Table S1.

HIV-1 primers used in the study

Primer set	Primer name	HXB2 coordinates	Expected size (bp)	Sequence (5′ → 3′)	Source
DNA first forward	DNA F1	623–649		AAATCTCTAGCAGTGGCGCCCGAACAG	(39)
DNA first reverse	DNA R1	9662–9686	9,064	TGAGGGATCTCTAGTTACCAGAGTC	(40)
DNA second forward	DNA F2	682–705		TCTCTCGACGCAGGACTCGGCTTG	(41)
DNA second reverse	DNA R2	9603–9632	8,951	GCACTCAAGGCAAGCTTTATTGAGGCTTA	(40)
DNA second forward	DNA F3	646–666		ACAGGGACCTGAAAGCGAAAG	(13)
DNA second reverse	DNA R3	9650–9676	9,031	CTAGTTACCAGAGTCACACAACAGACG	(13)
RNA first forward	RNA F1	760–777		TTTTGACTAGCGGAGGCT	Newly designed
RNA first reverse	RNA R1	9603–9632	8,873	GCACTCAAGGCAAGCTTTATTGAGGCTTA	(40)
RNA second forward	RNA F2	796–816		GCGAGAGCGTCAGTATTAAGC	Newly designed
RNA second reverse	RNA R2	9145–9171	8,376	CTGCCAATCAGGGAAGTAGCCTTGTGT	(42)
RNA second reverse	RNA R2'	9438–9458	8,663	GGAAAGTCCCCAGCGGAAAGT	(29)