Table 2 Sequences of primers used for alternate polymerase chain reactions
Genome region | Primer name | Sequence (5´ to 3´) | Reference |
|---|---|---|---|
Group M pol | |||
Protease (RT PCR) | Outer sense : 5´Prot1 | TAATTTTTTAGGGAAGATCTGGCCTTCC | Ref. 8 |
Outer antisense : 3´Prot1 | GCAAATACTGGAGTATTGTATGGATTTTCAGG | Ref. 8 | |
(nested PCR) | Inner sense : 5´Prot2 | TCAGAGCAGACCAGAGCCAACAGCCCCA | Ref. 8 |
Inner antisense : 3´Prot2 | AATGCTTTTATTTTTTCTTCTGTCAATGGC | Ref. 8 | |
Reverse transcriptase (RT PCR) | Outer sense : MJ3 | AGTAGGACCTACACCTGTCA | Ref. 8 |
Outer antisense : MJ4 | CTGTTAGTGCTTTGGTTCCTCT | Ref. 8 | |
(nested PCR) | Inner sense : A35 | TTGGTTGCACTTTAAATTTTCCCATTAGTCCTATT | Ref. 8 |
Inner antisense : NE135 | CCTACTAACTTCTGTATGTCATTGACAGTCCAGCT | Ref. 8 | |
Group M env | |||
Gp41 (RT PCR) | Outer sense : 1S | TGGAGGAGGAGATATGAGG | |
Outer antisense : AS1 | GTGAGTATCCCTGCCTAACTCTAT | Ref. 9 | |
(nested PCR) | Inner sense : T20S1 | GAGGGACAATTGGAGAAGTGAATT | Ref. 9 |
Inner antisense : 2AS | CTACCAAGCCTCCTACTATC | Ref. 9 | |
Group O pol | |||
Pol (RT PCR) | Outer sense : ProtO | TTCAAYTGTGGRAAAGAGGGAC | Ref. 3 |
Outer antisense : PolOL1 | CTAATTCCTTGATAGATTTGACT | Ref. 3 | |
*Protease (nested PCR) | Inner sense : Prot4 | CAGCCCCACCRATGGAGG | Ref. 3 |
Inner antisense : NouvL | CATTGTTTTACTTTTGGTCCAT | Ref. 3 | |
*Reverse transcriptase (nested PCR) | Inner sense : PolOF1 | CAGTATTRGTGGGACCTACTCCTGTT | Ref. 3 |
Inner antisense : PolOL2 | GGCTGTACTGTCCAYTTGTCTG | Ref. 3 | |
Group O env | |||
Gp41 (RT PCR) | Outer sense : V3DURA | ATTCCAATACACTATTGTGCTCCA | Ref. 3 |
Outer antisense : gp41NE3 | TAAGTTGCTCAAGAGGTGGTA | Ref. 3 | |
(nested PCR) | Inner sense : OFU | TAAAACCTTTTAGTGTRGCAC | Ref. 3 |
Inner antisense : 8393L | GTTGATATCCCTGCCTAATG | Ref. 3 | |
Group O and M-specific PCR (integrase region) | Outer sense : 4235 | CCCTACAATCCCCAAAGTCAAGG | Ref. 7 |
Outer antisense : 4538 | TACTGCCCCTTCACCTTTCCA | Ref. 7 | |
(nested PCR) | Inner sense : 4327 | TAAGACAGCAGTACAAATGGCAG | Ref. 7 |
Inner antisense : 4481 | GCTGTCCCTGTAATAAACCCG | Ref. 7 |