Table 2.

The primer sets used for RT-LAMP, RT-PCR and real-time RT-PCR. The F1c and B1c regions of the FIP and BIP primers are indicated by lower-case letters, and the F2 and B2 regions of the FIP and BIP primers are shown as upper-case letters

Name	Positiona (nt)	Sequence
		RT-LAMP Y4 set
Y4F3b	8802-8820	TGC CAA CTG TGA TGA ATG G
Y4B3b	9105-9085	GTT CGT GAT GTG ACC TCA TAA
Y4FIP	F1c 8934-8917 F2 8865-8884	gca ttc tca acg att ggt ACG GAG TTT GGG TTA TGA TG
Y4BIP	B1c 8950-8968 B2 9027-9008	gca aat cat ggc aca ttt c CG TGG CAT ATA TGG TTC CTT
Y4LF	8914-8893	CAA TGG GTA TTC GAC TTG TTC A
Y4LB	8969-8987	TCA GAT GTT GCA GAA GCG T
		RT-LAMP Y5 set, Przewodowska et al. [ 11 ]
Y5F3	8910-8931	CGT TGA AAC CAA TCG TTG AGA A
Y5B3	9241-9224	GAC ATC CTC GGT GGT GTG
Y5FIP	F1c 9001-8981 F2 8938-8958	gcg cat ttc tat ata cgc ttc ACC AAC CCT TAG GCA AAT CAT
Y5BIP	B1c 9145-9162 B2 9217-9169	cgc agc att gaa atc agc TGT GTT CTC CTC TTG TGT ACT G
Y5LF	8980-8960	TGC AAC ATC TGA GAA ATG TGC
Y5LB	9168-9184	CTC GAC TTT TCG GGT TGG A
		RT-LAMP N set, Nie [ 10 ]
NF3	8779-8799	ATA CGA CAT AGG AGA AAC TGA
NB3	8987-8968	ACG CTT CTG CAA CAT CTG AG
NFIP	F1c 8859-8841 F2 8808-8829	gtt tgg cga ggt tcc att ttc TGT GAT GAA TGG GCT TAT GGT
NBIP	B1c 8913-8933 B2 8965-8945	tga aac caa tcg ttg aga atg ATG TGC CAT GAT TTG CCT AAG
		TM real time RT-PCR set, Singh et al. [ 13 ]
Y1 FP	8918-8939	CCA ATC GTT GAG AAT GCA AAA C
Y1 RP	8991-8967	FAM-ATA TAC GCT TCT GCA ACA TCT GAG A-BHQ1
Y1 probe	8946-8965	TTA GGC AAA TCA TGG CAC AT

^a The nucleotide position corresponds to the genome of PVY isolate N Nysa with accession number FJ666337

^b Primers used as forward (Y4F3) and reverse (Y4B3) primers in conventional RT-PCR, in SG-based real-time RT-PCR, and in TM-based real-time RT-PCR with probe Y1