“Rapid diagnosis of Cucumber mosaic virus in banana plants using a fluorescence-based real-time isothermal reverse transcription-recombinase polymerase amplification assay”

Cucumber mosaic virus (CMV) is a widespread plant virus infecting important vegetables, plantation and flower crops. Currently, CMV is detected by enzyme-linked immunosorbent assays (ELISA) and reverse transcription-polymerase chain reaction (RT-PCR) assays. ELISA requires polyclonal antibodies and is time-consuming. PCR requires skilled manpower and complex procedures of RNA isolation as well as a thermal cycler. To overcome these difficulties, a portable rapid, simple and visual fluorescence-based reverse transcription-recombinase polymerase amplification (portable RT-exo-RPA) assay for the detection of CMV was developed. A specific primer pair of 30–33 bp targeting a conserved region of the coat protein (CP) gene of CMV and a probe to function in the RT-exo-RPA assays were designed and synthesized. A total of 62 symptomatic as well as 58 asymptomatic banana plant samples, collected from banana orchards located in Jalgaon, Maharashtra, India, were evaluated for CMV infections using crude leaf extracts as templates by a reverse transcription-recombinase polymerase amplification (RT-RPA) assay as well as a real-time RT-exo-RPA assay and the results were compared with those of a reverse transcription-polymerase chain reaction (RT-PCR) assay using purified total plant RNAs as templates. CMV was as efficiently detected using the crude leaf extract template in the RT-RPA and real-time RT-exo-RPA assays as using the purified RNA template in the RT-PCR assay. To dispense with the use of real-time PCR, a portable RT-exo-RPA assay was developed and the alternative methods for the visualization of CMV detection using either a fluorometer or direct viewing with a UV transilluminator were evaluated. To our knowledge, this is the first report of the rapid and reliable diagnosis of CMV infections by a real-time RT-exo-RPA assay using a crude leaf extract as template.