Skip to main content

Advertisement

Table 1 Comparison of designed two degenerate primer sets and three probes containing wobble and LNA bases in six combinations for detection of the different flavivirus RNA

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

Sample No Virus Ct value obtained through testing the combination of Flavi all degenerate primers and probe
S/AS1/probe1 S/AS1/probe2 S/AS1/probe3 S/AS2/probe1 S/AS2/probe2 S/AS2/probe3
1 DENV-1 31.50 17.57 15.66 27.95 17.84 15.61
2 DENV-2 22.69 22.21 19.76 22.27 22.19 19.92
3 DENV-3 No Ct 21.25 19.14 No Ct 20.63 18.57
4 DENV-4 No Ct 35.50 35.48 No Ct No Ct No Ct
5 JEV 20.40 21.63 20.93 18.99 19.98 19.27
6 RSSEV 27.69 29.38 27.31 24.67 26.13 23.81
7 TBEV K23 17.68 21.81 16.99 16.73 18.63 16.32
8 TBEV Louping ill 26.00 28.75 23.78 22.13 24.8 21.22
9 Usutu virus 25.63 33.96 25.91 22.96 30.3 23.48
10 WNV Uganda 30.22 30.27 30.68 28.46 28.45 28.26
11 WNV Israel 21.76 21.83 20.78 20.06 21.68 19.8
12 SLEV 25.85 26.95 25.57 24.41 24.90 23.49
13 YFV 17D 19.82 22.48 18.41 20.03 22.12 18.92
14 YFV Asibi 23.71 26.98 22.82 24.17 26.83 23.53
15 YFV Brasil 21.35 23.73 20.48 21.75 23.82 21.43
16 YFV Ivory Coast 21.35 23.98 20.36 21.47 23.94 21.44
18 Chikungunya virus No Ct No Ct No Ct No Ct No Ct No Ct
19 RVFV No Ct No Ct No Ct No Ct No Ct No Ct
20 Sindbis virus No Ct No Ct No Ct No Ct No Ct No Ct
21 H1N1 Influenza A No Ct No Ct No Ct No Ct No Ct No Ct
22 H5N1 Influenza A No Ct No Ct No Ct No Ct No Ct No Ct
17 Negative control No Ct No Ct No Ct No Ct No Ct No Ct
  1. DENV: Dengue virus, JEV: Japanese encephalitis virus, RSSEV: Russian spring-summer encephalitis virus, WNV: West Nile virus, TBEV: Tick-borne encephalitis virus, SLEV: Saint Louis encephalitis virus, RVFV: Rift valley fever virus, YFV: Yellow fever virus.
  2. S: Flavi all S, AS1: Falvi all AS1, AS2: Flavi all AS2, probe1: Flavi all probe 1, probe 2: Flavi all probe 2, probe 3: Flavi all probe 3.