TABLE 4.
RT-qPCR assays for deletion and substitution sites in SARS-CoV-2 variants of concern
| Assay | Manufacturer | Names and 5′ → 3′ Sequences | Fluorophore |
|---|---|---|---|
| SΔ69-70 | IDT | SΔ69-70 Fw primer; TCAACTCAGGACTTGTTCTTACCT Rv primer; TGGTAGGACAGGGTTATCAAAC Ref probe; Cy5668/CCATGCTAT/TAO/ACATGTCTCTGGGAC/IBRQ Del probe; HEX/CCATGCTAT/ZEN/CTCTGGGACCAATG/IABkFQ |
-a - Cy5 HEX |
| †ORF1aΔ3675-3677 | IDT | ORF1aΔ3675-3677 Fw primer; TGCCTGCTAGTTGGGTGATG Rv primer; TGCTGTCATAAGGATTAGTAACACT Ref probe; SUN/CTAGTTTGT/ZEN/CTGGTTTTAAGCTAA/IABkFQ Del probe; Cy5668/GGTTGATAC/TAO/TAGTTTGAAGCTAA/IAbRQ |
- - Cy5 SUN |
| K417N, E484K, L452R, E484Q | ThermoFisher TaqMan | Reference probeb Substitution probeb |
FAM VIC |
a
-, indicates that there is no fluorophore for those entries.
b
Sequences are unavailable from the manufacturer.