Development and Evaluation of an Enhanced LAMP Primer Set for Detection of Potato Virus Y

Abstract

Abstract: Whilst molecular methods for plant virus detection are usually based on PCR amplification, loop mediated isothermal amplification (LAMP) is a rapid and sensitive molecular diagnostic tool increasingly used for plant virus detection, particularly in field conditions and resource-limited laboratories. In this study, a novel LAMP primer set (ID: 334) was developed for the specific detection of Potato virus Y (PVY), a globally significant pathogen responsible for yield losses of up to 80% in potatoes. Primer set 334 was designed based on conserved regions identified across 30 complete PVY genomes. It was evaluated against 33 PVY isolates representing 5 strain groups. The assay demonstrated 100% inclusivity, successfully detecting all isolates, including both recombinant and non-recombinant strains. Specificity testing confirmed no cross amplification with related potyviruses (Potato virus A (PVA) and Potato virus V (PVV)) or unrelated potato viruses (Potato virus X (PVX), Potato leafroll virus (PLRV), and Potato mop-top virus (PMTV)), further validating the exclusiveness of the assay. Moreover, the assay was validated on multiple host matrices, including leaves and tuber tissues of potato. Compared to a previously published LAMP assay, primer set 334 exhibited 2.6-fold greater sensitivity, detecting PVY at four orders of magnitude lower concentrations, with performance comparable to qPCR but with faster time-to-result. This improved LAMP assay provides a rapid, specific, and sensitive tool for PVY detection in leaves and tubers, supporting both laboratory, field, and post-harvest diagnostics.