Phenotypic susceptibility and virological outcome in nucleoside-experienced patients receiving three or four antiretroviral drugs

Regimen selection in the OPTIONS trial of HIV salvage therapy: drug resistance, prior therapy, and race-ethnicity determine the degree of regimen complexity

BACKGROUND

Regimen selection for highly treatment-experienced patients is complicated.

METHODS

Using a web-based utility, study team members reviewed antiretroviral (ARV) history and resistance data and recommended individual ARV regimens and nucleoside reverse transcriptase inhibitor (NRTI) options for treatment-experienced participants consisting of 3-4 of the following agents: raltegravir (RAL), darunavir (DRV)/ritonavir, tipranavir (TPV)/ritonavir, etravirine (ETR), maraviroc (MVC), and enfuvirtide (ENF). We evaluated team recommendations and site selection of regimen and NRTIs. Associations between baseline factors and the selection of a complex regimen (defined as including four ARV agents or ENF) were explored with logistic regression.

RESULTS

A total of 413 participants entered the study. Participants initiated the first or second recommended regimen 86% of the time and 21% of participants started a complex regimen. In a multivariable model, ARV resistance to NRTI (odds ratio [OR] = 2.2), non-nucleoside reverse transcriptase inhibitor (NNRTI, OR = 6.2) or boosted protease inhibitor (PI, OR = 6.6), prior use of integrase strand transfer inhibitor (INSTI, OR = 25), and race-ethnicity (all P ≤ 0.01) were associated with selection of a complex regimen. Black non-Hispanic (OR = 0.5) and Hispanic participants from the continental US (OR = 0.2) were less likely to start a complex regimen, compared to white non-Hispanics.

CONCLUSIONS

In this multi-center trial, we developed a web-based utility that facilitated treatment recommendations for highly treatment-experienced patients. Drug resistance, prior INSTI use, and race-ethnicity were key factors in decisions to select a more complex regimen.

In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis

BACKGROUND

Effectiveness of ART regimens strongly depends upon complex interactions between the selective pressure of drugs and the evolution of mutations that allow or restrict drug resistance.

METHODS

Four clinical isolates from NRTI-exposed, NNRTI-naive subjects were passaged in increasing concentrations of NVP in combination with 1 µM 3 TC and 2 µM ADV to assess selective pressures of multi-drug treatment. A novel parameter inference procedure, based on a stochastic viral growth model, was used to estimate phenotypic resistance and fitness from in vitro combination passage experiments.

RESULTS

Newly developed mathematical methods estimated key phenotypic parameters of mutations arising through selective pressure exerted by 3 TC and NVP. Concentrations of 1 µM 3 TC maintained the M184V mutation, which was associated with intrinsic fitness deficits. Increasing NVP concentrations selected major NNRTI resistance mutations. The evolutionary pathway of NVP resistance was highly dependent on the viral genetic background, epistasis as well as stochasticity. Parameter estimation indicated that the previously unrecognized mutation L228Q was associated with NVP resistance in some isolates.

CONCLUSION

Serial passage of viruses in the presence of multiple drugs may resemble the selection of mutations observed among treated individuals and populations in vivo and indicate evolutionary preferences and restrictions. Phenotypic resistance estimated here "in silico" from in vitro passage experiments agreed well with previous knowledge, suggesting that the unique combination of "wet-" and "dry-lab" experimentation may improve our understanding of HIV-1 resistance evolution in the future.

Bacterial pore-forming proteins as anthelmintics

Crystal (Cry) proteins are made by the Gram-positive bacterium Bacillus thuringiensis (Bt). Cry proteins are pore-forming proteins and are the most widely used biological insecticides in the world. Our laboratory found some Cry proteins are highly effective against a broad range of nematodes (roundworms). Here, we discuss our results of Cry protein activity against intestinal roundworms. Both Cry5B and Cry21A have therapeutic activities against infections of the roundworm Heligmosomoides polygyrus bakeri in mice. Cry5B also shows highly therapeutic activity against Ancylostoma ceylanicum infection in hamsters. A. ceylanicum is a minor hookworm parasite of humans, and it is closely related to the more prevalent Ancylostoma duodenale. In addition, Cry proteins show excellent combinatorial therapeutic properties with nicotinic acetylcholine receptor (nAChR) agonists, one of the two classes of compounds approved by the World Health Organization for the treatment for intestinal roundworms in humans. Given their non-toxicity to humans and their broad spectrum of nematicidal action, Cry proteins show great potential as next-generation anthelmintics.

Predictive value of HIV-1 replication capacity and phenotypic susceptibility scores in antiretroviral treatment-experienced patients

OBJECTIVES

The aim of the study was to determine the prognostic value of HIV replication capacity (RC) for subsequent antiretroviral (ARV) treatment response in ARV-experienced patients.

METHODS

RC and phenotypic resistance testing were performed at baseline and week 12 on plasma samples from patients randomized to undergo a 12-week ARV drug-free period (ARDFP) or initiate immediate salvage therapy (no-ARDFP group) in the Options in Management with Antiretrovirals (OPTIMA) trial. Dichotomous and incremental phenotypic susceptibility scores (dPSSs and iPSSs, respectively) were calculated. The predictive value of RC and PSS for ARV therapy response and/or ARDFP was evaluated using multivariate regression analysis and Pearson correlations.

RESULTS

In 146 no-ARDFP subjects, baseline RC (50.8%) did not change at week 12 and was not correlated with CD4 cell count or viral load changes at week 12 (P=0.33 and P=0.79, respectively) or at week 24 (P=0.96 and P=0.14, respectively). dPSS predicted virological but not CD4 cell count response to ARV therapy at weeks 12, 24 and 48 (P=0.002, P<0.001 and P=0.005, respectively). RC was significantly correlated with dPSS and iPSS at baseline, but did not increase their predictive value. In the 137 ARDFP patients, RC increased significantly (from 52.4 to 85.8%), but did not predict CD4 cell count and viral load changes during ARDFP (P=0.92 and P=0.26, respectively). RC after ARDFP did not predict subsequent CD4 cell count and viral load changes 12 weeks following ARV treatment reinitiation (P=0.90 and P=0.29, respectively).

CONCLUSIONS

We found no additional predictive value of replication capacity for virological or immunological responses (above what PSS provides) in patients undergoing salvage ARV treatment.

Clinical cut-offs for HIV-1 phenotypic resistance estimates: update based on recent pivotal clinical trial data and a revised approach to viral mixtures

The clinical utility of HIV-1 resistance testing is dependent upon accurate interpretation and application of results. The development of clinical cut-offs (CCOs) for most HIV antiretroviral drugs assessed by the vircoTYPE HIV-1 resistance test has been described previously. Updated CCOs based on new methodology and new data from clinical cohorts and pivotal clinical studies are presented in this communication. Data for analysis included the original records for CCO derivation from eight clinical trials and two cohort studies plus new records from the clinical cohorts and from the TITAN, POWER, and DUET clinical studies. Drug-specific linear regression models were developed to describe the relationship between baseline characteristics (phenotypic resistance as estimated by virtualPhenotype-LM using methods revised recently for handling mixed viral sequences; viral load; and treatment history), new treatment regimen, and 8-week virologic outcome. The clinical cut-offs were defined as the estimated phenotypic resistance levels (fold change, FC) associated with a 20% and 80% loss of drug activity. The development dataset included 6550 records with an additional 2299 reserved for validation. The updated, v.4.2 CCOs were generally close to the v4.1 values, with a trend observed toward marginally higher cut-offs for the NRTIs. These results suggest that the updated CCOs provide a relevant tool for estimating the contribution to virological response of individual antiviral drugs in antiretroviral drug combinations as used currently in clinical practice.

Determination of clinically relevant cutoffs for HIV-1 phenotypic resistance estimates through a combined analysis of clinical trial and cohort data

BACKGROUND

Clinically relevant cutoffs are needed for the interpretation of HIV-1 phenotypic resistance estimates as predicted by "virtual" phenotype HIV resistance analysis.

METHODS

Using a clinical data set containing 2596 treatment change episodes in 2217 patients in 8 clinical trials and 2 population-based cohorts, drug-specific linear regression models were developed to describe the relation between baseline characteristics (resistance, viral load, and treatment history), new treatment regimen selected, and 8-week virologic outcome.

RESULTS

These models were used to derive clinical cutoffs (CCOs) for 6 nucleoside/nucleotide reverse transcriptase inhibitors (zidovudine, lamivudine, stavudine, didanosine, abacavir, and tenofovir), 3 unboosted protease inhibitors (PIs; indinavir, amprenavir, and nelfinavir), and 4 ritonavir-boosted PIs (indinavir/ritonavir, amprenavir/ritonavir, saquinavir/ritonavir, lopinavir/ritonavir). The CCOs were defined as the phenotypic resistance levels (fold change [FC]) associated with a 20% and 80% loss of predicted wild-type drug effect and depended on the drug-specific dynamic range of the assay.

CONCLUSIONS

The proposed CCOs were better correlated with virologic response than were biological cutoffs and provide a relevant tool for estimating the resistance to antiretroviral drug combinations used in clinical practice. They can be applied to diverse patient populations and are based on a consistent methodologic approach to interpreting phenotypic drug resistance.

Association of efavirenz hypersusceptibility with virologic response in ACTG 368, a randomized trial of abacavir (ABC) in combination with efavirenz (EFV) and indinavir (IDV) in HIV-infected subjects with prior nucleoside analog experience

PURPOSE

To evaluate the association of efavirenz hypersusceptibility (EFV-HS) with clinical outcome in a double-blind, placebo-controlled, randomized trial of EFV plus indinavir (EFV+IDV) vs. EFV+IDV plus abacavir (ABC) in 283 nucleoside-experienced HIV-infected patients.

METHOD AND RESULTS

Rates of virologic failure were similar in the 2 arms at week 16 (p = .509). Treatment discontinuations were more common in the ABC arm (p = .001). Using logistic regression, there was no association between virologic failure and either baseline ABC resistance or regimen sensitivity score. Using 3 different genotypic scoring systems, EFV-HS was significantly associated with reduced virologic failure at week 16, independent of treatment assignment. In some patients on the nucleoside-sparing arm, the nucleoside-resistance mutation L74V was selected for in combination with the uncommonly occurring EFV-resistance mutations K103N+L100I; L74V was not detected as a minority variant, using clonal sequence analysis, when the nucleoside-sparing regimen was initiated.

CONCLUSION

Premature treatment discontinuations in the ABC arm and the presence of EFV-HS HIV variants in this patient population likely made it difficult to detect a benefit of adding ABC to EFV+IDV. In addition, L74V, when combined with K103N+L100I, may confer a selective advantage to the virus that is independent of its effects on nucleoside resistance.

[Recommendations from the GESIDA/Spanish AIDS Plan regarding antiretroviral treatment in adults with human immunodeficiency virus infection (update January 2007)]

OBJECTIVE

This consensus document is an update of antiretroviral therapy (ART) recommendations for adult patients infected with the human immunodeficiency virus (HIV-1).

METHODS

To formulate these recommendations, a panel composed of members of the Grupo de Estudio de Sida (GESIDA; AIDS Study Group) and the Plan Nacional sobre el Sida (PNS; Spanish AIDS Plan) reviewed the advances in the current understanding of the pathophysiology of HIV, the safety and efficacy findings from clinical trials, and the results from cohort and pharmacokinetic studies published in biomedical journals or presented at scientific meetings over the last years. Three levels of evidence were defined according to the source of the data: randomized studies (level A), cohort or case-control studies (level B), and expert opinion (level C). The decision to recommend, consider or not recommend ART was established in each situation.

RESULTS

Currently, the treatment of choice for chronic HIV infection is the combination of three drugs of two different classes, including 2 nucleosides or nucleotide analogs (NRTI) plus 1 non-nucleoside (NNRTI) or 1 boosted protease inhibitor (PI/r). Initiation of ART is recommended in patients with symptomatic HIV infection. In asymptomatic patients, initiation of ART is recommended on the basis of CD4+ lymphocyte counts and plasma viral load, as follows: 1) therapy should be started in patients with CD4+ counts of < 200 cells/microl; 2) therapy should be started in most patients with CD4+ counts of 200-350 cells/microl, although it can be delayed when CD41 count persists at around 350 cells/microL and viral load is low, and 3) initiation of therapy can be delayed in patients with CD4+ counts of > 350 cells/microL. The initial objective of ART is to achieve an undetectable viral load. Adherence to therapy plays an essential role in maintaining the antiviral response. Therapeutic options are limited with the development of cross resistance and ART failure. Genotype studies are useful in these cases. More information regarding the studies analyzed and the panel recommendations for adherence, toxicity, treatment during pregnancy, patients with hepatitis B or C virus co-infection, and post-exposure prophylaxis can be accessed at www.gesida.seimc.org.

CONCLUSIONS

CD4+ lymphocyte count is the most important reference factor for initiating ART in asymptomatic patients. The large number of available drugs, the increased sensitivity of tests to monitor viral load, and the ability to determine viral resistance is leading to a more individualized approach to therapy.

Interactions between non-nucleoside reverse transcriptase inhibitor and nucleoside reverse transcriptase inhibitor mutations: phenotypes and mechanisms

PURPOSE OF REVIEW

Antiretroviral regimens that combine nucleoside reverse transcriptase inhibitors and non-nucleoside reverse transcriptase inhibitors have consistently been the most effective regimens for the initial treatment of HIV-1 infection. Such combinations have been manufactured in several fixed-dose combinations and are the most commonly used treatments worldwide. The success of these regimens may partly be a result of the synergistic manner in which the two classes of compounds inhibit the HIV-1 reverse transcriptase enzyme.

RECENT FINDINGS

Multiple synergistic effects have been described in the mechanisms and pathways of drug resistance. This review outlines what is currently known about the interactions between nucleoside reverse transcriptase inhibitor and non-nucleoside reverse transcriptase inhibitor resistance.

SUMMARY

These synergistic interactions are likely to be the driving force behind the potency and durability of the nucleoside reverse transcriptase inhibitor/non-nucleoside reverse transcriptase inhibitor combinations used in clinical practice.

Immunovirologic characteristics of human immunodeficiency virus-infected patients consisting mainly of injecting drug users on highly active antiretroviral treatment with prolonged virologic failure

Immunovirologic parameters of 24 heavily antiretroviral drug-pretreated patients with prolonged virologic treatment failure under highly active antiretroviral therapy, and who harbored highly resistant human immunodeficiency virus (HIV) isolates, were studied in this retrospective cross-sectional study. Most of the patients were injecting drug users (71%) and male (88%). All patients were studied for CD4(+) cell count, HIV viral load, resistance mutations, and viral phenotype. The patients showed a high accumulation of resistance-associated mutations, their CD4(+) cell count and viral load directly correlated with their respective values at initiation of therapy, and the presence of K103N was inversely associated with lower viral load. On the other hand, patients with K103N had the same level of CD4(+) cell count compared with patients without this mutation. Among the patients, a majority with a specific viral phenotype was not present. Rather, a dual-tropic virus was found most frequently, suggesting a preferential suppression of X4-specific strains and less cytopathogenicity during antiretroviral therapy and a greater proportion of R5X4 viruses due to an adaptation to that pressure.

Efavirenz/emtricitabine/tenofovir disoproxil fumarate fixed-dose combination: first-line therapy for all?

ATRIPLA (Bristol-Myers Squibb and Gilead Sciences) is a complete regimen in a single, fixed-dose combination tablet that contains: efavirenz 600 mg, emtricitabine 200 mg and tenofovir disoproxil fumarate 300 mg. Current treatment guidelines recommend this triple combination for initial therapy because of its excellent potency, tolerability and favorable safety profile. Individually, these agents have long half-lifes that allow for once-daily dosing and may provide a pharmacologic bridge for the occasional missed dose. Although several options for once-daily regimens are available, comparative clinical trials are still in progress. This article reviews relevant efficacy and safety data of efavirenz, emtricitabine and tenofovir disoproxil fumarate, compared with other once-daily agents or certain common alternate drugs presently used as initial therapy in treatment-naive patients.

Barriers to accessing antiretroviral therapy in Kisesa, Tanzania: a qualitative study of early rural referrals to the national program

This community-based, qualitative study conducted in rural Kisesa District, Tanzania, explores perceptions and experiences of barriers to accessing the national antiretroviral programme among self-identified HIV-positive persons. Part of wider operations research around local introduction of HIV therapy, the study involved consultation with villagers and documented early referrals' progress through clinical evaluation and, if eligible, further training and drug procurement. Data collection consisted of 16 participatory group discussions with community members and 18 in-depth interviews with treatment-seekers. Although participants welcomed antiretroviral therapy, they feared that transportation and supplementary food costs, the referral hospital's reputation for being unfriendly and confusing, and difficulties in sustaining long-term treatment would limit accessibility. Fear of stigma framed all concerns, posing challenges for contacting referrals who did not want their status disclosed or expressed reluctance to identify a "treatment buddy" as required by the programme. To mitigate logistical barriers, transportation costs were paid and hospital visits facilitated. Participants reported satisfaction with eligibility testing, finding the process easier than anticipated. Most were willing to join a support group and some changed attitudes toward disclosure. However, both experienced and anticipated discrimination continue to hinder widespread antiretroviral therapy (ART) uptake. While simple measures to reduce perceived barriers improved initial access to treatment and helped overcome anxiety among early referrals, pervasive stigma remains the most formidable barrier. Encouraging successful referrals to share their positive experiences and contribute to nascent community mobililzation could start to address this seemingly intractable problem.

Approach to salvage antiretroviral therapy in heavily antiretroviral-experienced HIV-positive adults

Despite dramatic declines in HIV-associated morbidity and mortality as a result of highly active antiretroviral therapy, management of heavily treatment-experienced patients remains complex and challenging. Treatment response rates with subsequent antiretroviral regimens are lower than with initial antiretroviral therapy. Additionally, increased mortality has been associated with multidrug-resistant HIV. We review data relevant to management of such patients and offer a systematic approach to constructing a salvage antiretroviral regimen.

[Clinical use of HIV-1 resistance genotyping. Predictive factors of poor virological evolution in salvage treatments]

OBJECTIVES

To describe the use of genotype resistance testing (GRT) for virological failure in clinical practice, and the long-term clinical and virological evolution in patients for whom it is requested. To identify the predictive factors of virological failure in patients with antiretroviral (ARV) salvage therapy.

METHODS

Observational study in HIV-infected patients for whom GRT was requested for virological failure (VF) in the period of 1 October 1999 to 31 December 2001. Logistic regression analysis was used to determine the predictive factors of virological progression.

RESULTS

Over the period studied, 196 patients required GRT for VF (15%) among those monitored in specific units. GRT was mainly requested for patients who had been extensively pretreated for a mean of 5 years and with a median of 5 ARV combinations. Half the patients presented 3 or more mutations associated with thymidine analogs (TAMs), mutations associated with non-nucleoside analogs (NNRTIs), and 5 or more mutations associated with protease inhibitors (PIs). In 143 (74%) patients, the RTV regimen was changed on the basis of GRT results. In the intent-to-treat analysis, the percentage of patients with plasma VL < 400 cop/mL at 6, 12 and 18 months was 41%, 29% and 17%, respectively. In the on-treatment analysis, the results were 50%, 48% and 46%, respectively. Mean CD4 lymphocyte increase was 59.74 and 94 cells/mm 3. The variables predicting virological failure (plasma VL > 400 cop/mL) at 12 months were plasma VL > 30,000 cop/mL (OR 6, 1.8-19.5) and accumulation of 3 or more TAMs (OR 4.4, 1.3-15) at the start of ARV salvage therapy.

CONCLUSION

Even though in clinical practice GRT is requested for patients with various treatment failures, when ART salvage treatment was started, plasma VL was undetectable and immunological response persisted in 40% of patients followed-up for 18 months. The factors best predicting virological evolution were VL and the number of baseline TAMs.

Reverse transcriptase mutations 118I, 208Y, and 215Y cause HIV-1 hypersusceptibility to non-nucleoside reverse transcriptase inhibitors

BACKGROUND

HIV-1 hypersusceptibility to non-nucleoside reverse transcriptase inhibitors (NNRTI) improves the response to NNRTI-containing regimens. The genetic basis for NNRTI hypersusceptibility was partly defined in our earlier analyses of a paired genotype-phenotype dataset of viral isolates from treatment-experienced patients, in which we identified reverse transcriptase mutations V118I, H208Y, and T215Y as being strongly associated with NNRTI hypersusceptibility.

OBJECTIVES

We evaluated the role of these mutations in NNRTI hypersusceptibility by site-directed mutagenesis and phenotypic analysis of HIV-1 recombinants.

METHODS

Drug susceptibility and replication capacity were determined in single cycle assays. Hypersusceptibility was defined by a statistically significant (P < 0.01; Student's t-test) mean fold-change in 50% inhibitory concentration (IC50) of less than 0.4.

RESULTS

The single mutations V118I, H208Y, and T215Y did not show hypersusceptibility to efavirenz with mean fold-change of 0.58, 0.55, and 0.70, respectively (P < 0.01 and P = 0.12). The H208Y/T215Y and V118I/H208Y/T215Y mutants showed marked hypersusceptibility to efavirenz, having mean fold-change values of 0.27 and 0.20, respectively (P < 0.001). In addition, H208Y/T215Y, V118I/T215Y, and V118I/H208Y/T215Y were hypersusceptible to delavirdine and nevirapine. The V118I/T215Y mutant was not replication impaired; whereas H208Y/T215Y and V118I/H208Y/T215Y had significantly (P < 0.01) reduced replication capacities of 40 and 35% of wild-type, respectively.

CONCLUSION

Different combinations of V118I, H208Y, and T215Y produce NNRTI hypersusceptibility. The V118I/T215Y mutant is hypersusceptible to delavirdine and nevirapine without reduced replication capacity, whereas the H208Y/T215Y and V118I/H208Y/T215Y mutants are hypersusceptible to all NNRTI and show impaired replication. These findings suggest that more than one mechanism is involved in NNRTI hypersusceptibility.

Role of the Inhibitory Quotient in HIV Therapy

A systemic review is presented of all studies that have evaluated the inhibitory quotient (IQ). The IQ is defined as the ratio between (trough) drug concentration and level of drug resistance of the HIV isolate. From the studies presented, it can be concluded that for protease inhibitors (PIs) and efavirenz, the phenotypic IQ is associated with virological response. The genotypic IQ (GIQ) for PIs was also demonstrated to be associated with virological response. An intrinsic limitation of the GIQ is that it is only applicable for PIs, of which resistance is based on the cumulative effect of mutations. As the IQ can be modified by adjustment of the drug dosage, it may be of clinical value. Its application in patient care should therefore be further investigated.

Nonnucleoside reverse transcriptase inhibitor phenotypic hypersusceptibility can be demonstrated in different assays

BACKGROUND

HIV-1 isolates harboring multiple nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations are more susceptible ("hypersusceptible") to the nonnucleoside reverse transcriptase inhibitors (NNRTIs) than isolates lacking NRTI resistance mutations, but this has only been reported with a single-cycle replication phenotypic assay. In fact, there was a report that a commercial multicycle assay did not readily detect hypersusceptibility.

OBJECTIVE

To see whether NNRTI hypersusceptibility can be demonstrated in other types of phenotypic assays, including multicycle assays and enzyme inhibition assays.

METHODS

The susceptibility of HIV-1 clones derived from different patients in multicycle assays was tested in peripheral blood mononuclear cells (PBMCs) and in an established cell line. In addition, the reverse transcriptase (RT) of many of these clones was expressed and their susceptibility tested in an RT inhibition assay. Nevirapine and efavirenz susceptibilities were tested and compared with a control wild-type virus or RT.

RESULTS

Hypersusceptibility to nevirapine and efavirenz was detected using each of the methods described above. R values correlating the other methods with single-cycle assay values were between 0.66 and 0.96. In addition to the high correlations, the different methods gave similar numeric results.

CONCLUSIONS

NNRTI hypersusceptibility is readily seen in multicycle susceptibility assays and in enzyme inhibition assays.

Efavirenz for HIV-1 infection in adults: an overview

Efavirenz (Sustiva), Bristol-Myers Squibb) is a non-nucleoside reverse transcriptase inhibitor that has been used successfully since the late 1990s to treat HIV-1 infection, and has since become a cornerstone of antiretroviral therapy. The efficacy and potency of efavirenz has been established in many clinical trials and cohort studies, where it has been compared with unboosted or ritonavir (Norvir, Abbott Laboratories Ltd)-boosted protease inhibitors, nevirapine (Viramune, Boehringer Ingelheim Ltd); and three nucleoside analog-based regimens. Pharmacokinetics allowing for a convenient once-daily administration make efavirenz one of the first agents to be included in once-daily regimens. Tolerability of efavirenz is satisfactory, although CNS-related toxicity can occur, and is still poorly understood. New insights into the pharmacokinetics of efavirenz could help to manage this unwanted toxicity. This drug profile will examine the principal data concerning the efficacy, pharmacokinetics and safety that have made efavirenz a standard of care in HIV-1 therapy, and will comment on new data that could change the way efavirenz is used in the near future.

Correlation between rules-based interpretation and virtual phenotype interpretation of HIV-1 genotypes for predicting drug resistance in HIV-infected individuals

Drug resistance testing provides useful information for managing HIV-infected patients. Phenotyping could add complementary information to genotyping and occasionally be more useful, although is less available to clinicians. Large paired geno-pheno databases have allowed the prediction of phenotypes from genotypes. However, the accuracy of these virtual phenotypes (vPT) in a clinical setting has not been well assessed yet. We analyzed the concordance between vPT and interpreted genotype (GT) in 105 samples belonging to treatment-experienced HIV-infected patients. A high concordance was seen when examining both non-nucleoside reverse transcriptase inhibitors (NNRTI) and protease inhibitors (PI) (r = 0.95 either), while it was lower for nucleoside analogs (r = 0.79). The drugs with lower concordance were abacavir (71.1%), tenofovir (71.5%) and didanosine (71.9%). In 20% of specimens (21/105), the vPT did not provide results for all approved drugs. These were mainly samples with a high number of drug resistance mutations or rare genotypes, which seem to be underepresented in the VircoNET database. Overall, there is good correlation between vPT/GT, especially for PI and NNRTI. The inclusion of additional sequences in the VircoNET database, mainly those derived from heavily treatment-experienced patients and/or from patients failing the most recently approved drugs might improve its performance.

Genetic correlates of efavirenz hypersusceptibility

BACKGROUND

Non-nucleoside reverse transcriptase inhibitor (NNRTI) hypersusceptibility is seen in approximately 30% of HIV isolates with nucleoside reverse transcriptase inhibitor (NRTI) resistance. NNRTI hypersusceptibility has been associated with improved outcomes to NNRTI-based therapy.

OBJECTIVE

To determine the genetic correlates of efavirenz hypersusceptibility.

METHODS

Paired baseline genotypes and phenotypes were obtained from 444 NRTI-experienced, NNRTI-naive patients. Fisher's exact tests, recursive partitioning (classification and regression trees; CART), and stepwise binary regression were used to identify specific reverse transcriptase (RT) mutations associated with efavirenz hypersusceptibility.

RESULTS

In univariate analyses, 26 RT codons were associated with efavirenz hypersusceptibility (P < 0.05), the top five were 215 > 41 > 210 > 118 > 208 (all P < 0.000001). From stepwise model selection, the 215, 208 and 118 mutations remained independently predictive of efavirenz hypersusceptibility. A final binary regression model to predict efavirenz hypersusceptibility included one covariate for the 215 mutation (relative risk 2.6, P < 0.0001) and a second covariate representing either the 208 or 118 mutation (relative risk 1.8, P < 0.0001). Similarly, in a CART analysis, a mutation at codon 215 was the first split selected, followed by mutations at 208 and 118. An efavirenz hypersusceptibility genotypic score using the three mutations 208, 118 and 215 was as accurate at predicting efavirenz hypersusceptibility as a more complex scoring system using 26 mutations.

CONCLUSION

Mutations at 215, 208 and 118 were independently associated with NNRTI hypersusceptibility. After confirmatory studies using other large datasets, incorporating a hypersusceptibility score into genotype interpretation algorithms will improve the prediction of NNRTI hypersusceptibility.

Natural variation of drug susceptibility in wild-type human immunodeficiency virus type 1

Wild-type viruses from the ViroLogic phenotype-genotype database were evaluated to determine the upper confidence limit of the drug susceptibility distributions, or "biological cutoffs," for the PhenoSense HIV phenotypic drug susceptibility assay. Definition of the natural variation in drug susceptibility in wild-type human immunodeficiency virus (HIV) type 1 isolates is necessary to determine the prevalence of innate drug resistance and to assess the capability of the PhenoSense assay to reliably measure subtle reductions in drug susceptibility. The biological cutoffs for each drug, defined by the 99th percentile of the fold change in the 50% inhibitory concentration distributions or the mean fold change plus 2 standard deviations, were lower than those previously reported for other phenotypic assays and lower than the clinically relevant cutoffs previously defined for the PhenoSense assay. The 99th percentile fold change values ranged from 1.2 (tenofovir) to 1.8 (zidovudine) for nucleoside reverse transcriptase RT inhibitors (RTIs), from 3.0 (efavirenz) to 6.2 (delavirdine) for nonnucleoside RTIs, and from 1.6 (lopinavir) to 3.6 (nelfinavir) for protease inhibitors. To evaluate the potential role of intrinsic assay variability in the observed variations in the drug susceptibilities of wild-type isolates, 10 reference viruses with different drug susceptibility patterns were tested 8 to 30 times each. The median coefficients of variation in fold change for the reference viruses ranged from 12 to 18% for all drugs except zidovudine (32%), strongly suggesting that the observed differences in wild-type virus susceptibility to the different drugs is related to intrinsic virus variability rather than assay variability. The low biological cutoffs and assay variability suggest that the PhenoSense HIV assay may assist in defining clinically relevant susceptibility cutoffs for resistance to antiretroviral drugs.

Novel single-cell-level phenotypic assay for residual drug susceptibility and reduced replication capacity of drug-resistant human immunodeficiency virus type 1

Human immunodeficiency virus type 1 (HIV-1)-infected individuals who develop drug-resistant virus during antiretroviral therapy may derive benefit from continued treatment for two reasons. First, drug-resistant viruses can retain partial susceptibility to the drug combination. Second, therapy selects for drug-resistant viruses that may have reduced replication capacities relative to archived, drug-sensitive viruses. We developed a novel single-cell-level phenotypic assay that allows these two effects to be distinguished and compared quantitatively. Patient-derived gag-pol sequences were cloned into an HIV-1 reporter virus that expresses an endoplasmic reticulum-retained Env-green fluorescent protein fusion. Flow cytometric analysis of single-round infections allowed a quantitative analysis of viral replication over a 4-log dynamic range. The assay faithfully reproduced known in vivo drug interactions occurring at the level of target cells. Simultaneous analysis of single-round infections by wild-type and resistant viruses in the presence and absence of the relevant drug combination divided the benefit of continued nonsuppressive treatment into two additive components, residual virus susceptibility to the drug combination and selection for drug-resistant variants with diminished replication capacities. In some patients with drug resistance, the dominant circulating viruses retained significant susceptibility to the combination. However, in other cases, the dominant drug-resistant viruses showed no residual susceptibility to the combination but had a reduced replication capacity relative to the wild-type virus. In this case, simplification of the regimen might still allow adequate suppression of the wild-type virus. In a third pattern, the resistant viruses had no residual susceptibility to the relevant drug regimen but nevertheless had a replication capacity equivalent to that of wild-type virus. In such cases, there is no benefit to continued treatment. Thus, the ability to simultaneously analyze residual susceptibility and reduced replication capacity of drug-resistant viruses may provide a basis for rational therapeutic decisions in the setting of treatment failure.

Virological significance, prevalence and genetic basis of hypersusceptibility to nonnucleoside reverse transcriptase inhibitors

Nonnucleoside reverse transcriptase inhibitors (NNRTI) are used to treat HIV-infected individuals in combination with nucleoside analogues (NRTI) and protease inhibitors. Long-term treatment with antiretroviral agents results in the emergence of strains with decreased susceptibility (resistance) to the drugs and is one of the major factors in loss of drug efficacy. Conversely, there have been recent reports of HIV strains with increased susceptibility (hypersusceptibility) to NNRTIs. These isolates emerge in patients on long-term antiretroviral therapy particularly in individuals receiving NRTIs. The prevalence of NNRTI hypersusceptibility ranges between 17.5 and 50% in NRTI-treatment experienced compared to 10% in NRTI-naïve patients. There is an inverse correlation between NNRTI hypersusceptibility and phenotypic NRTI resistance and a direct correlation between the number of NRTI resistance mutations present in the HIV reverse transcriptase. Re-sensitisation of phenotypic NNRTI resistance has been reported by NRTI mutations and is not likely to be detected using genotypic resistance assays. Recent studies demonstrate that NNRTI hypersusceptible virus at baseline is likely to predict better virological outcomes in patients on NNRTI-based salvage regimens compared to patients with NNRTI susceptible virus. These studies have implications for the sequence of antiretroviral drug use where patients may benefit from NRTI therapy before the introduction of NNRTIs, however more studies are needed to examine this treatment rationale.