Table 3.
Specific and degenerate primers used for PCR amplification of either RNA1, RNA2 and/or RNA3 segment of each Ilarvirus species.
| Virus | Primers | Primer sequence (5′−3′) | Annealing temp. | RNA (Gene*) | Amplicon length | References |
|---|---|---|---|---|---|---|
| American plum line pattern virus (APLPV) | APLPV- 2-F | AAATCACAGGGACGACTTCA | 56°C | RNA2 (RdRp gene) | 730 bp | This study |
| APLPV- 2-R | TCCGACTCTTCCTACAATGC | |||||
| APLPV3-F | GATCAGACGCTTTTGCAGTT | 54°C | RNA3 (CP gene) | 357 bp | This study | |
| APLPV3-R | CCTCCAGCTACCAAAACAGA | |||||
| Apple mosaic virus (ApMV) | ApMV-Rd-F | GCAGAGGTTGCATCATTTGA | 55°C | RNA2 (RdRp gene) | 347 bp | This study |
| ApMV-Rd-R | GAAATTTGGCCTCAAAGTTG | |||||
| ApMV-F | TGGATTGGGTTGGTGGAGGAT | 53°C | RNA3 (CP gene) | 261 bp | Petrzik and Svoboda, 1997 | |
| ApMV-R | TAGAACATTCGTCGGTATTTG | |||||
| Parietaria mottle virus (PMoV) | PMoVf | GATGTTGCCGCCGACGATTCTA | 54°C | RNA1 (MT gene) | 475 bp | Janssen et al., 2005 |
| PMoVr | TTTTCCCACAACCCGCAACAC | |||||
| PMoV-Rd-F | GATTGAAGAGTGATACGCAC | 55°C | RNA2 (RdRp gene) | 372 bp | This study | |
| PMoV-Rd-R | CAGGGTCGACTACACCACGAT | |||||
| Prune dwarf virus (PDV) | PDV-Rd-F | CGACGTTTGATAAGTCGC | 54°C | RNA2 (RdRp gene) | 360 bp | This study |
| PDV-Rd-R | ATTTGGCTTCGAAATTGAAC | |||||
| PDV-F | TAGTGCAGGTTAACCAAAAGGAT | 62°C | RNA3 (CP gene) | 172 bp | Parakh et al., 1994 | |
| PDV-R | ATGGATGGGATGGATAAAATAAT | |||||
| Prunus necrotic ringspot virus (PNRSV) | PNRSV-Rd-F | GCAAAGGTTACATCACCTGATTC | 60°C | RNA2 (RdRp gene) | 363 bp | This study |
| PNRSV-Rd-R | TTGGTTATGTGGAAATTTCGCTTC | |||||
| PNRSV-C537 | ACGCGCAAAAGTGTCGAAATCTAAA | 54°C | RNA3 (CP gene) | 455 bp | MacKenzie et al., 1997 | |
| PNRSV-H83 | TGGTCCCACTCAGAGCTCAACAAAG | |||||
| Raphanus latent virus (RaLV) | RaLV-Rd-F | AAGGGAAGTTACACCATGATG | 52°C | RNA2 (RdRp gene) | 347 bp | This study |
| RaLV-Rd-R | GAATTTGGTTTCGAAATTAAAGA | |||||
| RaLV-F | TGAGATCAGTTAACCGATGC | 58°C | RNA3 (CP gene) | 307 bp | This study | |
| RaLV-R | GCATCTATCAAGGTACCCAC | |||||
| Ilarvirus genus sub group 1 | Ilar-grp1-MT-F | AWTCITCICAYAGTTTTGCYGC | 52°C | RNA1 (MT gene) | 870 bp | This study |
| Ilar-grp1-MT-R | ATIGTIGCIATRTAITGVAC | |||||
| Ilarvirus genus sub group 1 | Ilar-grp1-CP-F | TGATICCAAIGAIGCNAT | 50°C | RNA3 (CP gene) | 271 bp | This study |
| Ilar-grp1-CP-R | TYIAGICACCAIACIAIDG |
*
MT = methyl transferase; RdRp = RNA dependent RNA polymerase; CP = coat protein.