Table 1.
Spike SNP assay primers and probes used in the current study.
| Name | Sequence a | Concentration (nM) b | Location (5′–3′) c |
|---|---|---|---|
| Primers | |||
| SpikeSNP Ext d | TGAAGTCAGACAAATCGCTCC | 400 | 22,777–22,797 |
| SpikeSNP R1 d | TGGTGCATGTAGAAGTTCAAAAG | 400 | 23,103–23,125 |
| LNA Probes | |||
| K417 d | FAM-CAAACTGGA+A+A+G+ATTGCTG-3IABkFQ | 200 | 22,802–22,820 |
| 484K d | Cy5-ACCTTGTAATGGTGT+T+A+AAGGTTTT-3IAbRQSp | 200 | 22,996–23,020 |
| 501Y d | HEX-CCCAC+T+T+ATGGTGTTGG-3IABkFQ | 200 | 23,057–23,073 |
| Unmodified Probes | |||
| 452R d | CFR610-ATAATTACCGGTATAGATTGTTTAGGAAGT-BHQ-2 | 200 | 22,908–22,937 |
| 484K | Q670-CACCTTGTAATGGTGTTAAAGGTTTTAA-BHQ-2 | 200 | 22,995–23,022 |
| 484Q | Q670-CACCTTGTAATGGTGTTCAAGGTTTTAA-BHQ-2 | 200 | 22,995–23,022 |
| 501Y | CFO560-CAACCCACTTATGGTGTTGGTTAC-BHQ-1 | 200 | 23,054–23,077 |
| 452Q | CFR610-ATAATTACCAGTATAGATTGTTTAGGAAGT-BHQ-2 | 200 | 22,908–22,937 |
| 490S | FAM-ACTCTCCTTTACAATCATATGGTTTCC-BHQ-1 | 200 | 23,028–23,054 |
| 478K (original) | CFO560-CGGTAGCAAACCTTGTAATGGTG-BHQ-1 | 200 | 22,987–23,009 |
| 478K (revised) | CFO560-CGGTARCAAACCTTGTAATGGTG-BHQ-1 | 200 | 22,987–23,009 |
Abbreviations: BHQ, black hole quencher; CFO560, CAL Fluor Orange 560; CFR610, CAL Fluor Red 610; Cy5, Cyanine 5; FAM, Fluorescein; IABkFQ/IAbRQSp, Iowa Black quenchers; Q670, Quasar 670; a probe sequences listed 5′-fluorophore-sequence-quencher-3′; “+” before base indicates a locked nucleic acid, bold and underlined base indicates the targeted single nucleotide change; b concentration in the final reaction mixture; c location in Wuhan-Hu-1 complete genome sequence (NCBI Reference Sequence: NC_045512.2); d previously published, presented for clarity.