TABLE 2.
Detection and differentiation of various flaviviruses using dengue group- and serotype-specific primer pairsa
| Strain | DEN Genotype | Detection (ct) with primer pair:
|
||||
|---|---|---|---|---|---|---|
| DN-F-DN-R | DN-F-D1-R | DN-F-D2-R | DN-F-D3-R | DN-F-D4-R | ||
| DEN-1 Hawaii | I | + (25) | + (24) | − (no Ct) | − (no Ct) | − (no Ct) |
| DEN-1 157001 | I | + (24) | + (22) | − (no Ct) | − (no Ct) | − (no Ct) |
| DEN-1 8500660 | I | + (26) | + (25) | − (no Ct) | − (no Ct) | − (no Ct) |
| DEN-1 8600098 | I | + (27) | + (25) | − (no Ct) | − (no Ct) | − (no Ct) |
| DEN-2 NGC | IA | + (17) | − (no Ct) | + (20) | − (no Ct) | − (no Ct) |
| DEN-2 466177 | IB | + (21) | − (no Ct) | + (24) | − (no Ct) | − (no Ct) |
| DEN-2 454009 | IC | + (19) | − (no Ct) | + (23) | − (no Ct) | − (no Ct) |
| DEN-2 454021 | IC | + (19) | − (no Ct) | + (24) | − (no Ct) | − (no Ct) |
| DEN-3 8700829 | I | + (26) | − (no Ct) | − (no Ct) | + (25) | − (no Ct) |
| DEN-3 H87 | II | + (22) | − (no Ct) | − (no Ct) | + (23) | − (no Ct) |
| DEN-3 466322 | II | + (28) | − (no Ct) | − (no Ct) | + (27) | − (no Ct) |
| DEN-3 333137 | II | + (26) | − (no Ct) | − (no Ct) | + (25) | − (no Ct) |
| DEN-4 H241 | I | + (19) | − (no Ct) | − (no Ct) | − (no Ct) | + (21) |
| DEN-4 768346 | I | + (23) | − (no Ct) | − (no Ct) | − (no Ct) | + (25) |
| DEN-4 8900508 | II | + (25) | − (no Ct) | − (no Ct) | − (no Ct) | + (26) |
| DEN-4 8700544 | ? | + (24) | − (no Ct) | − (no Ct) | − (no Ct) | + (27) |
| JEV (JaGAr) | − (no Ct) | − (no Ct) | − (no Ct) | − (no Ct) | − (no Ct) | |
| West Nile virus | − (no Ct) | − (no Ct) | − (no Ct) | − (no Ct) | − (no Ct) | |
| Yellow fever virus | − (no Ct) | − (no Ct) | − (no Ct) | − (no Ct) | − (no Ct) | |
| NTCb | − (no Ct) | − (no Ct) | − (no Ct) | − (no Ct) | − (no Ct) | |
a
A total of 45 cycles of amplification were carried out using the one-step SYBR Green-based RT-PCR assay for dengue virus detection and differentiation. Ct values were measured by adding dengue virus at 500 to 5,000 PFU/ml. Negative results were defined as Ct values greater than 40 cycles of amplification.
b
Nontemplate control.