Skip to main content

Advertisement

Table 5 Oligonucleotide sequence of primers and probes used in Pan-Flavi qRT-PCR assay

From: Development of one-step quantitative reverse transcription PCR for the rapid detection of flaviviruses

Primer & Probe Sequence Concentration Orientationa Positionb Tm (°C)
Flavi all S TACAACATgATggggAARAgAgARAA 10 pmol S 8993–9019 54.7
DEN4 F TACAACATgATgggRAAACgTgAGAA 10 pmol S 8996–9019 60.18
Flavi all AS 1 gTCCCANCCDgCKgTRTC 10 pmol AS 9236–9253 52.5
  gTCCCATCCAgCKgTRTCATC 5 pmol AS 9236–9256 57.1
Flavi all AS 2 gTgTCCCAgCCNgCKgTgTCATCWgC 10 pmol AS 9232–9260 69.6
Flavi all probe 1 FAM-AARggHAgYMgNgCCA + T H + T + g + g + T-BBQ 5 pmol S 9044–9065 69–83
Flavi all probe 2 FAM-Tg + g TWYATgTggYTNg + g RgC--BBQ 5 pmol S 9062–9082 62–75
Flavi all probe 3 mix FAM-Tg + g TWYATgT + g gYTNg + g RgC—BBQc 5 pmol S 9062–9082 66-79
  FAM-CCgTgCCATATggTATATgTggCTgggAgC-BBQd 0.5 pmol S 9052–9081 74.7
  FAM-TTTCTggAATTTgAAgCCCTgggTTT-BBQe 0.5 pmol S 9086–9012 68
Flavi all S2 TACAACATgATgggMAAACgYgARAA 10 pmol S 8996–9019 58.2
Flavi all AS4 gTgTCCCAGCCNgCKgTRTCRTC 10 pmol S 9235–9260 64.1
  1. Tm: temperature, Locked-Nucleic Acid bases are written as ‘ + _’, e.g., +A.
  2. Degenerate bases: R = (A/G), W = (A/T), K = (T/G), Y = (C/T), N = (A/G/T/C).
  3. a S: sense orientation, AS: antisense orientation.
  4. b YFV strain; accession no: NC 002031.
  5. c Flavi all probe, d Flavi probe YFV, e Flavi probe DEN4.
  6. Final Pan-Flavi assay comprise of Flavi all S, Flavi all S2 & Flavi all AS4 primer and Flavi all probe 3 mix.