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 | ||