Table 2.
Probes and primers used for the detection of DENV serotype.
| Primer Name | Sequence | Genome Postition | Gen | Amplicon Size |
|---|---|---|---|---|
| Probes | ||||
| Texas RedDENV-1 | 5′-(Texas Red) AGTTTCTTTTCCTAAACACCTCG-3′ | 5045–5067 | NS3 | |
| 6FAMDENV-2 | 5′-(_6 FAM) CCGGTGTGCTCRGCYCTGAT-3′ | 5260–5279 | NS3 | |
| CY5DENV-3 | 5′-(_CY5) TTAGAGTYCTTAAGCGTCTCTTG-3′ | 5152–5174 | NS3 | |
| YakimaYellowDENV-4 | 5′-(_Yakima Yellow) CCTGGTTGATGACAAAAGTCTTG-3′ | 5320–5342 | NS3 | |
| Primers | ||||
| AD3 (-) [14] | 5′-CTGATTTCCAT(A, C,G,T)CC(A,G)TA-3′ | 3412–3428 | NS1 | |
| AD4 (+) | 5′-GA(C,T)ATGGG(C,G,T)TA(C,T)TGGATAGA-3′ | 3010–3029 | NS1 | 419(AD3 and AD4) |
| D1 | 5′-GAGGACCAATATCTCAG-3′ | 3135–3151 | NS1 | 265 (D1 and AD3) |
| D2 (+) | 5′-AAGCTTGAGATGGACTTT-3′ | 3235–3151 | NS1 | 194 (D2 and AD3) |
| D3 (+) | 5′-GTCTAGCTGGTCCCATT-3′ | 3150–3166 | NS1 | 271 (D3 and AD3) |
| D4 (+) | 5′-ATCATATGCGGGCCCTT-3′ | 3155–3171 | NS1 | 273 (D4 and AD3) |
| D1 [15] | 5′-TCAATATGCTGAAACGCGCGAGAAACCG-3′ | 134–161 | C-prM | |
| D2 | 5′-TTGCACCAACAGTCAATGTCTTCAGGTTC-3′ | 616–644 | C-prM | 511 (D1 and D2) |
| TS1 | 5′-CGTCTCAGTGATCCGGGGG-3′ | 568–586 | C-prM | 482 (Dl and TS1) |
| TS2 | 5′-CGCCACAAGGGCCATGAACAG-3′ | 232–252 | C-prM | 119 (Dl and TS2) |
| TS3 | 5′-TAACATCATCATGAGACAGAGC-3′ | 400–421 | C-prM | 290 (Dl and TS3) |
| TS4 | 5′-CTCTGTTGTCTTAAACAAGAGA-3′ | 506–527 | C-prM | 392 (Dl and TS4) |
| Bio-CFDJ9977a [12] | 5′- GCATGTCTTCCGTCGTCATCC-3′ | 9952–9977 | NS5 | |
| DEN1-J9243 | 5′-GCCTGAACATGCTCTATTGGCT-3′ | 9243–9264 | NS5 | 761 (J9243 and CFDJ) |
| DEN2-J9452 | 5′-TCTTCAAAAGCATTCAGCACCT-3′ | 9452–9473 | NS5 | 546 (J9452 and CFDJ) |
| DEN1-J9243 | 5′-GCCTGAACATGCTCTATTGGCT-3′ | 9243–9264 | NS5 | 761 (J9243 and CFDJ) |
| DEN2-J9452 | 5′-TCTTCAAAAGCATTCAGCACCT-3′ | 9452–9473 | NS5 | 546 (J9452 and CFDJ) |
| DEN3-9471 | 5′-CCCATCCGCTAGAGAAGAAAATTACAC-3′ | 9471–9497 | NS5 | 522 (J9471 and CFDJ) |
| DEN4-9580 | 5′- GGTTTGGCACTTCCCTCCTCTTCTTG-3′ | 9580–9605 | NS5 | 411 (9580 and CFDJ) |
| DV1 (+) [30] | 5′-GGRACKTCAGGWTCTCC-3′ | 4918–4934 | NS3 | |
| DV3 | 5′-AARTGIGCYTCRTCCAT-3′ | 5368–5384 | NS3 | 470 (DV1 and DV3) |
| DSP1 (-) [16] | 5′-AGTTTCTTTTCCTAAACACCTCG-3′ | 5067–5045 | NS3 | 169 (DV1 and DSP1) |
| DSP2 (-) | 5′-CCGGTGTGCTCRGCYCTGAT-3′ | 5279–5260 | NS3 | 362 (DV1 and DSP2 |
| DSP3 (-) | 5′-TTAGAGTYCTTAAGCGTCTCTTG-3′ | 5174–5152 | NS3 | 265 (DV1 and DSP3 |
| DSP4 (-) | 5′-CCTGGTTGATGACAAAAGTCTTG-3′ | 5342–5320 | NS3 | 426 (DV1 and DSP4) |