Kinetics of HIV-1 drug resistance mutations in vivo

Abstract: Antiretroviral therapy (ARV) exert a selective pressure on HIV-1 and may select viral drug resistant strains which have competitive advantage in the presence of the drug. Knowledge about the appearance and disappearance of these mutations is important when choosing ARV.The aim of this thesis was to study the kinetics of drug induced resistance mutations and the relevance of the mutational patterns in minor and major viral populations at ARV cessation, change and failure in a clinical setting. Paper 1. To study the kinetics if HIV-1 RNA and drug-induced mutations after cessation of ARV therapy in 26 patients. After cessation of ARV a phase of varying length with undetectable virus was followed by a rapid viral increase before a plateau, corresponding to pretreatment levels, was reached. A significant larger number of primary protease inhibitor (PI) associated mutations reverted to wild-type, as compared with primary reverse transcriptase inhibitor (RTI) associated mutations, suggesting that they may cause a more impaired viral fitness. During the phase of rapid viral increase mutated and wild-type virus replicated equally good, indicating that mutated stains still may replicate efficiently. Paper 2. To study the reappearance of drug resistance mutations detected earlier at a new virological failure during second or third line antiretroviral therapy. Genotypic resistance testing was carried out in 66 patients before change of therapy and at the next treatment failure. The majority of primary and secondary resistance mutations persisted at new failures with modified treatment in both the RT and the PI genes. The results suggest that clinical cross-resistance may develop via common pathways within all categories of drugs in heavily treated patients. Paper 3. To describe the pattern of resistance mutations in Pl-naive HIV-1 infected patients experiencing their first treatment failure on nelfinavir(NFV) containing therapy. 172 patient were studied. Virus from base-line was sequenced in 29 patients, the V82A mutation was found in four patients without any epidemiological connections. Treatment-naïve patients in Sweden may thus harbour PI-resistant virus and resistance testing should be considered before treatment. 43 patients failed treatment.. A diverse pattern of primary PI mutations was seen: 461 (n= 7), 30N (n= 6), 90M (n= 5) and 82A (n= 4). The finding of 461 was unexpected and is associated with a higher degree of PI cross-resistance than the common 30N. Paper 4. To investigate the kinetics of M1841/V in the minor HIV-1 populations. Sixteen HIV-1 infected patients with treatment failure on 3TC and/or doI containing regimens were analysed by direct sequencing and selective PCR (SPCR). In five samples, SPCR detected mutated virus, at low proportions, when direct sequencing showed a wild-type sequence. The good correlation between direct sequencing and SPCR is in line with that M184V mutants rapidly become dominating during 3TC failure, although a few patients may harbour 3TC resistant virus in minor populations only. Eleven patients with treatment failure on ddI containing treatment exhibited wild-type virus by both methods suggesting M184V does not cause any clinical significant decrease in sensitivity to ddI in vivo.