Table 3.
Primers and PCR conditions used for the efficient detection of targeted viruses.
| Target virusa | Primer name and combinations | Primer concentration (μM) | Annealing temperature (ºC) | Expected PCR product (bp) |
|---|---|---|---|---|
| Uniplex PCR | ||||
| CBSIs | CBSVF3 CBSVR3 |
0.4 0.4 |
52 | 283 |
| CBSIs | CBSVF5 CBSVR3 |
0.4 0.4 |
52 | 520 |
| CBSV | CBSVF2 CBSVR7 |
0.4 0.4 |
52 | 345 |
| UCBSV | CBSVF2 CBSVR8 |
0.4 0.4 |
52 | 441 |
| CMBs | Deng A Deng B |
0.6 0.6 |
52 | 520 |
| ACMV | CMBRep/F ACMVRep/R |
0.4 0.4 |
52 | 368 |
| ACMV | CMBCP/F ACMVCP/R |
0.4 0.4 |
52 | 650 |
| EACMV | CMBRep/F EACMVRep/R |
0.4 0.4 |
52 | 524 |
| EACMV-UG | CMBCP/F EACMV-UG/R |
0.4 0.4 |
52 | 1000 |
| Duplex and multiplex PCR | ||||
| CBSIs + CMBs | CBSVF3 CBSVR3 Deng A Deng B |
0.4 0.4 0.6 0.6 |
52 | 283 520 |
| CBSV + UCBSV | CBSVF2 CBSVR7 CBSVR8 |
0.4 0.1 0.4 |
50 | 345 441 |
| CBSIs + EACMV | CBSVF3 CBSVR3 CMBRepF EACMVRep/R |
0.4 0.4 0.4 0.4 |
52 | 283 524 |
| CBSIs + ACMV + EACMV-Ug | CBSVF3 CBSVR3 CMBCP/F ACMVCP/R EACMV-UG/R |
0.4 0.4 0.4 0.4 0.4 |
52 | 230 650 1000 |
| Real-time PCR | ||||
| CBSIs | CBSVF3 CBSVR4 | 0.7 | 68 | 130 |
| Ribulose biphosphate carboxylase oxygenase gene | RubiscoLF RubiscoLR |
0.7 | 68 | 171 |
| Ribosomal protein (L2) | L2F L2R |
0.7 | 68 | 135 |
a
ACMV – African cassava mosaic virus; EACMV – East African cassava mosaic virus; EACMV-Ug – East African cassava mosaic virus-Uganda; CBSIs – cassava brown streak ipomoviruses; CMBs – cassava mosaic begomoviruses; CBSV – Cassava brown streak virus; UCBSV – Ugandan Cassava brown streak virus.