Table 1.
The reverse transcription-PCR and qPCR assays most commonly used to detect PMMoV in (waste)water and food matrices.
| Assay type | Oligonucleotide name | Sequence (5’ – 3’) | Target gene | Amplicon size (bp) | Thermocycler conditions |
Citation |
|---|---|---|---|---|---|---|
| PCR | PMMV-F | AACCTTTCCAGCACTGCG | Replication- associated protein |
201 | 94°C 5 min, 40x (94°C 1 min, 50°C 45 s, 72°C 1 min), 72°C 5 min |
Zhang et al. 2006 |
| PMMV-R | GCGCCTATGTCGTCAAGACT | |||||
| PCR | PMMoV-CP forward | ATGGCTTACACAGTTTCCAGT | Capsid protein |
474 | 94°C 3 min, 40x (94°C 30 s, 55°C 30 s, 72°C 30 s) |
Peng et al. 2015 |
| PMMoV-CP reverse | CTAAGGAGTTGTAGCCCAGGTG | |||||
| PCR | CP/s | ATGGCATACACAGTTACCAGT | Capsid protein |
470 | 94°C 2 min, 40x (94°C 1 min, 49°C 45 s, 72°C 1 min), 72°C 7 min |
Çağlar et al. 2013 |
| CP/a | TTAAGGAGTTGTAGCCCACGTA | |||||
| qPCR (SYBR green) |
Ha-PMMV1 | GTGGCAGCAAAGGTAATGGT | Replication- associated protein |
80 | 95°C 15 min, 45x (58°C 45 s, 72°C 15 s) |
Hamza et al. 2011 |
| Ha-PMMV2 | ATTTGCTTCGGTAGGCCTCT | |||||
| PM1602 | TGTTTCGGAAAAGGCTCTTG | |||||
| qPCR (hydrolysis probe) |
PMMV-FP1 | GAGTGGTTTGACCTTAACGTTGA | Replication- associated protein |
68 | 95°C 10 min, 40x (95°C 30 s, 60°C 1 min) |
Zhang et al. 2006 |
| PMMV-RP1 | TTGTCGGTTGCAATGCAAGT | |||||
| PMMV-probe1 | 6FAM-CCTACCGAAGCAAATG-TAMRA | |||||
| PMMV-FP1-rev | GAGTGGTTTGACCTTAACGTTTGA | Haramoto et al. 2013 | ||||
| PMMV- Taqman MGB probe | 6FAM-CCTACCGAAGCAAATG-MGB-NFQ |