Table 1.
New PCR primers designed to amplify HIV-1 group M or group O isolates.
| Primer name | Location on HIV-1 reference strains | Targeted HIV region | Sequence 5′-3′ |
|---|---|---|---|
| Universal primers | HIV-1 B_HXB2 | ||
| PR2 | 1557–1583 | pol (protease-RT) | CCTAGRAAAARGGGCTGTTGGAAATGT |
| PR3 | 1590–1615 | pol (protease-RT) | GARGGACAYCAAATGAAAGAYTGYAC |
| TR2 | 1905–1930 | pol (protease-RT) | TAGAYACAGGAGCAGATGATACAGTA |
| PR2as | 2294–2322 | pol (protease-RT) | TTTATRGCAAAYAYTGGRGTRTTRTATGG |
| TR3as | 2885–2912 | pol (protease-RT) | CTAAYTTYTGTATRTCATTGACAGTCCA |
| TR2as | 2915–2941 | pol (protease-RT) | AATYTGACTTGCCCARTTTARTTTTCC |
| Group M specific primers | |||
| 41UM-1 | 7108–7133 | env (gp41) | GGACAAGCAATGTATGCCCCTCCCAT |
| 41UM-2 | 7231–7256 | env (gp41) | GGAGGARAYATGARGGACAATTGGAG |
| 41UM-1r | 8099–8125 | env (gp41) | GGYGGTAGCTGAAGAGGCACAGGYTCC |
| 41UM-2r | 8016–8044 | env (gp41) | TGYCTTGCTCKCCACCTYCTTCTTCGATT |
| Group O specific primers | HIV-1 O_ANT-70 | ||
| IN-O-1s | 4154–4183 | pol (integrase) | TAGTTCARCAGATAATAGARGAACTRACAA |
| IN-O-2s | 4234–4262 | pol (integrase) | GGAAATGAAAAAATAGATAAATTAGTAAG |
| IN-O-1as | 5380–5408 | pol (integrase) | CTRTCTGCTGTTTCAGGGTCAATCTGTGT |
| IN-O-2as | 5299–5323 | pol (integrase) | TTTCYCCTGGCATYAATCCCCAATA |
| gp41O_1 | 7679–7704 | env (gp41) | GGGGGAGAYATGNRAGATATATGGAG |
| gp41O_2 | 7844–7870 | env (gp41) | CTAAGTGCAGCAGGWAGCACTATGGGC |
| gp41O_1r | 8565–8593 | env (gp41) | TAAGYTGCTCAAGAGGTGGTARNTCCACA |
| gp41O_2r | 8468–8496 | env (gp41) | CTGYCTYCKTCTCCACCTYCTTCTCCTGT |
pol: polymerase; RT: reverse transcriptase; env: envelope; gp41: glycoprotein 41.