Altered Viral Fitness of HIV-1 Following Failure of Protease Inhibitor-Based Therapy:

Retrovirus Reverse Transcriptases Containing a Modified YXDD Motif

The YXDD motif, where X is a variable amino acid, is highly conserved among various viral RNA-dependent DNA polymerases. Mutations in the YXDD motif can abolish enzymatic activity, alter the processivity and fidelity of enzymes and decrease virus infectivity. This review provides a summary of the significant documented studies on the YXDD motif of HIV-1, simian immunodeficiency virus, feline immunodeficiency virus and murine leukaemia virus and the impact of mutation that this motif has had on viral pathogenesis and drug treatment.

In Vivo validation of a bioinformatics based tool to identify reduced replication capacity in HIV-1

Although antiretroviral drug resistance is common in treated HIV infected individuals, it is not a consistent indicator of HIV morbidity and mortality. To the contrary, HIV resistance-associated mutations may lead to changes in viral fitness that are beneficial to infected individuals. Using a bioinformatics-based model to assess the effects of numerous drug resistance mutations, we determined that the D30N mutation in HIV-1 protease had the largest decrease in replication capacity among known protease resistance mutations. To test this in silico result in an in vivo environment, we constructed several drug-resistant mutant HIV-1 strains and compared their relative fitness utilizing the SCID-hu mouse model. We found HIV-1 containing the D30N mutation had a significant defect in vivo, showing impaired replication kinetics and a decreased ability to deplete CD4+ thymocytes, compared to the wild-type or virus without the D30N mutation. In comparison, virus containing the M184V mutation in reverse transcriptase, which shows decreased replication capacity in vitro, did not have an effect on viral fitness in vivo. Thus, in this study we have verified an in silico bioinformatics result with a biological assessment to identify a unique mutation in HIV-1 that has a significant fitness defect in vivo.

The utilization of humanized mouse models for the study of human retroviral infections

The development of novel techniques and systems to study human infectious diseases in both an in vitro and in vivo settings is always in high demand. Ideally, small animal models are the most efficient method of studying human afflictions. This is especially evident in the study of the human retroviruses, HIV-1 and HTLV-1, in that current simian animal models, though robust, are often expensive and difficult to maintain. Over the past two decades, the construction of humanized animal models through the transplantation and engraftment of human tissues or progenitor cells into immunocompromised mouse strains has allowed for the development of a reconstituted human tissue scaffold in a small animal system. The utilization of small animal models for retroviral studies required expansion of the early CB-17 scid/scid mouse resulting in animals demonstrating improved engraftment efficiency and infectivity. The implantation of uneducated human immune cells and associated tissue provided the basis for the SCID-hu Thy/Liv and hu-PBL-SCID models. Engraftment efficiency of these tissues was further improved through the integration of the non-obese diabetic (NOD) mutation leading to the creation of NODSCID, NOD/Shi-scid IL2rγ^-/-, and NOD/SCID β2-microglobulin^null animals. Further efforts at minimizing the response of the innate murine immune system produced the Rag2^-/-γ_c^-/- model which marked an important advancement in the use of human CD34+ hematopoietic stem cells. Together, these animal models have revolutionized the investigation of retroviral infections in vivo.

Optimal timing and duration of induction therapy for HIV-1 infection

The tradeoff between the need to suppress drug-resistant viruses and the problem of treatment toxicity has led to the development of various drug-sparing HIV-1 treatment strategies. Here we use a stochastic simulation model for viral dynamics to investigate how the timing and duration of the induction phase of induction–maintenance therapies might be optimized. Our model suggests that under a variety of biologically plausible conditions, 6–10 mo of induction therapy are needed to achieve durable suppression and maximize the probability of eradicating viruses resistant to the maintenance regimen. For induction regimens of more limited duration, a delayed-induction or -intensification period initiated sometime after the start of maintenance therapy appears to be optimal. The optimal delay length depends on the fitness of resistant viruses and the rate at which target-cell populations recover after therapy is initiated. These observations have implications for both the timing and the kinds of drugs selected for induction–maintenance and therapy-intensification strategies.

Clinicians treating HIV infection must balance the need to suppress viral replication against the harmful side effects and significant cost of antiretroviral therapy. Inadequate therapy often results in the emergence of resistant viruses and treatment failure. These difficulties are especially acute in resource-poor settings, where antiretroviral agents are limited. This has prompted an interest in induction–maintenance (IM) treatment strategies, in which brief intensive therapy is used to reduce host viral levels. Induction is followed by a simplified and more easily tolerated maintenance regimen. IM approaches remain an unproven concept in HIV therapy. We have developed a mathematical model to simulate clinical responses to antiretroviral drug therapy. We account for latent infection, partial drug efficacy, cross-resistance, viral recombination, and other factors. This model accurately reflects expected outcomes under single, double, and standard three-drug antiretroviral therapy. When applied to IM therapy, we find that (1) IM is expected to be successful beyond 3 y under a variety of conditions; (2) short-term induction therapy is optimally started several days to weeks after the start of maintenance; and (3) IM therapy may eradicate some preexisting drug-resistant viral strains from the host. Our simulations may help develop new treatment strategies and optimize future clinical trials.

Clinical implications of discordant viral and immune outcomes following protease inhibitor containing antiretroviral therapy for HIV-infected children

Many HIV-infected children treated with protease inhibitors (PI) reconstitute immunity despite viral breakthrough predicting disease progression. We studied a unique cohort of PI treated children with advanced disease who demonstrated sustained CD4 T cell counts but median post therapy viral load rebounded to >4.0 log(10) copies/ml. Phylogenetic relationships between pre- and post-therapy viruses reveals significant bottlenecks for quasispecies with natural polymorphisms mapping outside of protease active site providing selective advantage for emergence. Among discordant subjects post-therapy viruses fell into two phenotypes; high viral loads (median >5.0 log(10) copies/ml) and attenuated post-therapy replication (median <4.0 log(10) copies/ml). Both groups showed similar degrees of CD4 T cell immune reconstitution and were similar to children who optimally suppressed virus to <400 copies/ml. Both high fit and low fit discordant response groups showed high reconstitution of naïve CD4 CD45RA T cells (median 388 and 357 cells/microl, respectively). Naïve T cells increases suggest virus replicating under PI selective pressure do not impair thymic output. If therapeutic options are limited, selection of therapy which allows immune reconstitution despite suboptimal viral control may be beneficial. This novel paradigm for virus/host interactions may lead to therapeutic approaches to attenuate viral pathogenesis.

A multidrug-resistant (MDR) HIV type 1 infection in a homosexual man and identified source patient

We report a case (IC) of multidrug-resistant (MDR) HIV-1 infection in which the identification of the source patient (S) was supported by phylogenetic analysis of the pol gene and by the similarity of env sequences. HIV isolates from IC and S were characterized as non-syncytium viruses: a X4 variant (R(11) E(26)) was identified in both cases according to the V3 loop sequence. The pol mutational profile of IC included multiple protease and reverse-transcriptase inhibitor mutations similar to those in S. The lamivudine/tenofovir/tipranavir/ritonavir/enfuvirtide association was effective for IC but not for S.

Clinical significance of human immunodeficiency virus type 1 replication fitness

The relative fitness of a variant, according to population genetics theory, is that variant's relative contribution to successive generations. Most drug-resistant human immunodeficiency virus type 1 (HIV-1) variants have reduced replication fitness, but at least some of these deficits can be compensated for by the accumulation of second-site mutations. HIV-1 replication fitness also appears to influence the likelihood of a drug-resistant mutant emerging during treatment failure and is postulated to influence clinical outcomes. A variety of assays are available to measure HIV-1 replication fitness in cell culture; however, there is no agreement regarding which assays best correlate with clinical outcomes. A major limitation is that there is no high-throughput assay that incorporates an internal reference strain as a control and utilizes intact virus isolates. Some retrospective studies have demonstrated statistically significant correlations between HIV-1 replication fitness and clinical outcomes in some patient populations. However, different studies disagree as to which clinical outcomes are most closely associated with fitness. This may be in part due to assay design, sample size limitations, and differences in patient populations. In addition, the strength of the correlations between fitness and clinical outcomes is modest, suggesting that, at present, it would be difficult to utilize these assays for clinical management.

Functional correlation between a novel amino acid insertion at codon 19 in the protease of human immunodeficiency virus type 1 and polymorphism in the p1/p6 Gag cleavage site in drug resistance and replication fitness

Population-based sequence analysis revealed the presence of a variant of human immunodeficiency virus type 1 (HIV-1) containing an insertion of amino acid Ile in the protease gene at codon 19 (19I) and amino acid substitutions in the protease at codons 21 (E21D) and 22 (A22V) along with multiple mutations associated with drug resistance, M46I/P63L/A71V/I84V/I93L, in a patient who had failed protease inhibitor (PI) therapy. Longitudinal analysis revealed that the P63L/A71V/I93L changes were present prior to PI therapy. Polymorphisms in the Gag sequence were only seen in the p1/p6 cleavage site at the P1' position (Leu to Pro) and the P5' position (Pro to Leu). To characterize the role of these mutations in drug susceptibility and replication capacity, a chimeric HIV-1 strain containing the 19I/E21D/A22V mutations with the M46I/P63L/A71V/I84V/I93L and p1/p6 mutations was constructed. The chimera displayed high-level resistance to multiple PIs, but not to lopinavir, and grew to 30% of that of the wild type. To determine the relative contribution of each mutation to the phenotypic characteristic of the virus, a series of mutants was constructed using site-directed mutagenesis. A high level of resistance was only seen in mutants containing the 19I/A22V and p1/p6 mutations. The E21D mutation enhanced viral replication. These results suggest that the combination of the 19I/E21D/A22V mutations may emerge and lead to high-level resistance to multiple PIs. The combination of the 19I/A22V mutations may be associated with PI resistance; however, the drug resistance may be caused by the presence of a unique set of mutations in the p1/p6 mutations. The E21D mutation contributes to replication fitness rather than drug resistance.

Biological characterization of human immunodeficiency virus type 1 subtype C protease carrying indinavir drug-resistance mutations

Human immunodeficiency virus type 1 subtype C isolates belong to one of the most prevalent strains circulating worldwide and are responsible for the majority of new infections in the sub-Saharan region and other highly populated areas of the globe. In this work, the impact of drug-resistance mutations in the protease gene of subtype C viruses was analysed and compared with that of subtype B counterparts. A series of recombinant subtype C and B viruses was constructed carrying indinavir (IDV)-resistance mutations (M46V, I54V, V82A and L90M) and their susceptibility to six FDA-approved protease inhibitor compounds (amprenavir, indinavir, lopinavir, ritonavir, saquinavir and nelfinavir) was determined. A different impact of these mutations was found when nelfinavir and lopinavir were tested. The IDV drug-resistance mutations in the subtype C protease backbone were retained for a long period in culture without selective pressure when compared with those in subtype B counterparts in washout experiments.

Virus fitness: concept, quantification, and application to HIV population dynamics

Viral fitness has been broadly studied during the past three decades, mainly to test evolutionary models and population theories difficult to analyze and interpret with more complex organisms. More recent studies, however, are focused in the role of fitness on viral transmission, pathogenesis, and drug resistance. Here, we used human immunodeficiency virus (HIV) as one of the most relevant models to evaluate the importance of viral quasispecies and fitness in HIV evolution, population dynamics, disease progression, and potential clinical implications.

Evolution of human immunodeficiency virus type 1 protease genotypes and phenotypes in vivo under selective pressure of the protease inhibitor ritonavir

We examined the population dynamics of human immunodeficiency virus type 1 pro variants during the evolution of resistance to the protease inhibitor ritonavir (RTV) in vivo. pro variants were followed in subjects who had added RTV to their previously failed reverse transcriptase inhibitor therapy using a heteroduplex tracking assay designed to detect common resistance-associated mutations. In most cases the initial variant appeared rapidly within 2 to 3 months followed by one or more subsequent population turnovers. Some of the subsequent transitions between variants were rapid, and some were prolonged with the coexistence of multiple variants. In several cases variants without resistance mutations persisted despite the emergence of new variants with an increasing number of resistance-associated mutations. Based on the rate of turnover of pro variants in the RTV-treated subjects we estimated that the mean fitness of newly emerging variants was increased 1.2-fold (range, 1.02 to 1.8) relative to their predecessors. A subset of pro genes was introduced into infectious molecular clones. The corresponding viruses displayed impaired replication capacity and reduced susceptibility to RTV. A subset of these clones also showed increased susceptibility to two nonnucleoside reverse transcriptase inhibitors and the protease inhibitor saquinavir. Finally, a significant correlation between the reduced replication capacity and reduced processing at the gag NC-p1 processing site was noted. Our results reveal a complexity of patterns in the evolution of resistance to a protease inhibitor. In addition, these results suggest that selection for resistance to one protease inhibitor can have pleiotropic effects that can affect fitness and susceptibility to other drugs.

The impact of the M184V substitution on drug resistance and viral fitness

Treatment of HIV/AIDS with antiretroviral therapy can result in HIV-1 drug resistance, limiting its use. Resistance mutations arise prior to therapy due to errors in HIV-1 replication, and are also spread by sexual and other modes of transmission. However, it is also generally believed that resistance is due to multiple drug mutations to any single or combination of antiretroviral agents selected during viral replication in the presence of incompletely suppressive drug regimens. In the case of protease inhibitors and most nucleoside analog reverse transcriptase inhibitors, drug resistance is due to the accumulation of mutations in the HIV-1 protease and reverse transcriptase genes respectively. However, in the case of non-nucleoside reverse transcriptase inhibitors, a single primary drug mutation is usually sufficient to abrogate antiviral activity. This is also true of certain specific mutations, such as M184V in the reverse transcriptase enzyme, resulting in resistance to the nucleoside analog, lamivudine (Epivir, GlaxoSmithKline). However, it is thought that lamivudine may still contribute to the effectiveness of antiretroviral therapy, even after the appearance of the M184V mutation. M184V may affect sensitivity to other drugs, such as zidovudine (Retrovir, GlaxoSmithKline), in HIV-1 variants that already contain resistance mutations to zidovudine, during concomitant treatment with lamivudine. M184V also has a positive effect on HIV-1 RT fidelity, reducing spontaneous HIV mutagenesis. Processivity of the reverse transcriptase enzyme may be affected by mutations such as M184V, and this may be a major determinant of viral replication fitness.

Virological and immunological impact of non-nucleoside reverse transcriptase inhibitor withdrawal in HIV-infected patients with multiple treatment failures

No significant changes in viral load and CD4 cell count were observed 2-4 weeks after the withdrawal of non-nucleoside reverse transcriptase inhibitors (NNRTI) from the current therapy of patients exhibiting resistance mutations to this class of drugs. The data suggest that in the presence of specific resistance mutations NNRTIexert no residual antiretroviral activity and could be withdrawn without viral rebound.

Changes in Viral Load in People with Virological Failure who Remain on the Same Haart Regimen

Objectives

To assess the rate of change in viral load and CD4 count over time in HIV-infected patients experiencing virological failure on a HAART regimen.

Design

Study population included patients from EuroSIDA, a large, multicentre, observational study enrolling HIV-infected patients across Europe.

Methods

Median change in viral load and CD4 count per month were estimated using the viral load and CD4 measurements obtained over a 12-month period after confirmed virological failure between 3 and 4 log10 copies/ml in a population of 488 HIV-infected patients who were left on a failing HAART regimen.

Results

The estimated median viral load change in our study population was 0.024 log10 copies/ml per month, statistically different from 0 (P=0.0001). In 20.9% of the patients studied viral load showed a tendency to decrease, in 47.8% showed a tendency to increase by a positive rate no higher than 0.04 log10 copies/ml per month and in the remaining 31.3% showed a tendency to increase by a rate greater than 0.04 log10 copies/ml per month. On average, CD4 counts were estimated to remain stable (decrease at a slow rate of about –0.53 cells/μl per month).

Conclusions

In patients that remained on a stable, but virologically failing HAART regimen (with viral load ranging 1000–10000 copies/ml), the viral load over the ensuing 12-month period increased at a relatively slow rate. In contrast, the CD4 count remained stable, possibly because of partial but sustained viral suppression below the viral load natural set-point. The time-course of selecting more replication-competent virus in patients with virological failure remains to be fully clarified.

HIV-1 Fitness and Replication Capacity: What Are They and Can They Help in Patient Management?

The natural history of HIV-1 infection is characterized by persistent viremia, progressive CD4 lymphopenia, and profound immune suppression resulting in opportunistic infections, neoplasms, and death. Introduction of combination antiretroviral therapy has been effective in suppressing HIV-1 replication, reversing immunodeficiency to a degree, reducing HIV-1-associated complications, and thereby prolonging life. One of the most vexing challenges of prolonged antiretroviral therapy is the development of drug resistance. Antiretroviral therapies fail in a substantial number of cases, often with emergence of HIV-1 variants encoding mutations that confer potent drug resistance to individual agents or entire drug classes. Resistance testing methods have been introduced to evaluate drug resistance, and several studies have reported clinical benefits of genotyping and phenotyping assays in clinical decision-making. However, the genetic variability of HIV-1 to develop resistance exceeds the antiretroviral armamentarium, and the number of patients with drug experience and resistance to all classes of antiretrovirals continues to grow. From a clinical standpoint, it would be useful to have a more comprehensive grasp of pathogenic determinants of HIV-1 in all patients. One proposed in vitro correlate of HIV-1 pathogenic potential is the replication capacity of HIV-1. New techniques to assess HIV-1 replication potential are in development, with a commercial assay now available to analyze clinical samples. In this review we explore the experimental basis for replication capacity measurements and potential clinical applications of this methodology.

Nelfinavir-resistant, amprenavir-hypersusceptible strains of human immunodeficiency virus type 1 carrying an N88S mutation in protease have reduced infectivity, reduced replication capacity, and reduced fitness and process the Gag polyprotein precursor aberrantly

The evolution of human immunodeficiency virus type 1 (HIV-1) strains with reduced susceptibility to protease inhibitors (PIs) is a major cause of PI treatment failure. A subset of subjects failing a therapy regimen containing the PI nelfinavir developed mutations at position 88 in the protease region. The N88S mutation occurring in some of these subjects induces amprenavir hypersusceptibility and a reduction of fitness and replication capacity. Here we demonstrate that substitutions L63P and V77I in protease, in combination, partially compensate for the loss of fitness, loss of replication capacity, loss of specific infectivity, and aberrant Gag processing induced by the N88S mutation. In addition, these mutations partially ablate amprenavir hypersusceptibility. Addition of mutation M46L to a strain harboring mutations L63P, V77I, and N88S resulted in a reduction of fitness and infectivity without changing Gag-processing efficiency, while amprenavir hypersusceptibility was further diminished. The ratio of reverse transcriptase activity to p24 protein was reduced in this strain compared to that in the other variants, suggesting that the M46L effect on fitness occurred through a mechanism different from a Gag-processing defect. We utilized these mutant strains to undertake a systematic comparison of indirect, single, cycle-based measures of fitness with direct, replication-based fitness assays and demonstrated that both yield consistent results. However, we observed that the magnitude of the fitness loss for one of the mutants varied depending on the assay used.

Genotypic testing for human immunodeficiency virus type 1 drug resistance

There are 16 approved human immunodeficiency virus type 1 (HIV-1) drugs belonging to three mechanistic classes: protease inhibitors, nucleoside and nucleotide reverse transcriptase (RT) inhibitors, and nonnucleoside RT inhibitors. HIV-1 resistance to these drugs is caused by mutations in the protease and RT enzymes, the molecular targets of these drugs. Drug resistance mutations arise most often in treated individuals, resulting from selective drug pressure in the presence of incompletely suppressed virus replication. HIV-1 isolates with drug resistance mutations, however, may also be transmitted to newly infected individuals. Three expert panels have recommended that HIV-1 protease and RT susceptibility testing should be used to help select HIV drug therapy. Although genotypic testing is more complex than typical antimicrobial susceptibility tests, there is a rich literature supporting the prognostic value of HIV-1 protease and RT mutations. This review describes the genetic mechanisms of HIV-1 drug resistance and summarizes published data linking individual RT and protease mutations to in vitro and in vivo resistance to the currently available HIV drugs.

Development and significance of resistance to protease inhibitors in HIV-1-infected adults under triple-drug therapy in clinical practice

Development of drug resistance is considered a major cause for failure of antiretroviral therapy in human immunodeficiency virus type 1 (HIV-1)-infected patients adherent to treatment. However, the rate of emergence and the significance of HIV-1 drug resistance in clinical practice have been not investigated thoroughly. Selection of HIV-1 variants that are genotypically resistant to protease inhibitors was studied in all the patients (n = 169) who completed at least 18 months of treatment with a protease inhibitor plus two nucleoside reverse transcriptase inhibitors at two urban Italian hospitals. HIV-1 carrying primary protease inhibitor resistance mutations was detected in 70 (41.4%) patients. The estimated proportion of patients developing genotypic resistance to protease inhibitors at 12 and 24 months was 18.3% (95% CI, 12.5-24.2%) and 33.9% (95% CI, 26.4-41.5%), respectively. Independent predictors of development of resistance to protease inhibitors were higher HIV-1 RNA levels at the nadir (P < 0.0001) and inclusion of ritonavir or saquinavir versus indinavir in the starting regimen (P = 0.0313). Resistance to protease inhibitors was strongly associated with a lower response to treatment, as shown by HIV-1 RNA load (P = 0.0001) and CD4 cell counts (P = 0.005). However, a linear increase in CD4 cell counts was maintained up to the end of follow-up even in the protease inhibitor-resistant population. Resistance to protease inhibitors develops in a relevant proportion of patients under long-term triple-drug therapy in clinical practice and is associated with virological treatment failure and limitation of CD4 cell increase.