Table 3.
Performance of the Pan-Flavi assay to detect different flaviviruses. Five μl of viral RNA extracted from virus cell culture supernatant were applied to both pan-Flavi assay and RT-PCR
| Virus | Virus abbreviation |
Strain/Reference |
Pan-flavi assay |
RT-PCR * |
|---|---|---|---|---|
| Ct value | Confirmation by gel | |||
|
Flaviviridae |
||||
| St. Louis Encephalitis virus |
SLEV |
ATCC VR-1265 |
22.19 |
N.d. |
| Usutu virus |
USUV |
AY453411 |
22.48 |
N.d. |
| Kunjin virus |
KUNV |
PI.France |
24.97 |
N.d. |
| Kedougou virus |
KEDV |
ArD 14701 |
29.62 |
Positive |
| Koutango virus |
KOUV |
AnD 5443 |
30.29 |
Positive |
| Spondweni virus |
SPOV |
SA Ar 94 |
26.02 |
Negative |
| Uganda S virus |
UGSV |
ArD 109325 |
29.48 |
Positive |
| Wesselsbron |
WESSV |
ArB 4177 |
24.73 |
Positive |
| Zika virus |
ZIKV |
PI, Senegal |
22.45 |
Positive |
| Sepik virus |
SEPV |
MK 7148 |
16.77 |
Positive |
| Dakar bat virus |
DBV |
AnD 249 |
32.57 |
Positive |
| Yaounade virus |
YAOV |
ArY 276/68 |
17.52 |
Positive |
| Bouboui virus |
BOUV |
ArB 490 |
31.88 |
Negative |
| Saboya virus |
SABV |
AnD 4600 |
27.50 |
Negative |
| Nounane virus# |
NOUV |
B3 isolate |
No ct |
N.d. |
|
Bunya viridae |
||||
| Rift valley fever virus |
RVFV |
RKI |
No ct |
N.d. |
|
Togaviridae |
||||
| Chikungunya virus |
|
LR 2006 |
No ct |
N.d. |
| Chikungunya virus |
|
ST05,African isolate |
No ct |
N.d. |
| Sindbis virus |
|
RKI |
No ct |
N.d. |
|
Influneza virus |
||||
| H1N1 Hamburg |
|
A/Hamburg/04/2009 H1N1 |
No ct |
N.d. |
| H1N1 California |
|
A/California/04/2009 H1N1 |
No ct |
N.d. |
| H5N1 | A/dk/Germany R603/06 H5N1 | No ct | N.d. |
N.d.: not done, Ct: threshold cycle, * RNA of African flaviviruses were detected using reference method described previously [33].# Nounane virus was detected using final optimized primer sets Flavi all S/Flavi all S2/Flavi all AS4 and Flavi all probe 3 mix.