Generic and sequence-variant specific molecular assays for the detection of the highly variable Grapevine leafroll-associated virus 3

► Improved the molecular detection of Grapevine leafroll-associated virus 3. ► Developed a new variant-specific hexaplex RT-PCR assay. ► Successfully detected variants differing by more than 20% at the nucleotide level. ► Effectively detected GLRaV-3 from leaf, cane, and root samples. ► Hexaplex RT-PCR assay was successfully used to screen over 300 field samples.