First report of Spinach latent virus in tomato in the United Kingdom

In July 2020 two samples of tomato (Solanum lycopersicum) were submitted to Fera Science Ltd, from an organic greenhouse in south-west England. The samples were sent following the appearance of symptoms suggestive of virus infection, which had spread through around 5% of the crop. Symptoms included chlorotic ringspots (Figure 1) and “zippering” on fruits (Figure 2). The samples were initially tested by ELISA for Tomato brown rugose fruit virus, Tomato spotted wilt virus (DSMZ, Germany), Pepino mosaic virus and tospoviruses (serogroups I, II and III) (Bioreba, Switzerland), which were not detected.

FIGURE 1. Tomato fruit showing chlorotic ringspots

FIGURE 2. Tomato fruit showing “zippering” symptoms

The samples were then tested as a bulk by high throughput sequencing (HTS) on a MiSeq Sequencer (Illumina UK) (Fox et al., 2019), and Spinach latent virus (SpLV, genus Ilarvirus) and Southern tomato virus (STV, genus Amalgavirus) were identified. The total number of reads for the bulked sample was 2,170,994 with 129,566 (5.968%) being mapped to the SpLV genome with an average coverage of 3779.509. The whole tripartite genome of SpLV was obtained and uploaded to GenBank (Accession No. RNA1: OK044130, RNA 2: OK044131, RNA 3: OK044132). The sequences of each RNA obtained by HTS were checked by nucleotide comparison through BLAST against publicly available sequences which had a 99% identity to the following SpLV sequences; KY695012.1 (RNA 1, USA), KY695013.1 (RNA 2, USA), MT269815.1 (RNA 3, Serbia).

The finding was confirmed by RT-PCR using primers designed to detect a broad range of ilarviruses (Untiveros et al., 2010). A product of the expected size (380 bp) was obtained (OK044133), analysed by Sanger sequencing (MWG GmbH) and checked by nucleotide sequence comparison against publicly available sequences using BLAST. The sequence had 100% identity to four isolates of SpLV (KY695013.1, MT269814.1, GQ865659.1, U93193.1)

SpLV is known to be transmitted mechanically and in some hosts by seed and through pollen (Stefanac & Wrischer, 1983). SpLV has previously been reported in tomatoes from New Zealand (Lebas et al, 2007) and the United States (Vargas-Ascencio et al, 2013). It was also recently detected in diseased tomatoes in Serbia, in which other viruses were not detected by alternative methods (Vučurović el al 2021) using sRNA sequencing. This is the first known finding in the United Kingdom. These recent detections suggest SpLV may be more widely distributed in tomato than currently reported.

ACKNOWLEDGEMENTS

This work was funded under the Defra-Fera Long Term Service Agreement.