Table 1.
List of primers used in the study
| Total HIV LTR | |
| LTR F | TTAAGCCTCAATAAAGCTTGCC |
| LTR R | GTTCGGGCGCCACTGCTAGA |
| probe (for qPCR) | CCAGAGTCACACAACAGACGGGCACA |
| Total HIV gag | |
| gag F | AGTTGGAGGACATCAAGCAGCCATGCAAAT |
| gag R | TGCTATGTCAGTTCCCCTTGGTTCTCT |
| probe (for qPCR) | ACCATCAATGAGGAAGCTGCAGAATGGG |
| Alu-gag assay | |
| Alu F | GCCTCCCAAAGTGCTGGGATTACAG |
| Cell-associated HIV RNA | |
| Subject 1 preamplification | |
| gag1 | TCAGCCCAGAAGTAATACCCATGT |
| gag R | TGCTATGTCAGTTCCCCTTGGTTCTCT |
| HIV-rev | TCTCGACGCAGGACTCG |
| rev R | GCTGTCTCCGCTTCTTCCT |
| Subject 2 preamplification | |
| gag1 | TCAGCCCAGAAGTAATACCCATGT |
| gag R | TGCTATGTCAGTTCCCCTTGGTTCTCT |
| MS total | GAAGAAGCGGAGACAGCGACGA |
| MF83 | GGATCTGTCTCTGTCTCTCTCTCCACC |
| US RNA qPCR (Subjects 1 and 2) | |
| gag1 | TCAGCCCAGAAGTAATACCCATGT |
| gag2 | CACTGTGTTTAGCATGGTGTTT |
| gag3 probe | ATTATCAGAAGGAGCCACCCCACAAGA |
| Subject 1 MS RNA qPCR (exons 1–4) | |
| rev F | AGGACTCGGCTTGCTGAA |
| rev R | GCTGTCTCCGCTTCTTCCT |
| rev probe | CACRGCAAGAGGCGAGGGG |
| Subject 2 MS RNA qPCR (exons 4–7) | |
| Mf84 | ACAGTCAGACTCATCAAGTTTCTCTATCAAAGCA |
| Mf83 | GGATCTGTCTCTGTCTCTCTCTCCACC |
| Ks2-tq probe | TTCCTTCGGGCCTGTCGGGTCCC |
| Illumina sequencing primers | |
| First PCR F | CCTCAATAAAGCTTGCCTTGAGTGC |
| First PCR R | CCTAGTTAGCCAGAGAGCTCCCAG |
| Second PCR F | AAGTAGTGTGTGCCCGTCTGTTGTGTGAC |
| Second PCR R | GGAAAGTCCCCAGCGGAAAGTCCCTTGTAG |
| RT-PCR | |
| STAT5B 1 | CATTGTTGGCTTCTCGGACC |
| LTR 2 | GAGCTGTCTGGCTAACTAGG |
| STAT5B 2 | GGGCAGCGGTCATACGTG |
| LTR 3 | AGCTTGCCTTGAGTGCTTCA |
| STAT5B 3 | GCTTGGCTTTCAATCCACTG |
| D4 F | TATGGCAGGAAGAAGCGGAG |
| Pacbio sequencing primers | |
| PB5HChaviF | CCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGT |
| PB5HChaviR | CTTGCCACACAATCATCACCTGCCAT |
| VIF1C | GGGTTTATTACAGGGACAGCAGAG |
| Ofm19 | GCACTCAAGGCAAGCTTTATTGAGGCTTA |