Table 1. Primers and strand displaceable probes.

Reprinted with permission from Yaren et al. 2017²⁰. Sequences in bold represent the double-stranded region of strand displacing probes. FAM-labeled (seen as green fluorescence), HEX-labeled (seen as light green-yellow fluorescence), TAMRA-labeled (seen as orange-red fluorescence), and TET-labeled (seen as yellow fluorescence) probes were assigned to detect Zika, Chikungunya, Dengue 1, and mitochondrial DNA in urine, respectively. FAM has excitation and emission maxima at 495 nm and 520 nm, respectively. HEX has excitation and emission maxima at 538 nm and 555 nm, respectively. TAMRA has excitation and emission maxima at 559 nm and 583 nm, respectively. TET has the excitation and emission maxima at 522 nm and 539 nm, respectively. To enable the use of a single quencher for all fluorophores, Iowa Black-FQ was used due to its wide absorption range (420-620 nm).

Target virus	Name	Sequence (5′-3′)	Length	Start Position	End Position
Zika	ZV-F3	GAGACTGCTTGCCTAG	16	9905	9920
	ZV-B3	CTGGGGTCTTGTCTTC	16	10145	10130
	ZV-LF	CAGTTGGAACCCAGTCAAC	19	10028	10010
	ZV-LB	GTGGAACAGAGTGTGGATTG	20	10093	10112
	ZV-FIP	CCATGGATTGACCAGGTAGTTTTTTCGACTGATGGCCAATG	41	9974	10053
	ZV-BIP	ACCACTGARGACATGCTTGTTTTTCATGTGGTCGTTYTCC	40	10070	10129
	ZV-LB_NatTail	FAM-CGGGTTTGCGCTCAGCCATCCGTTCAGTCCGTCAGGTCAGGTGGAACAGAGTGTGGATTG	60	10093	10112
Chikungunya	CH-F3	CGTCAACGTACTCCTAAC	18	2891	2908
	CH-B3	ACGTTGGCTTTRTTTTGG	18	3094	3077
	CH-LF	AGCGTCTTTATCCACGGG	18	2968	2951
	CH-LB	AYGCATCRATAATGGCGGG	19	3025	3043
	CH-FIP	GAAGTTTCCTTTCGGTGGGTTTTTGGAAGACACTYTCYGG	40	2932	2993
	CH-BIP	AAGGAGTGGGAGGTGGATTTTTTCAYTTGGTGACTGCAG	39	3006	3063
	CH-LF_NatTail	HEX-CGGGTTTGCGCTCAGCCATCCGTTCAGTCCGTCAGGTCAGAGCGTCTTTATCCACGGG	58	2968	2951
Dengue-1	D1-F3	ACAGCYCTGAATGAYATGG	19	9583	9601
	D1-B3	GCAGTTTCTCTCAGGC	16	9803	9788
	D1-LF	CACTTGYTGCCARTCATTCC	20	9666	9647
	D1-LB	CCATGCCGYAACCAAG	16	9727	9742
	D1-FIP	CTGGTGGAARTGGTGTGATTTTTTGGGAACCTTCAAAAGG	40	9628	9693
	D1-BIP	GAAGGAYGGGAGGGAAATAGTTTTTTTAGCCCTRCCCACAAG	42	9702	9763
	D1-LB_NatTail	TAMRA-CGGGTTTGCGCTCAGCCATCCGTTCAGTCCGTCAGGTCAGCCATGCCGYAACCAAG	56	9727	9742
Mitochondrial DNA	MtDNA-F3	AGCCTACGTTTTCACAC	17	9183	9199
	MtDNA-B3	GCGCCATCATTGGTAT	16	9410	9395
	MtDNA-LB	GCCTAGCCATGTGATTTCAC	20	9322	9341
	MtDNA-LF	GGCATGTGATTGGTGGGT	18	9254	9237
	MtDNA-FIP	GTCATGGGCTGGGTTTTACTTTTTCTACCTGCACGACAAC	40	9213	9228
	MtDNA-BIP	CTCAGCCCTCCTAATGACCTTTTTGAGCGTTATGGAGTGG	40	9359	9344
	MtDNA-LB_NatTail	TET-CGGGTTTGCGCTCAGCCATCCGTTCAGTCCGTCAGGTCAGGCCTAGCCATGTGATTTCAC	60	9322	9341
	Common quencher	CTGACCTGACGGACTGAACGGATGGCTGAGCGCAAACCCG-lowa Black FQ	40