Persistence of earlier HIV-1 drug resistance mutations at new treatment failure

HIV-1 polymerase inhibition by nucleoside analogs: cellular- and kinetic parameters of efficacy, susceptibility and resistance selection

Nucleoside analogs (NAs) are used to treat numerous viral infections and cancer. They compete with endogenous nucleotides (dNTP/NTP) for incorporation into nascent DNA/RNA and inhibit replication by preventing subsequent primer extension. To date, an integrated mathematical model that could allow the analysis of their mechanism of action, of the various resistance mechanisms, and their effect on viral fitness is still lacking. We present the first mechanistic mathematical model of polymerase inhibition by NAs that takes into account the reversibility of polymerase inhibition. Analytical solutions for the model point out the cellular- and kinetic aspects of inhibition. Our model correctly predicts for HIV-1 that resistance against nucleoside analog reverse transcriptase inhibitors (NRTIs) can be conferred by decreasing their incorporation rate, increasing their excision rate, or decreasing their affinity for the polymerase enzyme. For all analyzed NRTIs and their combinations, model-predicted macroscopic parameters (efficacy, fitness and toxicity) were consistent with observations. NRTI efficacy was found to greatly vary between distinct target cells. Surprisingly, target cells with low dNTP/NTP levels may not confer hyper-susceptibility to inhibition, whereas cells with high dNTP/NTP contents are likely to confer natural resistance. Our model also allows quantification of the selective advantage of mutations by integrating their effects on viral fitness and drug susceptibility. For zidovudine triphosphate (AZT-TP), we predict that this selective advantage, as well as the minimal concentration required to select thymidine-associated mutations (TAMs) are highly cell-dependent. The developed model allows studying various resistance mechanisms, inherent fitness effects, selection forces and epistasis based on microscopic kinetic data. It can readily be embedded in extended models of the complete HIV-1 reverse transcription process, or analogous processes in other viruses and help to guide drug development and improve our understanding of the mechanisms of resistance development during treatment.

Nucleoside analogs (NAs) represent an important drug class for the treatment of viral infections and cancer. They inhibit DNA/RNA polymerization after being incorporated into nascent DNA/RNA, which prevents primer extension. Viruses are particularly versatile and frequently develop mutations enabling them to avert the effects of NAs. The mechanisms of resistance development are, however, still poorly understood. Through mathematical modeling, we assess the mechanisms by which HIV-1 can develop resistance against nucleoside analog reverse transcriptase inhibitors (NRTI). We quantify the effects of treatment and estimate the fitness of drug resistant mutants. We correctly predict that HIV-1 can develop resistance by decreasing NRTI incorporation rate, increasing its excision rate, or decreasing its affinity for the viral polymerase enzyme. Our model also allows quantification of the cell specific factors affecting NRTI efficacy. Resistance development also changes drug susceptibility distinctly and we show, for the first time, that selection of drug resistance can occur in particular target cells. This finding could provide an explanation of how clinically observed resistant viral mutants may arise. It also pin-points important parameters that may impact clinical efficacy of NAs used to treat other viruses.

Transmission of human immunodeficiency virus I drug resistance - a case report. What are the clinical implications?

The success of first-line antiretroviral therapy can be challenged by the acquisition of primary drug resistance. Here we report a case where baseline genotypic resistance testing detected resistance conferring nucleoside/nucleotide reverse transcriptase inhibitor (NRTI)-associated mutations, but no primary mutations for protease inhibitor (PI). Subsequent PI-based HAART with boosted saquinavir led to virological treatment success with persistently undetectable viral load. After treatment simplification from saquinavir to an atazanavir based PI-therapy and no change in backbone therapy rapid virological breakthrough occurred. Retrospective analysis displayed preexisting gag cleavage site mutations which may have reduced the genetic barrier in a clinical relevant manner in combination with the already existing NRTI resistance mutations. Alternatively, this effect could be explained with a different antiviral potency for the respective PIs used.

Significance of variation within HIV, EBV, and KSHV subtypes

Since their initial transmission to humans, viruses have diversified extensively through recombination and mutation. The presence of intra- and inter-individual viral diversity influences disease progression, drug resistance, and therapy and presumably explains the conflicting results in many studies, including the failure of peptide-based vaccination strategies. Although HIV is a small RNA virus, coinfection with large DNA viruses, notably the oncogenic gamma-herpesviridae human herpesvirus-8 and Epstein Barr virus, is common. This coinfection occurs secondary to immunosuppression and shared transmission routes with high-risk predisposing behavior. In addition, all 3 of these viruses can lead to chronic infections, long periods of latency, and reactivation characterized by pain and suffering. The efficient targeting of their genetic diversity represents one of the major challenges in their control, both in prophylactic and therapeutic strategies. An understanding of diversity will help delineate whether population-specific vaccine strategies are necessary.

The cost-effectiveness of counseling strategies to improve adherence to highly active antiretroviral therapy among men who have sex with men

OBJECTIVE

Inadequate adherence to highly active antiretroviral therapy (HAART) may lead to poor health outcomes and the development of HIV strains that are resistant to HAART. The authors developed a model to evaluate the cost-effectiveness of counseling interventions to improve adherence to HAART among men who have sex with men (MSM).

METHODS

The authors developed a dynamic compartmental model that incorporates HIV treatment, adherence to treatment, and infection transmission and progression. All data estimates were obtained from secondary sources. The authors evaluated a counseling intervention given prior to initiation of HAART and before all changes in drug regimens, combined with phone-in support while on HAART. They considered a moderate-prevalence and a high-prevalence population of MSM.

RESULTS

If the impact of HIV transmission is ignored, the counseling intervention has a cost-effectiveness ratio of $25,500 per quality-adjusted life year (QALY) gained. When HIV transmission is included, the cost-effectiveness ratio is much lower: $7400 and $8700 per QALY gained in the moderate- and high-prevalence populations, respectively. When the intervention is twice as costly per counseling session and half as effective as estimated in the base case (in terms of the number of individuals who become highly adherent, and who remain highly adherent), then the intervention costs $17,100 and $19,600 per QALY gained in the 2 populations, respectively.

CONCLUSIONS

Counseling to improve adherence to HAART increased length of life, modestly reduced HIV transmission, and cost substantially less than $50,000 per QALY gained over a wide range of assumptions but did not reduce the proportion of drug-resistant strains. Such counseling provides only modest benefit as a tool for HIV prevention but can provide significant benefit for individual patients at an affordable cost.

HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo

Genetic diversity plays a key role in human immunodeficiency virus (HIV) adaptation, providing a mechanism to escape host immune responses and develop resistance to antiretroviral drugs. This process is driven by the high-mutation rate during DNA synthesis by reverse transcriptase (RT), by the large viral populations, by rapid viral turnover, and by the high-recombination rate. Drugs targeting HIV RT are included in all regimens of highly active antiretroviral therapy (HAART), which helps to reduce the morbidity and mortality of HIV-infected patients. However, the emergence of resistant viruses is a significant obstacle to effective long-term management of HIV infection and AIDS. The increasing complexity of antiretroviral regimens has favored selection of HIV variants harboring multiple drug resistance mutations. Evolution of drug resistance is characterized by severe fitness losses when the drug is not present, which can be partially overcome by compensatory mutations or other adaptive changes that restore replication capacity. Here, we review the impact of mutations conferring resistance to nucleoside and nonnucleoside RT inhibitors on in vitro and in vivo fitness, their involvement in pathogenesis, persistence upon withdrawal of treatment, and transmission. We describe the techniques used to estimate viral fitness, the molecular mechanisms that help to improve the viral fitness of drug-resistant variants, and the clinical implications of viral fitness data, by exploring the potential relationship between plasma viral load, drug resistance, and disease progression.

Utility of repeat genotypic resistance testing and clinical response in patients with three class resistance and virologic treatment failure

We sought to determine the utility of repeat genotypic resistance testing (GRT) and the clinical response in HIV-1-infected patients with known resistance to three of the major classes of antiretroviral drugs. The HIV-1 genetic sequences for 20 patients who had high-level 3 class resistance demonstrated on a prior GRT (3C-GRT 1) measured during the period from November 1, 2000 through July 1, 2004 were retrospectively evaluated. At the time of 3C-GRT 1, the median CD4 count and HIV-1 RNA viral load were 168 cells/mm(3) and 4.5 log copies per milliliter, respectively. The median time to the second GRT (3C-GRT 2) was 17 months. At that time, the median CD4 count and VL were 140 cells/mm(3) and 4.9 log copies per milliliter (p = 0.8 and p = 0.12, respectively). On 3C-GRT 2, all patients retained essentially identical mutations, with the exception of the loss of the M184V mutation in 6 patients. After 3C-GRT 2, all patients continued on protease inhibitor-containing highly active antiretroviral therapy (HAART) regimens. At 24 weeks after 3C-GRT 2, there was no significant change in CD4 count or HIV-1 RNA viral load (p = 0.68 and p = 0.30, respectively). Repeat GRT in patients with documented high-level 3 class resistance does not provide new or clinically useful information. Under continued antiretroviral selective pressure, the viral genetic sequences in this patient population remained stable. In addition, continuing HAART regimens containing protease inhibitors appeared to forestall further immunological and virologic deterioration in patients with multiple resistance mutations. Providers should focus on obtaining access to combinations of novel agents for patients with 3 class resistance rather than repeated GRT.

Persistence of drug-resistant HIV-1 and possible implications for antiretroviral therapy

Antiretroviral therapy has significantly reduced the morbidity and mortality of subjects infected with HIV-1. However, the establishment of persistent infection and the development of drug-resistant variants are major obstacles facing the eradication of HIV-1. This review summarizes the current knowledge of the persistence of drug-resistant HIV-1 acquired by transmission, or due to therapy failure and the possible implications for antiretroviral therapeutic strategies.

Dawn of non-nucleoside inhibitor-based anti-HIV microbicides

The emergence of HIV/AIDS as a disease spread through sexual intercourse has prompted the search for safe and effective vaginal and rectal microbicides for curbing mucosal viral transmission via semen. Since endogenous reverse transcription is implicated in augmenting the sexual transmission of HIV-1 infection, potential microbicides should have the inherent ability to optimally inhibit both wild-type and drug-escape mutants. The non-nucleoside reverse transcriptase inhibitors (NNRTIs), which bind to an allosteric site on RT, are an important arsenal of drugs against HIV-1. The clinical success of NNRTI-based HIV/AIDS therapies has led to extensive structural and molecular modelling studies of enzyme complexes and chemical synthesis of second- and third-generation NNRTIs. Rationally designed NNRTIs deduced from changes in binding pocket size, shape and residue character that result from clinically observed NNRTI resistance-associated mutations exhibit high binding affinity for HIV-1 RT and robust anti-HIV activity against the wild-type and drug-escape mutants without cytotoxicity. Notably, membrane permeable tight binding NNRTIs have the ability to inactivate cell-free as well as cell-associated HIV-1 in semen without metabolic activation. Consequently, NNRTIs currently under development as experimental microbicides include thiourea-PETT (where PETT stands for phenethylthiazolylthiourea) derivatives (PHI-236, PHI-346 and PHI-443), urea-PETT derivatives (MIV-150), oxypyrimidines (S-DABOs), thiocarboxanilides (UC-781) and diarylpyrimidines (TMC-120). Mucoadhesive formulations of these NNRTIs have been studied for safety and efficacy in animal models and some have entered Phase I safety testing in humans. This review focuses on the structural, biological and preclinical studies relevant to the clinical development of these NNRTIs as molecular virucides intended to prevent the sexual transmission of HIV-1.

Study of antiretroviral mutants in HIV patients with treatment failures and the effect of risk factors in the virological failures

INTRODUCTION: Information about HIV phenotypes of resistant to available ART and the influence of different risk factors on virological failures (VF) in Costa Rican HIV positive patients prior or during HAART is unknown. MATERIALS AND METHODS: Eighty nine samples, 72 VF and 17 basal (before treatment) were analyzed by examining resistant mutants in reverse transcriptase (RT) and protease (PT) regions using Trugene or LIPA genotyping kits. Sixty eight control patients were selected and relevant information was collected in a questionnaire. RESULTS: Poor adherence, presence of resistant mutations and number of treatment's changes were the only significant factors found (p = 0.006, 0.04 and 0.01 respectively). From 66 sequenced samples, 78%, 50% and 50% showed resistance to NRTI (nucleoside reverse transcriptase inhibitors), NNRT (non-nucleoside reverse transcriptase inhibitors) and PI (protease inhibitors), respectively. The most frequent mutations were M41L, M184V, and T215FY in RT and L62PI, L10FIRV and M36I in PT. DISCUSSION: The most important factor related to treatment response in this study was adherence to treatment. Mutations in RT were related to the treatment failure while the ones found in PT were secondary mutations which have been previously described to influence the selection of primary resistance mutations in these regions. The study reveals the urgency to detect resistant mutations in VF to be considered by physicians for selection of treatment schedule, to analyze basal HIV patients for monitoring of the spread of resistant mutations and the importance to reinforce the adherence in the patients for overall treatment outcome.

Atazanavir plus ritonavir or saquinavir, and lopinavir/ritonavir in patients experiencing multiple virological failures

OBJECTIVE

To evaluate atazanavir/ritonavir (ATV/RTV) (300/100 mg) once daily, atazanavir/saquinavir (ATV/SQV) (400/1200 mg) once daily, and lopinavir/ritonavir (LPV/RTV) (400/100 mg) twice daily, each with tenofovir (300 mg) once daily and a nucleoside reverse transcriptase inhibitor in treatment-experienced HIV-infected patients.

METHODS

Randomized, open-label, 48-week multicenter trial of 358 randomized adult patients who had failed two or more prior HAART regimens with baseline HIV RNA > or = 1000 copies/ml and CD4 cell count > or = 50 x 10(6) cells/l.

RESULTS

The primary efficacy endpoint [plasma HIV RNA reduction assessed by time-averaged difference (TAD)] was similar for ATV/RTV and LPV/RTV [TAD 0.13; 97.5% confidence interval, -0.12 to 0.39] at 48 weeks. Mean reductions from baseline for ATV/RTV and LPV/RTV were comparable at 1.93 and 1.87 log10 copies/ml, respectively. Mean CD4 cell count increases were 110 and 121 x 10(6) cells/l for ATV/RTV, and LPV/RTV, respectively. The efficacy of ATV/SQV was lower than LPV/RTV by both these parameters. Declines in total cholesterol and fasting triglycerides were greater with ATV/RTV and ATV/SQV than with LPV/RTV (P < or = 0.005). Lipids in the LPV/RTV arm at week 48 generally increased from baseline. Lipid-lowering agents were used more frequently in the LPV/RTV arm than in the ATV arms (P < 0.05 versus ATV/RTV), as were antidiarrheal agents (P < or = 0.04 versus both ATV treatments). No new or unique safety findings emerged.

CONCLUSIONS

ATV boosted with RTV is as effective and well tolerated as LPV/RTV in treatment-experienced patients, with a more favorable impact on serum lipids. Pharmacokinetically enhanced ATV provides a suitable choice for therapy of treatment-experienced HIV-infected patients.

Analysis of HIV- type 1 protease and reverse transcriptase in Brazilian children failing highly active antiretroviral therapy (HAART)

The aim of this study was to evaluate the genotypic resistance profiles of HIV-1 in children failing highly active antiretroviral therapy (HAART). Forty-one children (median age = 67 months) receiving HAART were submitted to genotypic testing when virological failure was detected. cDNA was extracted from PBMCs and amplified by nested PCR for the reverse transcriptase and protease regions of the pol gene. Drug resistance genotypes were determined from DNA sequencing. According to the genotypic analysis, 12/36 (33.3%) and 6/36 (16.6%) children showed resistance and possible resistance, respectively, to ZDV; 5/36 (14%) and 4/36 (11.1%), respectively, showed resistance and possible resistance to ddI; 4/36 (11.1%) showed resistance to 3TC and D4T; and 3/36 (8.3%) showed resistance to Abacavir. A high percentage (54%) of children exhibited mutations conferring resistance to NNRTI class drugs. Respective rates of resistance and possible resistance to PIs were: RTV (12.2%, 7.3%); APV (2.4%, 12.1%); SQV(0%, 12.1%); IDV (14.6%, 4.9%), NFV (22%, 4.9%), LPV/RTV (2.4%, 12.1%). Overall, 37/41 (90%) children exhibited virus with mutations related to drug resistance, while 9% exhibited resistance to all three antiretroviral drug classes.

Differential maintenance of the M184V substitution in the reverse transcriptase of human immunodeficiency virus type 1 by various nucleoside antiretroviral agents in tissue culture

The M184V substitution in human immunodeficiency virus type 1 reverse transcriptase (RT) is rapidly selected in tissue culture following serial passage of wild-type virus in the presence of increasing concentrations of lamivudine (3TC). M184V is also associated with several alterations of RT enzymatic function in vitro that may adversely affect viral fitness or replication capacity, which creates a potential rationale for its maintenance once it has been selected by antiviral chemotherapy. However, the relative effectiveness of nucleoside RT inhibitors that are structurally unrelated to 3TC in selecting and/or maintaining M184V has not been investigated. In the present study, we have studied the abilities of a variety of drugs, i.e., zalcitabine (ddC), didanosine (ddI), abacavir (ABC), and the novel nucleoside SPD754, in addition to 3TC, to maintain the presence of M184V in tissue culture and have shown that SPD754, ABC, and 3TC are able to preserve M184V in mixed dual infections consisting of wild-type viruses and clinical isolates which contained the M184V mutation. Moreover, M184V could also be maintained in these cultures when a subtherapeutic concentration of 3TC (i.e., 0.05 microM) was used. In contrast, neither ddI nor ddC was able to maintain M184V to the same extent as the other drugs after 10 weeks of tissue culture in mixtures of wild-type viruses and isolates containing M184V in different proportions.