Development of a reverse transcription-recombinase polymerase amplification (RT-RPA) assay for the detection of onion yellow dwarf virus (OYDV) in onion cultivars

Onion yellow dwarf virus (OYDV) is an important virus affecting Allium species like onion and garlic worldwide. Enzyme-linked immunosorbent assays (ELISA) and reverse transcription polymerase chain reaction (RT-PCR) assays are two most commonly used assays for the detection of OYDV but the sensitivity of ELISA is less than that of RT-PCR. PCR based assays are often considered for their sensitivity, specificity but time consuming and require specific technical expertise and costly equipments. To counter these difficulties, a simple and rapid RT-RPA assay for the detection of OYDV was developed. A common set of primer was designed to amplify the coat protein region of OYDV to perform RT-PCR and RT-RPA. Specificity as well as sensitivity test using tenfold serial dilution series of the purified RNA was performed for both the assays. Both symptomatic and asymptomatic samples of different varieties of onion were collected from Delhi NCR region and evaluated for OYDV infection using RT-PCR along with RT-RPA assay. The comparative results have shown that sensitivity of RT-RPA was similar to RT-PCR. However, RT-RPA is simple, and rapid assay for the large scale virus indexing of onion.