A sensitive real-time RT-PCR reveals a high incidence of Southern tomato virus (STV) in Spanish tomato crops

Abstract

Southern tomato virus (STV) is a double-stranded RNA (dsRNA) virus belonging to genus Amalgavirus (family Amalgamaviridae). STV has been detected in tomato plants showing different symptoms although it has not been demonstrated that STV is the causal agent. To study the STV incidence and its pathogenic role, a sensitive and quantitative real-time reverse transcription-polymerase chain reaction assay (RT-qPCR) was developed. The standard curve performed with viral RNA transcripts allowed a wide dynamic range for STV quantitation from 104 to 1011 copies/ng of total RNA. STV detection by RT-qPCR was 102-fold more sensitive than conventional RT-PCR or RT-LAMP and 104-fold more sensitive than molecular hybridization. STV was detected in different tomato plant tissues, as well as in the coat and the embryo of individual seeds. Also, viral concentration remained constant over time in leaf tissues of STV-infected tomato plants. Surveys on different tomato fields from Spain revealed that STV was widespread. In addition, the virus was detected in almost every tomato variety and nursery analyzed. STV-infected tomato plants did not show any disease-related symptom suggesting that the virus was not directly the causal agent of any tomato disease. However, there is no information about the STV effect in mixed infections or in abiotic stressed conditions and further studies must be performed to clarify it. The RT-qPCR assay developed in this work could be implemented on sanitation programs in order to limit the virus spread and could be used to study the effect of STV in mix infections or abiotic stressed conditions.