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
| 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 |
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.
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.