TABLE 1.
The primer-probe sets used for qPCR
| Primer set target (segment) | Primer sequence |
Probe sequencea | Target region (positions) | |
|---|---|---|---|---|
| Forward | Reverse | |||
| N (S) | TGTCAGAGTGGTCCAGGATT | ACCTGTCTCCTTCAGCTTCT | FAM-TGGAGTTTGGTGAGCAGCAGC-BHQ1 | 1566–1702 |
| GPC (M) | GGCAGCTACATGCAGACATA | CCTATCACCCCCAGAATCCA | TexasRed-GCCCTGTTTGGCAATGGGCT-BHQ2 | 236–357 |
| TexasRed-GCCTTGTTTGGCAATGGGCT-BHQ2 | ||||
| RdRp (L) | AACATCCTGGACCTTGCATC | CAATGTGGCCATCTTCTCCA | Cy5-TGGGAGCTCTACTCAGAAGTCCA-BHQ3 | 3710–3832 |
| Cy5-TGGGAGCTCTACTCAGAGGTCCA-BHQ3 | ||||
| Cy5-TGGGAGATCTACTCAGAAGTCCA-BHQ3 | ||||
| Cy5-TGGGAGCTTTACTCAGAAGTCCA-BHQ3 | ||||
| Contamplicon | JOE (HEX)-AGTAGCTTGCTCTTTCATCTGTTACG-BHQ1 | |||
a
The bases in bold type indicate the mismatch of the sequences between the probes. FAM, 6-carboxyfluorescein; BHQ1, black hole quencher 1; JOE, 2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein; HEX, hexacholoro-6-carboxyfluorescein.