Table 1.

Primer sequences for Pepino mosaic virus genotype-specific loop mediated isothermal amplification and RT-PCR

Genotype	Primer designation	Sequence*	Position on genome	GenBank accession #
Primers for genotype-specific RT-LAMP
CH2	CH2_F3	5′-CGATGAAGCTGAACAACATTTCC-3′	4297-4319	DQ000985
	CH2_FIP	5′-CTTAATGGGTTGATCTTGGTGGAAGCTGTGAGAAAGCTTCACAAAC-3′	4403-4381 + 4321-4343
	CH2_BIP	5′-GGGTTAAGTTTTCCCCAGTTTGAAAATTCCTTCAGTGTTAATCTTGTG-3′	4404-4428 + 4498-4476
	CH2_B3	5′-TCCAGCAATTCCGTGCACAACAA-3′	4523-4501
	CH2_Loop F	5′-GGCCTCGCCTTGATGGA-3′	4360-4344
	CH2_Loop B	5′-TGGAAAGATCAACTTTGATCAATT-3′	4429-4452
EU	EU_F3	5′-ACCAAGAAGATACAAAATTTGC-3′	6090-6111	FJ940223
	EU_FIP	5′-TRAGACCATCAGCAGGCTGC TGCATTTGACTTCTTCGATG-3′	6173-6154 + 6112-6131
	EU_BIP	5′-TCAGGCARCCAAATGAGAAAGAAACCTGTGGAGATCTTTTGC-3′	6174-6196 + 6256-6238
	EU_B3	5′-TGACTTCTCCAAGTGTGG-3′	6284-6267
	EU_Loop F	5′-TGGCAGGGTTGGTGACTC-3′	6149-6132
	EU_Loop B	5′-CTAGCTGCTCACTCCGTAGCTAA-3′	6197-6219
US1	US1_F3	5′-GCATTCATACCAAATGGGAG-3′	4255-4274	FJ940225
	US1_ FIP	5′-TGCGAACAGCCAAGAAATGT-ATAAATTGCATGAATACCTTACTCC-3′	4334-4315 + 4275-4299
	US1_ BIP	5′-TTGCACAAACTCCACCAAGGACTTAACCCGTCAATGTGTT-3′	4337-4356 + 4415-4396
	US1_ B3	5′-CCATTTCGAACAGGGGAA-3′	4433-4416
	US1_ Loop F	5′-TGCTCAGCTTCATCA-3′	4413-4299
	US1_ Loop B	5′-TGAAGCCATGAGACTT-3′	4357-4372
Primers for genotype-specific RT-PCR
CH2	PeppMVCH2CPF	5′- caggaaacagctatgacGTTTTCCTCAATTGTGAAAT-3′	5568-5587	DQ000985
	PepMVCH2CPR	5′- tgtaaaacgacggccagtTTTTTTTTTTATTTAGTAGATTTAGATAC-3′	6412-6394
EU	PepMVEUCPF	5′ – caggaaacagctatgacGTTTTCCTAAATTTGAAAAT-3′	5572-5591	FJ940223
	PepMVEUCPR	5′ – tgtaaaacgacggccagtATTTCAAAGAAATAATTAGG-3′	6410-6391
US1	PepMVUS1CPF	5′ - caggaaacagctatgacGTTTTCCTAGTGTTTGAAA-3′	5570-5588	FJ940225
	PepMVUS1CPR	5′ - tgtaaaacgacggccagtAAATTACAAAAGCAATTTATTG-3′	6415-6394
Primers for full genome sequencing
CH2	KL11-124:CH2-1F	5′- caggaaacagctatgacGAAAACAAAACATAACACATAATATC-3′	1-26	DQ000985
	KL11-131: CH2-1226R	5′- tgtaaaacgacggccagtTCATGCACCTCCAGTCATGT-3′	1226-1207
	KL11-125: CH2-902F	5′- caggaaacagctatgacAAAAATAGCTTTGTGACCTTTCC-3′	902-924
	KL11-132: CH2-1741R	5′- tgtaaaacgacggccagtGCTGGAAGTGTCAGATGCAA-3′	1741-1722
	KL11-126: CH2-1395F	5′- caggaaacagctatgacCCAATTTAGTCAAACAAGGCGTA-3′	1395-1417
	KL11-133: CH2- 2719R	5′- tgtaaaacgacggccagtAATTGGCACTTTGCACTTTTG-3′	2719-2699
	KL11-127: CH2-2383F	5′- caggaaacagctatgacGATTCAACCTGGCTTTCCAA-3′	2383-2402
	KL11-134: CH2- 3738R	5′- tgtaaaacgacggccagtGTTTGGGCGGTTCTGTTAAA-3′	3738-3719
	KL11-128: CH2- 3379F	5′- caggaaacagctatgaCGACCTGGGAGATTTGTGCTG-3′	3379-3398
	KL11-135: CH2- 4734R	5′- tgtaaaacgacggccagtGACAGGGGTCACCAAAAATG-3	4734-4715
	KL11-129: CH2- 4381F	5′- caggaaacagctatgacTCCACCAAGATCAACCCATT-3′	4381-4400
	KL11-136: CH2- 5748R	5′- tgtaaaacgacggccagtAAATCACTTAGGGAAGGAGCTG-3′	5748-5727
	KL11-130: CH2- 5405F	5′- caggaaacagctatgacGCCGTAATATTCACCAGCATC-3′	5405-5425
	KL11-137: CH2-6412	5′- tgtaaaacgacggccagtTTTTTTTTTTATTTAGTAGATTTAGATAC-3′	6412-6394

*Primer adapters (M13 forward and reverse primer sequences, in lowercase) were added to specific viral sequences to facilitate direct sequencing of the amplified RT-PCR products.