Table 2.

Primers and probes used for HTLV-1 Gene expression, proviral load, and PCR for sequencing

mRNA	Plasmid standard	Primers and probe
Hbz	JA662	5′ Primer	[HBZMAP1] 5′-1905CTTCTAAGGATAGCAAACCGTCAAG1881-3′
		Probe	[TMP-13] 5′-/56-FAM/1782CCTGTGCCA/ZEN/TGCCCGGAGGA1801/3IABkFQ/-3′
		3′ Primer	[HBZMAP2] 5′-353ATGGCGGCCTCAG365^1765GGCT1768-3′
rGAPDH	rGAPDH	5′ Primer	[rGAPDH-S] 5′-GATGCTGGTGCCGAGTACGTG-3′
		Probe	[BY-1Z] 5′-/56-FAM/ACCACCATG/ZEN/GAGAAGGCCGGG/3IABkFQ/-3′
		3′ Primer	[rGAPDH-AS] 5′- GTGGTGCAGGATGCGTTGCTGA-3′
Gag/Pol	ACHneo	5′ Primer	[#20] 5′-938AGCCCCCAGTTCATGCAGACC958-3′
		Probe	[TMP-3] 5′-/56-FAM/990CTGCCAAAG/ZEN/ACCTCCAAGACCTCC1013/3IABkFQ/-3′
		3′ Primer	[#19] 5′-1036GAGGGAGGAGCAAAGGTACTG1016-3′
Gene
Gag/Pol	ACHneo	5′ Primer	[#20] 5′-938AGCCCCCAGTTCATGCAGACC958-3′
		Probe	[TMP-3] 5′-/56-FAM/990CTGCCAAAG/ZEN/ACCTCCAAGACCTCC1013/3IABkFQ/-3′
		3′ Primer	[#19] 5′-1036GAGGGAGGAGCAAAGGTACTG1016-3′

Region of interest	Plasmid standard	Primers
vCTCF-BS	NA	5′ Primer	[CTCF-F2] 5′-6826TAGCACTATGCTGTTTCGCCT6846-3′
		3′ Primer	[CTCF-R2] 5′-7211GGTGGACGGGCTATTATCTT7192-3′

All provided sequence numbering is in the context of the HTLV-1 molecular clone ACHneo