TABLE 1.

Oligonucleotide primers and probes used in this study

Assay	Genomic region	Primer or probe	Typea	Sequence (5′-3′)	Genomic locationb	Tm (°C)
usRNA, prDNA	gag	GAG1	Sense I, II	TCAGCCCAGAAGTAATACCCATGT	1280-1303	58.3
		SK431	Antisense I	TGCTATGTCAGTTCCCCTTGGTTCTCT	1474-1500	61.5
		GAG2	Antisense II	CACTGTGTTTAGCATGGTGTTT	1341-1362	55.1
		GAG3	Probe	FAM-ATTATCAGAAGGAGCCACCCCACAAGA-TAMRA	1311-1337	61.7
msRNA	tat/rev	ks1	Sense I	CTTAGGCATCTCCTATGGCAGGAA	5956-5979	59.0
		mf83	Antisense I, II	GGATCTGTCTCTGTCTCTCTCTCCACC	8433-8459	61.7
		mf84	Sense II	ACAGTCAGACTCATCAAGTTTCTCTATCAAAGCA	6012-6045	60.4
		ks2-tq	Probe	FAM-TTCCTTCGGGCCTGTCGGGTCCC-TAMRA	8399-8421	67.8

^aI, first PCR; II, second (real-time) PCR.

^bThat is, relative to the sequence of HXB2 reference strain of HIV-1.