Table 2.
Oligonucleotides and cycling conditions used during polymerase change reaction. A = adenine; C = cytosine; G = guanine; T = thymine; Rev = reverse; min = minute; s = second; RDRP = RNA-dependent RNA polymerase
| Primers | Sequence (5′-3′) |
|---|---|
| N CDS Fw XhoI | ATCATACTCGAGATGTCTGATAACGGACCCCA |
| N CDS Rev NotI | ATCATTGCGGCCGCGGCCTGAGTTGAGTCAGCAC |
| E-N fw BamHI | GGTGGTGGATCCTGAGCCTGAAGAACATGTCC |
| E-N Rev EcoRI | GGTGGTGAATTCAGCTCTCCCTAGCATTGTTC |
| Oligo(dT)20 | TTTTTTTTTTTTTTTTTTTT |
| Oligo(dA)20 | AAAAAAAAAAAAAAAAAAAA |
| 18S cDNA 1 | CCTTCCGCAGGTTCACCTAC |
| 18S cDNA 2 | CCTCCAATGGATCCTCGT |
| 18S cDNA 3 | TAATCATGGCCTCAGTTCCG |
| 18S qPCR | Fw: AAACGGCTACCACATCCA |
| Rev: CCTCCAATGGATCCTCGT | |
| N qPCR | Fw: GACCCCAAAATCAGCGAAAT |
| Rev: TCTGGTTACTGCCAGTTGAATCTG | |
| RDRP qPCR | Fw:CGTCTGCGGTATGTGGAAAG |
| Rev: TAAGACGGGCTGCACTTACA | |
| PCR cycling conditions: | Initial Denaturation: 95°C 5 Min (Ramp rate 4.4) |
| 45 Cycles: 95°C - 15 seconds (Ramp rate 4.4) | |
| 55°C - 10 seconds (Ramp rate 2.2) | |
| 72°C - 25 seconds (Ramp rate 4.4) |