, R. et al. (2013). Development and validation of a real‐time RT‐PCR assay for generic detection of pospiviroids. Journal of Virological Methods, 187, 43–50. [DOI: https://dx.doi.org/10.1016/j.jviromet.2012.09.004]
; Harju, V. 1