Phenotypic assays and sequencing are less sensitive than point mutation assays for detection of resistance in mixed HIV-1 genotypic populations

The sensitivity and discriminatory power of the 151 and 215 amplification r efractory mutation system (ARMS) were evaluated, and their performance for the detection of drug resistance in mixed genotypic populations of the reve rse transcription (RT) gene of HIV-1 were compared with T7 sequencing, cycl e sequencing, the line probe assay (LiPA) HIV-1 RT test, and the recombinan t virus assay (RVA). ARMS and the LiPA HIV-1 RT test were shown to be able to detect minor variants that in particular cases comprised only 1%, T7 seq uencing on an ALF semiautomated sequencer could correctly score mixtures on ly when variants were present at 50%. Cycle sequencing on an ABI PRISM 310 improved the sensitivity for mixtures to about 25%. Using RVA, it was shown that at least 50% of the virus population needed to carry the resistance m utation at codon 184 to afford phenotypic resistance against lamivudine. Th e two point mutation assays therefore proved to be more sensitive methods t han sequencing and RVA to reliably determine a gradual shift in HIV-1 drug resistance mutations in follow-up of patients infected with HIV-1. In 4 of 5 treated patients who were followed by ARMS, a gradual shift in resistant genotypic populations was observed during a period of 6 to 19 months. For 1 patient, a shift from wild to mutant type at position 151 occurred within 2 months, without mixed genotypic intermediate type's being detected.