Table 1 PCR and qPCR primers

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