Primer

Sequence

Notes

YF-F

   AAT TCC ACT CAT GAA ATG TAC

Yellow fever virus

Flav100F

5’-AAY TCI ACI CAI GAR ATG TAY-3’

Maher-Sturgess et al. (2008)

Flav200R

5’-CCI ARC CAC ATR WAC CA-3’

Forward primer

5’-AAR TAC ACA TAC CAR AAC AAA GTG GT-3’

Faye et al. 2013

Reverse primer

5’-TCC RCT CCC YCT YTG GTC TTG-3’

Faye et al. 2013

16 nt BNA/LNA-probe

FAM-CTY AGA CCA GCT GAA R-BBQ

Faye et al. 2013

E F1269-F

5’-GAG GCT GGG AAA TGG CTG-3’

Grubaugh et al., 2013

E F2225-R

5’-CCT CCA ACT GAT CCA AAG TCC CA-3’

Grubaugh et al., 2013

NS3 F5015-F

5’-GTG GTT GGN CTG TAT GGN AA-3’

Grubaugh et al., 2013

NS3 F5807-R

5’-CCC ATT TCT GAG ATG TCA GT-3’

Grubaugh et al., 2013

NS5 F8276d-F

5’-AAY TCN CAN CAN GAR ATG TAY-3’

Grubaugh et al., 2013

NS5 F9063d-R

5’-CCN ARC CAC ATR WAC CA-3’

Grubaugh et al., 2013

Unifor

5’-TGG GGN AAY SRN TGY GGN YTN TTY GG-3’

Faye et al. 2008

Unirev

5’-CCN CCH RNN GAN CCR AAR TCC CA-3’

Faye et al. 2008

Mounifor2

5’-GGR DRM DTB KWA AYV TGY GCN AWR TT-3’

Faye et al. 2008

Mounirev2

5’-CCN ATN SWR CTH CCH KHY YTR WRC CA-3’

Faye et al. 2008

ZIKVENVF

5’-GCT GGD GCR GAC ACH GGR ACT-3’

Faye et al. 2008

ZIKVENVR

5’-RTC YAC YGC CAT YTG GRC TG-3’

Faye et al. 2008

ZIKV 835

5’-TTG GTC ATG ATA CTG CTG ATT GC-3’

Lanciotti et al. 2007

ZIKV 911c

5’-CCT TCC ACA AAG TCC CTA TTG C-3’

Lanciotti et al. 2007

ZIKV 860-FAM

5’-CGG CAT ACA GCA TCA GGT GCA TAG GAG-3’

Lanciotti et al. 2007

ZIKV 1086

5’-CCGCTG CCC AAC ACA AG-3’

Lanciotti et al. 2007

ZIKV 1162c

5’-CCA CTA ACG TTC TTT TGC AGA CAT-3’

Lanciotti et al. 2007

ZIKV 1107-FAM

5’-AGC CTA CCT TGA CAA GCA GTC AGA CAC TCA A-3’

Lanciotti et al. 2007

3PNC-2R

5′-GCT CAG GGA GAA CAA GAA CCG-3′

Grard et al. 2007

X1

5′-YIR TIG GIY TIT AYG GIW WYG G-3′

4913–4935

X2

5′-RTT IGC ICC CAT YTC ISH DAT RTC IG-3′

5707–5733

TB-5′UTR-S F

5′-AAA AGA CAG CTT AGG AGA ACA AGA-3′

NS5 gene

TB-3′UTR-R

5′-AGA ACA AGA ACC GCC CCC CC-3′

FLAVI-1 S

5’-AAT GTA CGC TGA TGA CAC AGC TGG CTG GGA CAC-3’

Ayers et l. 2006

FLAVI-2 A

5’-TCC AGA CCT TCA GCA TGT CTT CTG TTG TCA TCC A-3’

FU1

5’-TAC AAC ATG ATGGGA AAG AGA GAG AA-3’

Kuno 1998

Cfd2

5’-GTG TCC CAG CCG GCG GTG TCA TCA GC-3’

Kuno 1998

MA

5’-CAT GAT GGG RAA RAG RGA RRA G-3’

Kuno 1998