Table 3 Primers for Pol and LTR amplification and sequencing
Amplification primers | ||||
|---|---|---|---|---|
Primer Number | Description | Co-ordinates (HXB2) /Length | Sequence (5'–3') | Product length |
Protease | ||||
 N1636 | EFP | 1978–2006, 29 | AAGGAAGGGCACCCAGCCAGAAATTGCAG | 864 |
 N1637 | ERP | 2813–2842, 30 | GCGGGATGTGGTATCCCTAATTGAACTTCC | |
 N1638 | IFP | 2075–2103, 29 | GACAGGCTAATTTTTTAGGGAARATTTGG | 530 |
 N1639 | IRP | 2577–2605, 29 | GGGCCATCCATTCCTGGCTTTAATTTTAC | |
RT | ||||
 N1641 | EFP | 2368–2395, 28 | CAGGAAGATGGAAACCAAAAATGATAGG | 2114 |
 N1642 | ERP | 4455–4482, 28 | CTATATATCCACTGGCTACATGAACTGC | |
 N1643 | IFP | 2489–2509, 21 | TACACCTGTCAACATAATTGG | 1816 |
 N1644 | IRP | 4285–4305, 21 | AATCACTAGCCATTGCTCTCC | |
RNaseH/Integrase | ||||
 N2244 | EFP | 3628–3660, 33 | CCCACACTAATGATGTAAAACAGTTAACAGAGG | 1659 |
 N2245 | ERP | 5257–5287, 31 | CCATGACCCAAATGCCAATCTCTTTCTCCTG | |
 N2246 | IFP | 3738–3765, 28 | ATGGGAAACATGGTGGACAGACTATTGG | 1476 |
 N2247 | IRP | 5185–5214, 30 | TGGGATGTGTACTTCTGAACTTAYTTTTGG | |
LTR | ||||
 N698 | EFP | 1–34, 34 | TGGAAGGGTTAATTTACTCYMAGAAAAGRCAAGA | 555 |
 N1032 | ERP | 538–556, 19 | TAGAGCACGCAAGGCAAGC | |
 N558 | IFP | 1–43, 43 | TGGAAGGGTTAATTTACTCTAAGGAAAGGCAAGAGATCCTTG | 431 |
 N1204 | IRP | 411–432, 21 | CTTATATGCAGGATCTGAGGG | |
Sequencing primers | gene | |||
 N1645 | Forward Primers | 2620–2635, 16 | GGCCATTGACAGAAGA | RT |
 N1646 | 3108–3124, 17 | TTGTATGTAGGATCTGA | ||
 N1647 | 3626–3642, 17 | TGCCCACACTAATGATG | ||
 N1648 | Reverse primers | 3870–3886, 17 | GCTGCCCCATCTACATA | |
 N1649 | 3345–3362, 18 | GTAAATCTGACTTGCCCA | ||
 N1650 | 2889–2906, 18 | GGGAACTGAAAAATATGC | ||
 9 M | Forward Primers | 4145–4167, 21 | CCTGTCATGGGTACCAGCACA | RNaseH/Integrase |
 10 M | 4664–4687, 24 | CCAAAGTCAGGGAGTAGTAGAATC | ||
 28 M | Reverse primers | 4957–4978, 22 | ACTACTGCCCCTTCACCTTTCC | |
 29 M | 4380–4401, 22 | GACTGCAGTCTACTTGTCCATG | ||