Abstract
In May 2018, tomato leaves (Solanum lycopersicum cv. Delisher) exhibiting symptoms of necrotic patches were collected from a glasshouse in Southern England. It was suspected that the samples were infected with Tomato chlorosis virus (ToCV), genus Crinivirus, as ToCV had been detected in a different variety on the same holding. Analysis was done by high throughput sequencing (Fox et al., 2019). The presence of ToCV could not be confirmed. A total of 3,453,344 reads were produced from the sample and 652 were found to represent the complete genome sequence of Southern tomato virus (STV), genus Amalgavirus (GenBank Accession No. MW266062) with an average coverage of 34 and with 100% nucleotide sequence identity to the original isolate of STV discovered in 2009 (EF442780.1). To confirm the presence of this virus, a specific real-time RT-PCR for STV (Table 1) was designed using PRIMER EXPRESS v.2 (Life Technologies Co., USA). The sample tested positive using this assay. During 2018, three tomato samples, cv. Dometica, from two different locations in northern England, with symptoms of severe leaf mottling and veinal necrosis (Fig. 1) had also been submitted to Fera Science Ltd. The samples tested negative by ELISA for common tomato viruses: Tomato mosaic virus, Tomato spotted wilt virus, Potyvirus (DSMZ, Germany); Alfalfa mosaic virus, Impatiens necrotic spot virus, Pepino mosaic virus, Potato virus Y, (Bioreba, Switzerland); Cucumber mosaic virus (Agdia, USA); and Potato virus X (Fera Science Ltd., UK). The samples also tested negative by PCR for Tomato torrado virus (Verbeek et al., 2012) and pospiviroids (Botermans et al., 2020). Mechanical inoculation to Chenopodium quinoa, Nicotiana benthamiana, N. hesperis, N. occidentalis P1 and Solanum lycopersicum) did not result in symptoms 21 days post inoculation. The samples were stored at -80°C. In 2019 samples were reanalysed using the STV real-time RT-PCR (Table 1), all samples tested positive. Seeds linked to the two northern outbreaks were also tested using the assay and found to be positive. STV, first detected in USA and Mexico (Sabanadzovic et al., 2009) has since been reported in several countries in Europe and Asia (Oh et al., 2018.). STV has been reported to be associated with mottling, yellowing and/or chlorotic spotting (Gaafar et al., 2019), this report records the virus as also being associated with veinal necrosis. Similar symptoms were observed in glasshouses across England, sporadically in 2018–9 and STV was subsequently detected. A further variety (cv. Lewis) was found to be co-infected with Pepino mosaic virus. STV has been detected from different tomato varieties in the UK. No management action is recommended in England or Wales unless symptoms are severe or STV is found in combination with other viruses. This work was supported by Defra under its Plant Health Long-Term Service Agreement with Fera Science Ltd.
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Claims 12
Claim · model-written summary
Southern tomato virus genome was detected in symptomatic tomato leaves.
- Taxon
- tomato
Solanum lycopersicume0 - Material
- Delishere0
- Interactor
- Southern tomato virusSouthern tomato viruse1pathogen
- Outcome
- complete genome sequence of Southern tomato virus (STV)e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“tomato leaves (Solanum lycopersicum cv. Delisher) exhibiting symptoms of necrotic patches”
e1“652 were found to represent the complete genome sequence of Southern tomato virus (STV)”
Claim · model-written summary
The STV genome had 100% nucleotide identity to the original isolate.
- Taxon
- tomatoSolanum lycopersicume1
- Interactor
- STVe0pathogen
- Outcome
- nucleotide sequence identitye0
- Value
- 100%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“100% nucleotide sequence identity to the original isolate of STV”
e1“tomato leaves (Solanum lycopersicum cv. Delisher)”
Claim · model-written summary
A specific STV real-time RT-PCR confirmed the sample positive.
- Taxon
- tomatoSolanum lycopersicume2
- Interactor
- STVe0pathogen
- Outcome
- tested positivee1
- Value
- positivee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a specific real-time RT-PCR for STV (Table 1) was designed”
e1“The sample tested positive using this assay”
e2“tomato leaves (Solanum lycopersicum cv. Delisher)”
Claim · model-written summary
Northern tomato samples were negative for listed common viruses and pospiviroids.
- Taxon
- tomatoSolanum lycopersicume0
- Material
- Dometicae0
- Outcome
- tested negativee2
- Setting
- northern Englande0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“three tomato samples, cv. Dometica, from two different locations in northern England”
e1“The samples also tested negative by PCR for Tomato torrado virus (Verbeek et al., 2012) and pospiviroids”
e2“The samples tested negative by ELISA for common tomato viruses”
Claim · model-written summary
Mechanical inoculation did not produce symptoms after 21 days.
- Taxon
- Solanum lycopersicumSolanum lycopersicume0
- Treatment
- Mechanical inoculatione0
- Outcome
- symptomse0
- Direction
- did not resulte0
- Value
- 21 dayse0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Mechanical inoculation to Chenopodium quinoa, Nicotiana benthamiana, N. hesperis, N. occidentalis P1 and Solanum lycopersicum) did not result in symptoms 21 days post inoculation”
Claim · model-written summary
All three northern samples tested positive for STV in 2019.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Dometicae1
- Interactor
- STVe0pathogen
- Outcome
- tested positivee0
- Setting
- northern Englande1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In 2019 samples were reanalysed using the STV real-time RT-PCR (Table 1), all samples tested positive”
e1“three tomato samples, cv. Dometica, from two different locations in northern England”
Claim · model-written summary
Seeds linked to northern outbreaks tested STV positive.
- Taxon
- tomatoSolanum lycopersicume1
- Organ / stage
- Seedse0
- Interactor
- STVe2pathogen
- Outcome
- found to be positivee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Seeds linked to the two northern outbreaks were also tested using the assay and found to be positive”
e1“three tomato samples, cv. Dometica”
e2“STV real-time RT-PCR”
Claim · model-written summary
STV was associated with veinal necrosis in tomato.
- Taxon
- tomatoSolanum lycopersicume1
- Interactor
- STVe2pathogen
- Outcome
- veinal necrosise0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“this report records the virus as also being associated with veinal necrosis”
e1“three tomato samples, cv. Dometica”
e2“STV has been reported”
Claim · model-written summary
STV was detected in glasshouses across England with similar symptoms.
- Taxon
- tomatoSolanum lycopersicume1
- Interactor
- STVe0pathogen
- Outcome
- STV was subsequently detectede0
- Setting
- Englande0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Similar symptoms were observed in glasshouses across England, sporadically in 2018–9 and STV was subsequently detected”
e1“tomato varieties in the UK”
Claim · model-written summary
Lewis tomato was coinfected with Pepino mosaic virus.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Lewise0
- Interactor
- Pepino mosaic virusPepino mosaic viruse0pathogen
- Outcome
- co-infectede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A further variety (cv. Lewis) was found to be co-infected with Pepino mosaic virus”
e1“tomato varieties in the UK”
Claim · model-written summary
STV was detected in different UK tomato varieties.
- Taxon
- tomatoSolanum lycopersicume0
- Interactor
- STVe0pathogen
- Outcome
- STV has been detectede0
- Setting
- UKe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“STV has been detected from different tomato varieties in the UK”
Claim · model-written summary
Management action was recommended only for severe symptoms or virus combinations.
- Taxon
- tomatoSolanum lycopersicume1
- Outcome
- No management actione0
- Qualifier
- unless symptoms are severe or STV is found in combination with other virusese0
- Setting
- England or Walese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“No management action is recommended in England or Wales unless symptoms are severe or STV is found in combination with other viruses”
e1“tomato varieties in the UK”
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