Table B.1.

PCR primers and Luminex probes in the six-fold multiplexed assays. These oligonucleotides were also used in (Glushakova et al., 2018, submitted to the J Virol Methods) and published here with permission. All reverse primers are 5’- biotinylated. All probes have 5’-amino-C12-modified.

Oligonucleotide identity	Sequences	Position, nucleotid es bases	GenBank accession number	Targeting region
DENV1 Forward primer	GGCCRGATTAAGCC*A*T*A*G	10267–10349	KY926849.1	UTR
DENV1 Probe	APAPCTATPCTPCCTPT
DENV1 Reverse primer	GCTTTCGGCCTGA*C*T*T*C
DENV2 Forward primer	CGTGTCRACTGTRCA*A*C*A*G	17–136	KY461768.1	Capsid/premembrane protein gene
DENV2 Probe	ATTCTCACTTPPAATPCTPC
DENV2 Reverse primer	ARTATCCCTGCTGTT*G*G*T*G
DENV3 Forward primer	AACACTCTGGGAAGGAT*C*A*C*C	7405–7507	KT726361.1	Non-structural Protein NS4B
DENV3 Probe	TTPPAACACCACPATAPCT
DENV3 Reverse primer	AGCAAGCCCAGCT*C*C*T*G
DENV4 Forward primer	GCAGGCAAAAGCCA*C*A*A*G	3289–3430	AH0119363.2	Non-structural protein NS2A
DENV4 Probe	APTPPACPPPATAACAPT
DENV4 Reverse primer	CATGACCTGCCCTA*A*T*T*G
CHIKV Forward primer	CAGATGGCAACGAA*C*A*G*G	6083–6273	KY575571.1	Non-structural protein NS4B
CHIKV FS-1 Probe	CCTTTPCAAPCTCCAPATC
CHIKV Reverse primer	GGGTCCTCTGAGCT*T*C*T*C
ZIKV Forward primer	AGGGACCTCCGACT*G*A*T*G	9981–10112	KY415991.1	Non-structural protein NS5
ZIKV Probe	PAAAPPPAPAATPPATPACC
ZIKV Reverse primer	CCTCAATCCACACTCT*G*T*T*C

P, AEGIS nucleotide.*, SAMRS nucleotides. R, mixed A and G bases. Position of primers and probes refer to the arbitrary chosen sequence of the viral strains.