Table 1.
PCR and qPCR primers
| Reference | Sequence | Primer name | Set | Size (bp) | Target |
|---|---|---|---|---|---|
| Lanciotti et al. [33] Region (C-prM) | TCAATATGCTGAAACGCGCGAGAAACCG | D1 | D1-D2 | 511 | DENV-all |
| TTGCACCAACAGTCAATGTCTTCAGGTTC | D2 | ||||
| CGTCTCAGTGATCCGGGGG | TS1 | D1-TS1 | 482 | DENV-1 | |
| CGCCACAAGGGCCATGAACAG | TS2 | D1-TS2 | 119 | DENV-2 | |
| TAACATCATCATGAGACAGAGC | TS3 | D1-TS3 | 290 | DENV-3 | |
| CTCTGTTGTCTTAAACAAGAGA | TS4 | D1-TS4 | 392 | DENV-4 | |
| Chow et al. [34] Region (NS3) | GGRACKTCAGGWTCTCC | upstream | up-down | 490 | DENV-all |
| AARTGIGCYTCRTCCAT | downstream | ||||
| Chang et al. [35] Region (NS5) | TTTGAGCATGTCTTCCGTCGTCATCC | Bio-CFD2-4 | FUD-CFD2-4 or FUD-CFDJ | 838 or 832 | DENV-all |
| GCATGTCTTCCGTCGTCATCC | Bio-CFDJ9977 | ||||
| GATGACACAGCAGGATGGGAC | FUDJ9166 | ||||
| GCCTGAACATGCTCTATTGGCT | DEN1-J9243 | DEN1-CFD2 | 761 | DENV-1 | |
| TCTTCAAAAGCATTCAGCACCT | DEN2-J9452 | DEN2-CFD2 | 546 | DENV-2 | |
| CCCATCCGCTAGAGAAGAAAATTACAC | DEN3-9471 | DEN3-CFD2 | 522 | DENV-3 | |
| GGTTTGGCACTTCCCTCCTCTTCTTG | DEN4-9580 | DEN4-CFD2 | 411 | DENV-4 | |
| Pierre et al. [37] Region (NS5/3'NC) | TGGATGACGACGGAAGACATG | EMF1 | EMF1-VD8 | 600 | DENV-all |
| GGGTCTCCTCTAACCTCTAG | VD8 | ||||
| Meiyu et al. [38] Region (NS1) | GACATGGGGTATTGGAT | DJS | DJS-DJA | 413 | DENV-all |
| TCCATCCCATACCTGCA | DJA | ||||
| ATGGATTACCAATATCT | DEN1 | DEN1-DJA | 262 | DENV-1 | |
| GTAAGCTTGAGATGGAC | DEN2 | DEN2-DJA | 189 | DENV-2 | |
| AGCCAAAAGAATGGAAG | DEN3 | DEN3-DJA | 392 | DENV-3 | |
| CTGCATCTGGAAAACTA | DEN4 | DEN4-DJA | 97 | DENV-4 | |
| Kuno et al. [39] Region (NS5) | TCAAGGAACTCCACACATGAGATGTACT | FG1-F | FG1-G4 | 1991 | FLAV |
| CCAGATGTTCTTWGCCCAYTCTGC | G4-R | ||||
| TACAACATGATGGGAAAGAGAGAGAA | FU1-F | FU1-cFD3 | 1084 | FLAV | |
| AGCATGTCTTCCGTGGTCATCCA | cFD3-R) | ||||
| GTGTCCCAGCCGGCGGTGTCATCAGC | cFD2 (R) | FU1-cFD2 | 220 | FLAV | |
| Shu et al. [40] Region (C) | CAATATGCTGAAACGCGAGAGAAAC | DN-F | DNF-DNR | 170 | DENV-all |
| CCCCATCTATTCAGAATCCCTGCTC | DN-R | ||||
| CGCTCCATACATCTTGAATGAGC | D1-R | DNF-D1R | 190 | DENV-1 | |
| AAGACATTGATGGCTTTTGAC | D2-R | DNF-D2R | 203 | DENV-2 | |
| AAGACGTAAATAGCCCCCGACC | D3-R | DNF-D3R | 201 | DENV-3 | |
| AGGACTCGCAAAAACGTGATGAATC | D4-R | DNF-D4R | 133 | DENV-4 | |
| Johnson et al. [41] Region (M/E/NS5) | CAAAAGGAAGTCGTGCAATA | DEN-1 F | FAM/BHQ-1 | 111 | DENV1 |
| CTGAGTGAATTCTCTCTACTGAACC | DEN-1 C | ||||
| CATGTGGTTGGGAGCACGC | DEN-1 probe | ||||
| CAGGTTATGGCACTGTCACGAT | DEN-2 F | HEX/BHQ-1 | 605 | DENV2 | |
| CCATCTGCAGCAACACCATCTC | DEN-2 C | ||||
| CTCTCCGAGAACAGGCCTCGACTTCAA | DEN-2 probe | ||||
| GGACTGGACACACGCACTCA | DEN-3 F | TR/BHQ-2 | 73 | DENV3 | |
| CATGTCTCTACCTTCTCGACTTGTCT | DEN-3 C | ||||
| ACCTGGATGTCGGCTGAAGGAGCTTG | DEN-3 probe | ||||
| TTGTCCTAATGATGCTGGTCG | DEN-4 F | Cy5/BHQ-3 | 88 | DENV4 | |
| TCCACCTGAGACTCCTTCCA | DEN-4 C | ||||
| TTCCTACTCCTACGCATCGCATTCCG | DEN-4 probe | ||||
| Ayers et al. [43] Region (NS5) | AATGTACGCTGATGACACAGCTGGCTGGGACAC | FLAVI-1 | FLAVI1-FLAVI2 | 863 | FLAV |
| TCCAGACCTTCAGCATGTCTTCTGTTGTCATCCA | FLAVI-2 | ||||
| Chien et al. [44] Region (C-prM) | TCAATATGCTGAAACGCGAGAGAAACCG | mD1 | mD1-D2 | 511 | DENV-all |
| TTGCACCAACAGTCAATGTCTTCAGGTTC | D2 | ||||
| CCCGTAACACTTTGATCGCT | rTS1 | mD1-rTS1 | 208 | DENV-1 | |
| CGCCACAAGGGCCATGAACAGTTT | mTS2 | mD1-mTS2 | 119 | DENV-2 | |
| TAACATCATCATGAGACAGAGC | TS3 | mD1-TS3 | 288 | DENV-3 | |
| TTCTCCCGTTCAGGATGTTC | Rts4 | mD1-rTS4 | 260 | DENV-4 | |
| Chien et al. [44] Region (NS5) | TACAACATGATGGGAAAGCGAGAGAAAAA | mFU1 | mFU1-CFD2 | 220 | FLAV |
| GTGTCCCAGCCGGCGGTGTCATCAGC | CFD2 | ||||
| TCAGAGACATATCAAAGATTCCAGGGGG | D1P | FAM/BHQ1 | 220 | DENV-1 | |
| AAGAGACGTGAGCAGGAAGGAAGGGGGAGC | D2P | Texas Red/BHQ2 | 220 | DENV-2 | |
| TGAGAGATATTTCCAAGATACCCGGAGGAG | D3P | CY5/BHQ3 | 220 | DENV-3 | |
| TGGAGGAGATAGACAAGAAGGATGGAGACC | D4P | HEX/BHQ1 | 220 | DENV-4 | |
| Salles et al. [42] Region (C-prM) | TTTATTTAGAGAGCAGATCTCTG | STD | STD-D2 | 572 | DENV-all |
| TTGCACCAACAGTCAATGTCTTCAGGTTC | D2 | ||||
| ACGGGTCGACCGTCTTTCAA | STD1 | STD1-rTS1 | 225 | DENV-1 | |
| CCCGTAACACTTTGATCGCT | rTS1 | ||||
| GCGAAAAACACGCCTTTCAA | STD2 | STD2-mTS2 | 140 | DENV-2 | |
| CGCCACAAGGGCCATGAACAGTTT | mTS2 | ||||
| ACGGGAAACCGTCTATCAA | STD3 | STD3-TS3 | 302 | DENV-3 | |
| TAACATCATCATGAGACAGAGC | TS3 | ||||
| GTGGTTAGACCACCTTTCAA | STD4 | STD4-rTS4 | 282 | DENV-4 | |
| TTCTCCCGTTCAGGATGTTC | rTS4 |