TABLE 1.
Oligonucleotides used in a ligation assay to detect mutations in HIV-1 pol associated with resistance to protease inhibitors
| Drug(s) | Codon | Amino acid substitution | Genotype detected | Sequence (5′→3′)a |
|---|---|---|---|---|
| Nelfinavir | 30 | WTb | dig-TATTAGATACAGGAGCAGATG | |
| D30N | Mutant | f-TATTAGATACAGGAGCAGATA | ||
| Common | p-ATACAGTATTAGAAGAAATGAAT-bio | |||
| 88 | WT | dig-CCTGTCAACATAATTGGAAGAA | ||
| N88D | Mutant | f-CCTGTCAACATAATTGGAAGAG | ||
| Common | p-ATCTGTTGACTCAGATTGGTTG-bio | |||
| Amprenavir | 50 | WT | dig-AAACCAAAAATGATAGGGGGAA | |
| I50V | Mutant | f-AAACCAAAAATGATAGGGGGAG | ||
| Common | p-TTGGAGGTTTTATCAAAGTAAGA-bio | |||
| Ritonavir, indinavir, lopinavirc | 82 | WT | dig-TATTAGTAGGACCTACACCTGT | |
| V82A | Mutant A | f-TATTAGTAGGACCTACACCTGC | ||
| V82S | Mutant S | f-TATTAGTAGGACCTACACCTAG | ||
| V82T | Mutant T | f-TATTAGTAGGACCTACACCTAC | ||
| Common | p-CAACATAATTGGAAGAAATCTGT-bio | |||
| Amprenavir, indinavir | 84 | WT | dig-AGGACCTACACCTGTCAACA | |
| Nelfinavir, ritonavir | I84V | Mutant | f-AGGACCTACACCTGTCAACG | |
| Saquinavir, lopinavirc | Common | p-TAATTGGAAGAAATCTGTTGACT-bio | ||
| Saquinavir, nelfinavir | 90 | WT | dig-CAACATAATTGGAAGAAATCTGT | |
| L90M | Mutant | f-CAACATAATTGGAAGAAATCTGA | ||
| Common | p-TGACTCAGATTGGTTGCACTTT-bio |
a
Bases comprising the codons of interest are in boldface type. dig, digoxigenin; f, fluorescein; p, phosphate; bio, biotin.
b
WT, wild-type.
c
Mutations associated with HIV-1 resistance to lopinavir in phenotypic susceptibility assays and with virologic failure in clinical trials (13; Harrigan et al., Antivir. Ther.; Kempf et al., Antivir. Ther.; Molla et al., Antivir. Ther.).