Assessment of SNaPshot and single step RT-qPCR methods for discriminating Potato virus Y (PVY) subgroups

► Molecular characterization of Potato virus Y (PVY) on field samples was done. ► SNaPshot and RT-qPCR successfully discriminate PVY strain groups. ► The tested RT-qPCR assay was more reliable in discriminating PVYNTN group members. ► The tested SNaPshot assay distinguished broader spectra of PVY strain groups. ► Molecular discrimination was compared with bioassay, ELISA and sequence analysis.