ABSTRACT
Southern tomato virus (STV) from genus Amalgavirus (Family Amalgaviridae) is a persistent virus infecting tomato crops worldwide. Information on genetic diversity and evolutionary mechanisms for plant persistent viruses are very scarce in comparison with plant acute viruses. In this work, the putative coat protein gene of worldwide STV isolates was analyzed showing very low nucleotide diversity (< 0.0100). Phylogenetic analysis separated STV isolates into two clades, but no correlation was found between genetic and geographic distances. Also, no recombination events among STV isolates were detected. Comparison of synonymous and nonsynonymous substitutions indicated negative selection at the amino acid level.
Subject(s)
Capsid Proteins/genetics , Plant Diseases/virology , Plant Viruses , RNA Viruses , Solanum lycopersicum/virology , Genetic Variation , Genome, Viral , Phylogeny , Phylogeography , Plant Viruses/classification , Plant Viruses/genetics , RNA Viruses/classification , RNA Viruses/genetics , RNA, Viral/genetics , Recombination, GeneticABSTRACT
Southern tomato virus (STV) is a double stranded RNA (dsRNA) virus belonging to genus Amalgavirus (family Amalgamaviridae) which has been detected in tomato plants showing stunting, fruit discoloration and size reduction. A one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of STV in total RNA or sap extracts (obtained just by grinding in buffer) from STV-infected tomato plants by using a set of three primers pairs which were designed to the sequence of the STV putative coat protein. Amplification products were visualized by gel electrophoresis or direct staining of DNA. The sensitivity of RT-LAMP was identical to that of the conventional RT-PCR and less affected by the presence of polymerase inhibitors. STV was detected by RT-LAMP in different tomato tissues, i.e. leaves, roots, fruits and seeds. Also the virus was successfully detected by RT-LAMP from sap extracts obtained from field tomato plants whereas conventional RT-PCR did not. Results of this work show that RT-LAMP is a specific, rapid and cheap procedure to detect STV and it could be implemented on field surveys and sanitation programs.
