Field deployable Reverse Transcriptase–Recombinase Polymerase Amplification (RT-RPA) for detection of Maize chlorotic mottle virus (MCMV)

Diagnosis of maize lethal necrosis (MLN)-causing viruses is key in MLN surveillance programs and in testing seed for zero tolerance of Maize chlorotic mottle virus (MCMV) in seed lots. This is crucial for MLN management in farmers’ fields and in commercial seed fields. A customized MCMV detection assay that is specific, sensitive, affordable, and portable is therefore important for this task. Reverse Transcriptase–Recombinase Polymerase Amplification (RT-RPA) meets those conditions earlier described. RPA is a rapid isothermal nucleic acid amplification and detection platform that is based on patented Recombinase Polymerase Amplification (RPA) technology. In this study, a real time endpoint analysis and field deployable RT-RPA diagnostic method for the detection of MCMV was developed. RPA primer sets with their complementary probes were designed, synthesized and tested through a series of primer set evaluations to determine the most efficient primer sets. The primer sets targeted the MCMV genome at position 2765-2948 bp (MCMV_gp2 replicase gene). The parameters evaluated were sensitivity, specificity and reproducibility for the assay with remarkable results. The assay discriminated against other maize infecting viruses hence specific to MCMV. The assay takes only 20 min and its detection limit of 10-4 is well comparable to RT-PCR and other molecular based detection assays. MCMV was also detected directly from leaf saps without the nucleic acid extraction step hence suitable for on-farm testing. RPA is a relatively inexpensive technique that requires minimal instrumentation. This assay is therefore suitable for the detection of MCMV in field surveys, routine MCMV testing for phytosanitary measures and in the seed certification procedures.