Skip to main content

Table 1 Primer sequences for Pepino mosaic virus genotype-specific loop mediated isothermal amplification and RT-PCR

From: Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification

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
  1. *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.