Table 2 Details of oligonucleotide sequences, fluorophores, optimal concentrations and annealing temperatures used for the detection of SARS-CoV-2 targeting Nsp10, N-gene, Nsp12, JUN and EICAS, collectively referred to as CoV2-ID.
Target | Target | Amplicon (bp) | Oligonucleotides (5′-3′) | Final conc. (µM) | Ta (°C) |
|---|---|---|---|---|---|
SARS-CoV-2 | Nsp10 | 85 | F: GGATCAAGAATCCTTTGGTGG | 1 | 64.0 |
R: GTCACAAAATCCTTTAGGATTTGGA | 1 | ||||
Pr: FAM-CATCGTGTTGTCTGTACTGCCGTTGCC-Q | 0.4 | ||||
N-gene | 88 | F: GCTGCTAGACAGATTGAAC | 1 | 60.5 | |
R: AGCAGATTTCTTAGTGACAGTTTG | 1 | ||||
Pr1:-TR-ATGTCTGGTAAAGGCCAACAACAACA-Q | 0.4 | ||||
Pr2: TR/FAM-TCTGGTAAAGGCCAACAACAACAAGG-Q | 0.4 | ||||
Nsp12 | 96 | F: CATCCCTACTATAACTCAAATGAA | 1 | 62.0 | |
R: GTCATAGTACTACAGATAGAGACAC | 1 | ||||
Pr: FAM-TGCAAAGAATAGAGCTCGCACCGT-Q | 0.4 | ||||
Mu-Nsp10 | 85 | (10Mu) GGATCAAGAATCTTTTGGTGG | 1 | 61.0 | |
Mu-N-gene | 88 | (NA) GCTGCTTGACAGTTTGAAC | 1 | 62.0 | |
(NB) GCTGCTTGATAGATTGAAC | 1 | 60.3 | |||
MuN: TR-TTTGGTAAAGGCCAACAACAACAAGG-Q | 0.4 | ||||
D614G mutation | 104 | F: CACCAGGAACAAATACTTC | 1 | ||
R: CCAAGTAGGAGTAAGTTGA | 1 | ||||
WT: FAM-ctttAtcAggAtgTtaact-Q | 0.4 | ||||
Mu: HEX-ctttAtcAggGtgTtaact-Q | 0.4 | ||||
mRNA control | JUN | 88 | F: CGCCTGATAATCCAGTCCA | 1 | 60.5 |
R: GCTCATCTGTCACGTTCTTG | 1 | ||||
Pr:- Cy5-CACATCACCACCACGCCGACC-Q | 0.4 | ||||
EICAS1 | – | 58 | F: AACAACCACACCAAAAC | ||
R: GGAGGTTTTAGTTTGG | |||||
Pr: HEX-CACACAACACCAACAAAACCAAACA-Q | |||||
rArArCrArArCrCrArCrArCrCrArArArArCrCrArCrArCrArArCrArCrCrArArCrArArArArCrCrArArArCrArCrCrArArArCrUrArArArArCrCrUrCrC | |||||
EICAS2 | – | 65 | Pr: HEX-CACACAACACCAACAAAACCAAACA-Q | ||
rCrGrCrCrUrGrArUrArArUrCrCrArGrUrCrCrArUrCrArCrArCrArArCrArCrCrArArCrArArArArCrCrArArArCrArCrArArGrArArCrGrUrGrArCrArGrArUrGrArGrC | |||||
