Generic and semi-generic tests
The generic plant virus tests listed below should not be considered as curated diagnostic protocols. These are rather tests that have been published for a first characterization of viral infections. They can allow, in particular together with direct sequencing of (RT-)PCR products, a first assignment of the viruses in a sample to a specific genus or possibly even down to the species level. However, further specific tests may be required for an unambiguous identification. Please note that indicated tests usually will not detect all species in a particular genus. For details see references.
Group targeted | Type | Oligo nucleotides (5’-3’) | Reference |
Badnavirus | PCR | BadnaFP: ATGCCITTYGGIAARAAYGCICC BadnaRP: CCAYTTRCAIACISCICCCCAICC | Yang IC et al (2003) |
Begomovirus DNA-A | PCR | PAL1v1978B: GCATCTGCAGGCCCACATBGTYTTHCCNGT PAR1c715H: GATTTCTGCAGTTDATRTTHTCRTCCATCCA | Tsai et al (2011) |
Begomovirus DNA-B | PCR | DNABLC1: GTVAATGGRGTDCACTTCTG DNABLC2: RGTDCACTTCTGYARGATGC DNABLV2: GAGTAGTAGTGBAKGTTGCA | Tsai et al (2011) |
Begomovirus ß-satellites | PCR | Beta01: GGTACCACTACGCTACGCAGCAGCC Beta02: GGTACCTACCCTCCCAGGGGTACAC | Briddon et al (2002) |
Begomovirus | PCR | DengA: TAATATTACCKGWKGVCCSC) DengB: TGGACYTTRCAWGGBCCTTCACA | Deng et al (1994) |
Begomovirus | PCR | AV494: GCCYATRTAYAGRAAGCCMAG AC1048: GGRTTDGARGCATGHGTACATG | Wyatt and Brown (1996) EPPO (2022) PM7/152(1) |
Begomovirus | PCR | SPG1: CCCCKGTGCGWRAATCCAT SPG2: ATCCVAAYWTYCAGGGAGCTAA | Li et al (2004) EPPO (2022) PM7/152(1) |
Begomovirus | PCR | Beg-CP-F: GCCCATGTAYMGRAARCC Beg-580-R: GGRTTAGARGCATGMGTACA | Saison and gentit (2015) EPPO (2022) PM7/152(1) |
Carlavirus | RT-PCR | Carla: CPGGBYTNGGBGTNCCNACNGA Poly-T: cctcgggcagtcctttttttttttttttttt | Gaspara et al (2008) |
Caulimovirus | PCR | Caulimo 3CPf: GAARRHCATTATGCMAAYGARTGTCC C4281: WWGGRTTTTCWRAACWWACT | Pappu and Druffel (2009) |
Nepovirus Subgroup A | RT-PCR | NepoA-F: ACDTCWGARGGITAYCC NepoA-R: RATDCCYACYTGRCWIGGCA | Wei and Clover (2008) EPPO (2017) PM7/2(2), Appendix 2 |
Nepovirus Subgroup B | RT-PCR | NepoB-F TCTGGITTTGCYTTRACRGT NepoB-R CTTRTCACTVCCATCRGTAA | Wei and Clover G (2008) |
Orthotospovirus | RT-PCR | gL3637 CCTTTAACAGTDGAAACAT gL4435c CATDGCRCAAGARTGRTARACAGA | Chu et al (2001) |
Orthotospovirus Asian clade 1 and Eurasian clade American clade 1 (not all TSWV isolates) Asian clade 2 LNRV American clade 2 | RT-PCR A B C D E | AS-EA-F: GGG GGA TCC AGA GCA ATC GAG G AS1-R: GCT TCA GTC CTC TTA AAT GTC C EA-R: TTG TTC AAT GAA GCA GCA CC AM1-F: GGG GGA TCC AGA GCA ATT GTG TC AM1-R: CTT TGC TTT TCA GCA CAG TGC A AS-EA-F: GGG GGA TCC AGA GCA ATC GAG G AS2-R: CTT TGA AGA TGA CCT CAT CT LNRV-F: CCA GTA AAA GAC GAA ATC CC LNRV-R: GAT TCA AAT CGC CCA GCA GTC C AM2-F: GGG GGA TCC AGA GCA ATC GG AM2-R1: GCA ACT CTA CCA GCT TG AM2-R2: GCA ACT TTA GCA GCT TG | Hassani-Mehraban et al (2016)
EPPO (2020) PM7/139(1), Appendix 4 |
Plant internal DNA control (COX) | Real-time PCR | COX-F: CGTCGCATTCCAGATTATCCA COX-R: CAACTACGGATATATAAGAGCCAAAACTG COX-P TGCTTACGCTGGATGGAATGCCCT-VIC | Weller et al (2000) |
Plant internal RNA control | RT-PCR | nad5-s: GATGCTTCTTGGGGCTTCTTGTT nad5-as: CTCCAGTCACCAACATTGGCATAA | Menzel et al (2002) |
Polerovirus | RT-PCR | Polero s2 ATCACITTCGGGCCGWSTCTATCAGA Polero as3 CACGCGTCIACCTATTTIGGRTTITG | Abraham et al (2006) |
Polerovirus | RT-PCR | Gen-1: CTCAARGCCTACCATGARTATAARATC Gen-2: CGTCTACCTATTTNGGRTTNTG | Knierim et al (2013) |
Pospiviroid | RT-PCR A B | Pospi1-FW: GGG ATCCCCGGGGAAAC Pospi1-RE: AGCTTCAGTTGTWTCCACCGGGT pCLVR4: GGGGCAACTCAGACCGAG C pCLV4: GGGGCTCCTGAGACCGCTCTTG |
EPPO (2021) PM7/138(1), Appendix 2 Verhoeven et al (2004)
Spieker (1996) |
Pospiviroid | RT-PCR | Pospi2-FW: ACCCGGTGGAWACAACTGAAGCT Pospi2-RE: GGTTTCCCCGGGGATCC | Verhoeven et al (2017) |
Potexvirus | RT-PCR | Potex 5: CAYCARCARGCMAARGAYGA Potex 1RC : TCAGTRTTDGCRTCRAARGT Potex 2RC: AGCATRGCNSCRTCYTG | Van der Vlugt and Berendsen M (2002) |
Potyvirus | RT-PCR | CPUP: TGAGGATCCTGGTGYATHGARAAYGG P9502: GCGGATCCTTTTTTTTTTTTTTTTT | Van der Vlugt et al (1999) |
Potyvirus | RT-PCR | Sprimer: GGNAAYAAYAGYGGNCARCC M4T: GTTTTCCCAGTCACGACTTTTTTTTTTTTTTT M4: GTTTTCCCAGTCACGAC | Chen et al (2001) |
Potyvirus | RT-PCR | CIFor: GGIVVIGTIGGIWSIGGIAARTCIAC CIRev: ACICCRTTYTCDATDATRTTIGTIGC | Ha et al (2008) |
Rhabdovirus | RT-PCR | Rhab-F: GGATMTGGGGBCATCC Rhab-R: GTCCABCCYTTTTGYC | Dietzgen et al. (2013) |
Tobamovirus | RT-PCR | Tobamo-s1: GGGAATCAGTTTCAAACRCA Tobamo-as1: GGGGGGATTCGAACCYCT | Menzel Wet al (2019) |
Tobamovirus | RT-PCR | TobamodF: TKGAYGGNGTBCCNGGNTGYGG TobamodR: ACNGAVTBNABCTGTAATTGCTAT | Li et al (2018) |
Tombusvirus | RT-PCR | Cir1: GACTCCGCCGTAGCTTGACC Cir2: GGTTTATTGACTTGTTCGTATTCA G | Koenig et al (2004) |
Torradovirus (RNA1) | RT-PCR | Torrado-1F: GCWGAYTAYTCMAGYTTTGATGG Torrado-1R: GGWACWGCMACHAGRTTGTCATC | Verbeek et al (2012) |
Torradovirus (RNA2) | RT-PCR | Torrado-2F: TGGGATGARTGYAATGTKCT Torrado-2R: CCWGTCCACCAYTTGCAATT | Verbeek et al (2012) |
Tymovirus | RT-PCR | EM13: CCTTCAACTGTGATGTTCATG EM14: TGCAGATTGTCCCACGC | Kreuze et al (2013) EPPO (2018) PM7/132(1), Appendix 3 |
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