Table 2.

Primer sequences and PCR conditions

Target	Primer	Sequences (5'-3')	PCR conditions
Integrated HIV-1
DNAa
• First round PCR	L-M667	ATGCCACGTAAGCGAAACTCTGGCTAACTAGGGAACCCACTG	95°C, 8 min and 95°C, 10 s, 60°C, 10 s, 72°C, 170 s for 12 cycles
	Alu 1	TCCCAGCTACTGGGGAGGCTGAGG
	Alu 2	GCCTCCCAAAGTGCTGGGATTACAG
• Second round PCR	Lambda T	ATGCCACGTAAGCGAAACT	95°C, 8 min and 95°C, 10 s, 60°C, 10 s, 72°C, 9 s for 40 cycles
	AA55M	GCTAGAGATTTTCCACACTGACTAA
Linear HIV DNAa	MH531	TGTGTGCCCGTCTGTTGTGT	95°C, 8 min and 95°C, 10 s, 60°C, 10 s, 72°C, 6 s for 40 cycles
	MH532	GAGTCCTGCGTCGAGAGAGC
2-LTR circlea	HIV F	GTGCCCGTCTGTTGTGTGTGACT	95°C, 8 min and 95°C, 10 s, 60°C, 10 s, 72°C, 10 s for 40 cycles
	HIV R	ACTGGTACTAGCTTGTAGCACCATCCA
U5-U3 RNAa	HIV F	GTGCCCGTCTGTTGTGTGTGACT	95°C, 2 min and 95°C, 5 s, 60°C, 10 s, 72°C, 10 s for 40 cycles
	HIV R	ACTGGTACTAGCTTGTAGCACCATCCA
Gag	For	CCCATAGTGCAGAACATCCA	50°C, 2 min, 95°C, 2 min, and 95°C, 15s and 60°C, 30s, for 50 cycles
	Rev	GGGCTGAAAGCCTTCTCTTC
Singly splicedb	M669	GTGTGCCCGTCTGTTGTGTGACTCTGGTAAC	50°C, 2 min, 95°C, 2 min, and 95°C, 15s and 60°C, 30s, for 50 cycles
	La 23	GCCTATTCTGCTATGTCGACACC
Multiply spliced HIV RNAa	P659	GACTCATCAAGTTTCTCTATCAAA	95°C, 4 min and 95°C, 5 s, 54°C, 10 s, 72°C, 8 s for 40 cycles
	P413MOD	AGTCTCTCAAGCGGTGGT
Unspliced HIV RNAa	La 9	GACGCTCTCGCACCCATCTC	95°C, 2 min and 95°C, 10 s, 60°C, 40 s for 40 cycles
	La 8.1	CTGAAGCGCGCACGGCAA
β-actin	Actin F	ATGGCCACGGCTGCTTCCAGC	95°C, 15 s, 55°C, 30 s, 72°C, 15 s for 30 cycles
	Actin R	CATGGTGGTGCCGCCAGACAG
GAPDH	GAPDH F	GAGTCAACGGATTTGGTCGT	95°C, 15 s, 60°C, 30 s, 72°C, 15 s for 30 cycles
	GAPDH R	TTGATTTTGGAGGGATCTCG

^a Primer sequences and PCR conditions were modified from [40]

^b Primer sequences and PCR conditions were modified from [74]