Table 1.

Primers and strand displaceable probes

Target virus	Name	Sequence (5′-3′)	Length	Start Pos	End Pos
Zika	ZV-F3	GAGACTGCTTGCCTAG	16	9905	9920
	ZV-B3	CTGGGGTCTTGTCTTC	16	10,145	10,130
	ZV-LF	CAGTTGGAACCCAGTCAAC	19	10,028	10,010
	ZV-LB	GTGGAACAGAGTGTGGATTG	20	10,093	10,112
	ZV-FIP	CCATGGATTGACCAGGTAGTTTTTTCGACTGATGGCCAATG	41	9974	10,053
	ZV-BIP	ACCACTGARGACATGCTTGTTTTTCATGTGGTCGTTYTCC	40	10,070	10,129
	ZV-LB_NatTail	FAM-CGGGTTTGCGCTCAGCCATCCGTTCAGTCCGTCAGGTCAG-GTGGAACAGAGTGTGGATTG	60	10,093	10,112
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-CGGGTTTGCGCTCAGCCATCCGTTCAGTCCGTCAGGTCAG-AGCGTCTTTATCCACGGG	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-CGGGTTTGCGCTCAGCCATCCGTTCAGTCCGTCAGGTCAG-CCATGCCGYAACCAAG	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-Iowa Black FQ	40
Aedes aegypti SSU rRNA	Aae-F3	GGTGTAGTGTGACCTG	16	2501	2524
	Aae-B3	GCTAGCTAATGACCAGC	17	2883	2866
	Aae-LB	AAGGGCCGGGAAATCG	16	2777	2793
	Aae-LF	TCTAAGGGCATCACGGAC	18	2705	2687
	Aae-FIP	CGTGCAGCCCAGAACATTTTTGCAAAATGAGATTGAGCG	39	2660	2678
	Aae-BIP	CAACGCGTATCCTTGCCTTTTTAATCCCGACTAAATGCG	38	2820	2803
	Aae-LF_NatTail-5IB-FQ	IowaBlack FQ- GGGTTTGCGCTCAGCCATCCGTTCAGTCCGTCAGGTCAG TCTAAGGGCATCACGGAC	57	2705	2687
	Aae-LF_NatTail_comp FAM	CTGACCTGACGGACTGAACGGATGGCTGAGCGCAAACCC-FAM	39

Underlined sequences are double strand segments of strand-displacing probes. FAM was used for Zika detection and positive control for Ae. aegypti ssu rRNA detection (λ_ex-λ_em = 495 nm-520 nm, color observed with excitation at 470 nm, green), HEX was used for chikungunya detection (λ_ex-λ_em = 538 nm-555 nm, color observed with excitation at 470 nm, yellow), TAMRA was used for dengue-1 detection (λ_ex-λ_em = 559 nm-583 nm, color observed with excitation at 470 nm, orange), TET was used for mitochondrial DNA detection as positive control in urine (λ_ex-λ_em = 522 nm-539 nm, color observed with excitation at 470 nm, yellow). IowaBlack-FQ was used as a common quencher with absorption range of 420-620 nm. Pos: position. SSU rRNA: small subunit ribosomal RNA