TABLE 1.

Oligonucleotide primer and probe sets for the triplex and 5′-UTR rRT-PCR assays

Assay	Oligonucleotide	Reference sequence positiona	Oligonucleotide sequence and modificationsb	Final concn (nM)
Triplex IA	HAVIA_F	2616−2639	ATAGAGGACCAYTGGAYTTGACAA	900
	HAVIA_P1	2648−2664	FAM-ACAGGAGCCACTGATGT-BHQ1	100
	HAVIA_P2	2647−2665	FAM-TCACAGGAGCTACTGATGT-BHQ1	100
	HAVIA_R	2712−2733	GCTGAYTYCTTTTCYACCCAAG	900
Triplex IB	HAVIB_F	5336−5355	GTTTGGAGTTGGAGAGAAGA	900
	HAVIB_P	5430−5449	VIC-AAATTTGAGAAAGATTATGA-MGBNFQ	200
	HAVIB_R	5479−5502	CAGCTGAAATTGAATAGTARGTTC	900
Triplex IIIA	HAVIIIA_F	4507−4530	TGCATCTGATTATTGGGATGGATA	300
	HAVIIIA_P	4575−4596	Q670-TCAGACCAATCCTCATCAGTTG-BHQ2	200
	HAVIIIA_R	4612−4632	AAYCTCATTGGACATCCAGAC	300
5′-UTR	HAV5UTR_F	249−265	CTAGGCTCTGGCCGTTG	800
	HAV5UTR_P	296−322	FAM-TCCCCAATT-NOVA-TAGACTCCTACAGCTCCA-BHQ1	150
	HAV5UTR_R	343−362	GCCAAGTTAACACTGCAAGG	800

^aGenome position relative to GenBank accession no. M14707 for the 5′-UTR and Triplex IB primer-probe set, GenBank accession no. AB020564 (HAVIA_F, HAVIA_R, and HAVIA_P1) and AB020568 accession no. (HAVIA_P2) for the Triplex IA primer-probe set, and GenBank accession no. AB279732 for the Triplex IIIA primer-probe set.

^bOligonucleotide modifications: BHQ1, black hole quencher 1; MGBNFQ, minor grove binder nonfluorescent quencher; Q670, Quasar 670; BHQ2, black hole quencher 2; NOVA, BHQnova double-quenched probe.