Table 1.
Primers and probes of qPCR assays used in this study.
| Assay | Function | Name | Sequence (5′–3′)a | Product length (bp) | Reference |
|---|---|---|---|---|---|
| N_Sarbeco | Forward primer | N_Sarbeco_F1 | CACATTGGCACCCGCAATC | 128 | Corman et al., 2020 |
| Reverse primer | N_Sarbeco_R1 | GAGGAACGAGAAGAGGCTTG | |||
| TaqMan probe | N_Sarbeco_P1 | FAM-ACTTCCTCAAGGAACAACATTGCCA-BHQ1 | |||
| NIID_2019-nCOV_N | Forward primer | NIID_2019-nCOV_N_F2 | AAATTTTGGGGACCAGGAAC | 158 | Shirato et al., 2020 |
| Reverse primer | NIID_2019-nCOV_N_R2ver3 | TGGCACCTGTGTAGGTCAAC | |||
| TaqMan probe | NIID_2019-nCOV_N_P2 | FAM-ATGTCGCGCATTGGCATGGA-BHQ1 | |||
| CDC-N1 | Forward primer | 2019-nCoV_N1-F | GACCCCAAAATCAGCGAAAT | 72 | CDC, 2020 |
| Reverse primer | 2019-nCoV_N1-R | TCTGGTTACTGCCAGTTGAATCTG | |||
| TaqMan probe | 2019-nCoV_N1-P | FAM-ACCCCGCATTACGTTTGGTGGACC-BHQ1 | |||
| CDC-N2 | Forward primer | 2019-nCoV_N2-F | TTACAAACATTGGCCGCAAA | 67 | CDC, 2020 |
| Reverse primer | 2019-nCoV_N2-R | GCGCGACATTCCGAAGAA | |||
| TaqMan probe | 2019-nCoV_N2-P | FAM-ACAATTTGCCCCCAGCGCTTCAG-BHQ1 | |||
| PMMoVb | Forward primer | PMMV-FP1 | GAGTGGTTTGACCTTAACGTTTGA | 68 | Zhang et al., 2006 |
| Reverse primer | PMMV-FP1-rev | TTGTCGGTTGCAATGCAAGT | Haramoto et al., 2013 | ||
| TaqMan MGB probe | PMMV-Probe1 | FAM-CCTACCGAAGCAAATG-NFQ-MGB | Zhang et al., 2006 | ||
| Coliphage MS2 | Forward primer | Not available | ATCCATTTTGGTAACGCCG | 68 | Friedman et al., 2011 |
| Reverse primer | Not available | TGCAATCTCACTGGGACATAT | |||
| TaqMan MGB probe | Not available | FAM-TAGGCATCTACGGGGACGA-NFQ -MGB |
a
FAM, 6-carboxyfluorescein; MGB, minor groove binder; NFQ, nonfluorescent quencher; BHQ1, black hole quencher 1.
b
PMMoV, pepper mild mottle virus.