Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated virus 3 variant groups I, II, III and VI

Table 5 List of primers used with the real-time RT-PCR HRM assay and the end-point multiplex RT-PCR protocol

Primer pair	Sequence (5'-3')	Target region	Amplicon size (bp)
LR3.HRM1.F	TAGACGTTAAAGATGTGAAGCG	GLRaV-3 ORF1a	167
LR3.HRM1.R	TCGTACACATCCACCATA
LR3.HRM2.F	GTCCTAGATTCGGATTTTGTCG	GLRaV-3 ORF1a	231
LR3.HRM2.R	GAATACTCTTCGCCCTATC
LR3.HRM3.F	CTGGTTGCTTTCGAGGTATATGAG	GLRaV-3 ORF1b	295
LR3.HRM3.R	CACTTCAAGGTGTTGCGCTT
LR3.HRM4.F	TAATCGGAGGTTTAGGTTCC	GLRaV-3 ORF4	226
LR3.HRM4.R	GTCGGTTCGTTAACAACAC
LR3.HRM5.F	TGTGTAAGAAGGTTATGGG	GLRaV-3 ORF6	224
LR3.HRM5.R	TACTGCCTTACCGGGTTTTC
LR3.HRM6.F	GTCACCAGGTGTTCCAAACC	GLRaV-3 ORF1a	305
LR3.HRM6.R	AACGCCCTGTATGTCCTCTC
LR3_Universal_F	TAAATGCTCTAGTAGGATTC	GLRaV-3 5'UTR
621_430R	TAACCCAACACGACGATGAG	GLRaV-3 5'UTR	429^a
623_564R	CTCACGCTAAACACACCAAG	GLRaV-3 5'UTR	563^a
PL20_315R	GTTTGTAACAAAGAAACACG	GLRaV-3 5'UTR	314^a
GH11_180R	CCAAAACGAAGACGAAAAGAAGAG	GLRaV-3 5'UTR	179^a
LR_ORF1aR	CGTCCGCTTCACCCCTTTGG	GLRaV-3 ORF1a
Vv_Actin_F [32]	CTTGCATCCCTCAGCACCTT	V. vinifera predicted actin-7	82
Vv_Actin_R [32]	TCCTGTGGACAATGGATGGA