Invasive Species Compendium

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Abstract

First report of Tomato mottle mosaic virus in Solanum lycopersicum seeds in the Netherlands and intercepted in seed imported from Asia.

Abstract

In October 2020, seeds of tomato (Solanum lycopersicum) were submitted to Fera Science Ltd. by inspectors from the Animal and Plant Health Agency in the Netherlands. The seeds were imported from Asia and samples were screened in compliance with import testing requirements. A total of 3000 seeds were tested for Tomato mottle mosaic virus (ToMMV; genus Tobamovirus) using the RT-PCR test. A product of the expected size (811 bp) was obtained in all subsamples (12 subsamples each of 250 seeds) and subsequently sent for Sanger sequencing. Sequences from 4 of these samples were compared against those in GenBank, and confirmed to be ToMMV (Accession Nos. OK334226, OK334230-32), with ≥99% nucleotide and 99-100% amino acid identity compared with the exemplar strain (KF477193; YP_008492931.1). To obtain the whole genome of the isolate, the 12 subsamples were bulked and sequenced by high throughput sequencing (HTS) and bioinformatic analysis. The whole genome of ToMMV was obtained (6375 bp; OK334224), and confirmed after a BLAST search (99.6% identity KF477193.1). The genome of Tomato mosaic virus (ToMV) was also found (OK334225). Additionally, 2 further seed samples imported from Asia were analysed and confirmed to be infected with ToMMV (OK334227-9). Separately, in April 2020 and July 2021, 3 seed samples of 3000 seeds of S. lycopersicum (36783676 origin Netherlands; 36783860 and 41106813 imported from China) were submitted to the NPPO of The Netherlands for Tomato brown rugose fruit virus (ToBRFV) testing and sequenced by HTS. Additionally, S. lycopersicum seeds received in 2015 (5785660, origin unknown), which were originally submitted for testing for presence of Potato spindle tuber viroid (PSTVd), were also analysed by HTS. Both ToBRFV and PSTVd were identified in these samples respectively in addition to the nearly complete (MZ713255-7) or partial (MZ964897-9) genomes of ToMMV, confirmed after BLAST searches (99.1-99.7 % identity KF477193.1). Furthermore, the genome of ToMV was identified in samples 36783860 and 5785660 (OL652662, OL652661). This is thought to be the first report of ToMMV in S. lycopersicum seeds in the Netherlands and intercepted in seed imported from Asia.