HIV-1 RNA serum-load and resistant viral genotypes during early zidovudine therapy

Estimating HIV-1 fitness characteristics from cross-sectional genotype data

Despite the success of highly active antiretroviral therapy (HAART) in the management of human immunodeficiency virus (HIV)-1 infection, virological failure due to drug resistance development remains a major challenge. Resistant mutants display reduced drug susceptibilities, but in the absence of drug, they generally have a lower fitness than the wild type, owing to a mutation-incurred cost. The interaction between these fitness costs and drug resistance dictates the appearance of mutants and influences viral suppression and therapeutic success. Assessing in vivo viral fitness is a challenging task and yet one that has significant clinical relevance. Here, we present a new computational modelling approach for estimating viral fitness that relies on common sparse cross-sectional clinical data by combining statistical approaches to learn drug-specific mutational pathways and resistance factors with viral dynamics models to represent the host-virus interaction and actions of drug mechanistically. We estimate in vivo fitness characteristics of mutant genotypes for two antiretroviral drugs, the reverse transcriptase inhibitor zidovudine (ZDV) and the protease inhibitor indinavir (IDV). Well-known features of HIV-1 fitness landscapes are recovered, both in the absence and presence of drugs. We quantify the complex interplay between fitness costs and resistance by computing selective advantages for different mutants. Our approach extends naturally to multiple drugs and we illustrate this by simulating a dual therapy with ZDV and IDV to assess therapy failure. The combined statistical and dynamical modelling approach may help in dissecting the effects of fitness costs and resistance with the ultimate aim of assisting the choice of salvage therapies after treatment failure.

Mutations conferring drug resistance represent major threats to the therapeutic success of highly active antiretroviral therapy (HAART) against human immunodeficiency virus (HIV)-1 infection. Viral mutants differ in their fitness and assessing viral fitness is a challenging task. In this article, we estimate drug-specific mutational pathways by learning from clinical data using statistical techniques and incorporate these into mathematical models of in vivo viral infection dynamics. This approach enables us to estimate mutant fitness characteristics. We illustrate our method by predicting fitness characteristics of mutant genotypes for two different antiretroviral therapies with the drugs zidovudine and indinavir. We recover several established features of mutant fitnesses and quantify fitness characteristics both in the absence and presence of drugs. Our model extends naturally to multiple drugs and we illustrate this by simulating a dual therapy with ZDV and IDV to assess therapy failure. Additionally, our modelling approach relies only on cross-sectional clinical data. We believe that such an approach is a highly valuable tool in assisting the choice of salvage therapies after treatment failure.

Cumulative viral load and virologic decay patterns after antiretroviral therapy in HIV-infected subjects influence CD4 recovery and AIDS

BACKGROUND

The impact of viral load (VL) decay and cumulative VL on CD4 recovery and AIDS after highly-active antiretroviral therapy (HAART) is unknown.

METHODS AND FINDINGS

Three virologic kinetic parameters (first year and overall exponential VL decay constants, and first year VL slope) and cumulative VL during HAART were estimated for 2,278 patients who initiated HAART in the U.S. Military HIV Natural History Study. CD4 and VL trajectories were computed using linear and nonlinear Generalized Estimating Equations models. Multivariate Poisson and linear regression models were used to determine associations of VL parameters with CD4 recovery, adjusted for factors known to correlate with immune recovery. Cumulative VL higher than the sample median was independently associated with an increased risk of AIDS (relative risk 2.38, 95% confidence interval 1.56-3.62, p<0.001). Among patients with VL suppression, first year VL decay and slope were independent predictors of early CD4 recovery (p = 0.001) and overall gain (p<0.05). Despite VL suppression, those with slow decay during the first year of HAART as well as during the entire therapy period (overall), in general, gained less CD4 cells compared to the other subjects (133 vs. 195.4 cells/µL; p = 0.001) even after adjusting for potential confounders.

CONCLUSIONS

In a cohort with free access to healthcare, independent of established predictors of AIDS and CD4 recovery during HAART, cumulative VL and virologic decay patterns were associated with AIDS and distinct aspects of CD4 reconstitution.

Stealth nucleosides: mode of action and potential use in the treatment of viral diseases

Riboviruses and retroviruses have been shown to spontaneously mutate at an extraordinarily high rate. While this genetic diversity allows viral subpopulations to escape conventional antivirals, it also has a cost. Indeed, this high mutation rate results in the synthesis of many defective virions. Stealth nucleosides are nucleoside analogues that are designed to increase the already high spontaneous mutation rate of viruses to the point where the virus cannot further replicate, a process known as "lethal mutagenesis". Rather than causing chain termination and attempting to immediately halt viral replication, as with conventional nucleoside reverse transcriptase inhibitors (NRTI), stealth nucleosides are incorporated into the viral genome during replication and, by mispairing, cause mutations to the viral genome. These mutations affect all viral proteins and cumulatively, over a number of replication cycles, are lethal to the virus. There are two distinct stealth nucleoside platforms: DNA stealth nucleosides and RNA stealth nucleosides. DNA stealth nucleosides are currently being screened for activity against HIV and may have activity against hepatitis B virus and smallpox virus, with the clinical lead DNA stealth nucleoside demonstrating activity in the low nanomolar range. In addition, DNA stealth nucleosides have been shown to be able to effectively treat NRTI-resistant HIV strains in vitro, which is not surprising given that the two principal modes of resistance (low affinity of reverse transcriptase for a modified sugar or pyrophosphorolysis) should not be applicable to DNA stealth nucleosides. RNA stealth nucleosides are being developed for the treatment of ribovirus infections, and particularly hepatitis C virus infection. RNA stealth nucleosides are selected for their broad spectrum of antiviral activity, and current lead RNA stealth nucleosides have potency in the same range as ribavirin.

Short-term effect of zidovudine on plasma and genital human immunodeficiency virus type 1 and viral turnover in these compartments

The effect of zidovudine on plasma and genital human immunodeficiency virus type 1 (HIV-1) was determined in 42 antiretroviral-naive HIV-1-seropositive women in Nairobi. After 7 days of zidovudine treatment, HIV-1 RNA levels decreased by 0.5 to 1.1 log(10) in plasma and genital secretions. HIV-1 RNA half-life following zidovudine treatment was 4.7, 1.3, and 0.9 days in plasma, cervix, and vagina, respectively, and significantly shorter in genital secretions than in plasma (P < 0.001). Defining the short-term effect of zidovudine on plasma and genital HIV-1 is important for improving perinatal HIV-1 interventions.

HIV-1 genotypic and phenotypic resistance

Antiretroviral failure caused by the development of drug resistance in HIV-1 is an increasingly common clinical problem. Two types of resistance assays are available to clinicians. Genotypic assays determine the presence of mutations associated with drug resistance. The interpretation of mutations is often complicated, however, and may require expert opinion. Phenotypic assays provide a direct measure of the drug susceptibility of the virus. The magnitude of increase, however, in viral drug inhibitory concentration that is predictive of clinical drug failure remains unknown for several antiretroviral drugs. The mutational patterns underlying resistance to each antiretroviral drug are often diverse, and cross-resistance patterns within each of the currently available classes are complex. Currently, resistance testing is recommended for patients who have virologic failure on an antiretroviral regimen. Furthermore, testing should also be considered in treatment-native patients when the prevalence of transmitted drug-resistant virus is expected to be high.

Origin of human immunodeficiency virus type 1 quasispecies emerging after antiretroviral treatment interruption in patients with therapeutic failure

The emergence of antiretroviral (ARV) drug-resistant human immunodeficiency virus type 1 (HIV-1) quasispecies is a major cause of treatment failure. These variants are usually replaced by drug-sensitive ones when the selective pressure of the drugs is removed, as the former have reduced fitness in a drug-free environment. This was the rationale for the design of structured ARV treatment interruption (STI) studies for the management of HIV-1 patients with treatment failure. We have studied the origin of drug-sensitive HIV-1 quasispecies emerging after STI in patients with treatment failure due to ARV drug resistance. Plasma and peripheral blood mononuclear cell samples were obtained the day of treatment interruption (day 0) and 30 and 60 days afterwards. HIV-1 pol and env were partially amplified, cloned, and sequenced. At day 60 drug-resistant variants were replaced by completely or partially sensitive quasispecies. Phylogenetic analyses of pol revealed that drug-sensitive variants emerging after STI were not related to their immediate temporal ancestors but formed a separate cluster, demonstrating that STI leads to the recrudescence and reemergence of a sequestrated viral population rather than leading to the back mutation of drug-resistant forms. No evidence for concomitant changes in viral tropism was seen, as deduced from env sequences. This study demonstrates the important role that the reemergence of quasispecies plays in HIV-1 population dynamics and points out the difficulties that may be found when recycling ARV therapies with patients with treatment failure.

Observations of HIV-1 Genotypic Drug Resistance in a Trial of Four Reverse Transcriptase Inhibitors (Quattro Trial)

The Quattro Trial compared the use of four HIV-1 reverse transcriptase (RT) inhibitors (zidovudine, lamivudine, loviride and zalcitabine), given either as four-drug combination therapy or monotherapy, with 8-week cycles of each drug, with zidovudine/lamivudine dual therapy. Observations of resistance associated and other mutations in the RT gene were made to determine whether therapy failure could be explained by acquisition of these mutations and whether novel mutation patterns developed. As in the intent-to-treat analysis, the use of cyclical monotherapy gave a smaller reduction in plasma virus load at 64 weeks (0.4 log10 copies/ml below baseline) than the quadruple or dual therapy arms (1.3 and 0.8 log10 copies/ml below baseline). Cyclical therapy appeared to generate less genotypic resistance to zidovudine, loviride or zalcitabine than the other arms. Resistance to lamivudine (mutation M184V) developed rapidly in all three arms. Resistance to zidovudine was acquired by a larger proportion of subjects on dual therapy than on quadruple therapy. Resistance to loviride or zalcitabine was rarely observed. During lamivudine monotherapy the M184V mutation was rapidly acquired and viral load rebounded. Zalcitabine monotherapy initially selected M184V mutants, but these were lost as therapy continued. Novel mutations that may have been associated with combination or cyclical quadruple therapy were observed infrequently. There was no clear correlation between changes in response to therapy and the development of previously described resistance mutations or with novel mutations in the RT gene.

Vaccination with CTL epitopes that escape: an alternative approach to HIV vaccine development?

This article describes a novel approach to HIV vaccine design that is, as yet, unproven and still in preliminary development. In rhesus macaques infected with simian immunodeficiency virus (SIV), we have identified particular cellular immune responses that select for viral variants during primary infection. We speculate that the detection of viral variants with altered amino acids in CTL epitopes implies the successful clearance of cells harboring wild-type virus. Here, we present our rationale suggesting why such potent early CTL responses that exert an antiviral effect may be particularly attractive targets for induction by candidate vaccines. Conventional wisdom suggests that regions of the virus that are structurally and functionally important will generally be well-conserved both among clades and within an infected host. Amino acid replacements within these well-conserved regions should be difficult for the virus to accommodate. Therefore, these regions are traditionally considered ideal targets for vaccine induced immune responses because they are refractory to CTL escape mutations. Many examples of these regions have been identified in both HIV-1 and SIV(mac) (J. Immunol. 162 (1999) 3727; J. Virol. 67 (1993) 438) and have been included in candidate vaccine formulations. Human clinical trials testing these vaccines are currently underway. Our proposed method of vaccination with CTL epitopes that escape explores an alternative hypothesis. Rather than engendering responses to regions of the virus that do not escape, we reason that vaccination needs to accelerate the development of the initial immune responses that effectively select for amino acid variants during acute infection. By examining CTL escape during the acute phase, we will identify CTL responses that the virus cannot tolerate and incorporate these responses into vaccines.

International perspectives on antiretroviral resistance. Nucleoside reverse transcriptase inhibitor resistance

Nucleoside reverse transcriptase inhibitors (NRTIs) comprise the first class of drug with proven antiretroviral efficacy against HIV-1, and the first in which drug resistance was reported. Ongoing research in the area of NRTI resistance and cross-resistance contributes much to what we know about the failure of antiretroviral therapy. The genetic mutation patterns responsible for resistance to the available NRTIs have been well documented. This information is being used to plan rational drug therapy. Furthermore, it serves as the standard against which to evaluate response patterns to multiple-drug regimens, ultimately enabling more accurate prediction of outcome with combination therapies. Other features of NRTI resistance, such as the theoretic reversal of zidovudine resistance associated with the M184V mutation or the powerful influence of the Q151M multiple-drug resistance mutation, have revealed the unpredictable nature of HIV resistance and how much we still need to learn. Although NRTIs are the cornerstone of antiretroviral therapy at present and are used to control disease progression for extended periods, it is clear that eventually resistance occurs with all antiretroviral regimens. Future research into NRTI-resistance mutations, mutational interactions, treatment sequencing, and viral fitness and fidelity will continue to refine our understanding of drug resistance and improve our ability to delay or eliminate resistance and advance HIV control.

A solid phase plate assay for HIV-1 genotyping

A prototype solid phase plate assay (SPPA) for the detection and genotyping of HIV-1 subtypes was developed using a PCR-based capture hybridization format. Well characterized HIV-1 reference controls of known subtypes and subtype specific capture oligonucleotide probes targeting several regions of the envelope (env) gene of HIV-1 were selected to develop the assay. The subtype specific oligonucleotide probes were covalently bound to microtubes in an ordered pattern and biotin labelled primers were used to amplify the target sequences. The PCR products were hybridized to the corresponding oligonucleotide probes, and colorimetrically detected by a chromogenic reaction using a standard microplate reader. All the HIV-1 subtype reference controls specifically hybridized to the corresponding capture probes and negligible cross-hybridization between subtypes was observed. To demonstrate the performance and reproducibility of the SPPA system and its validation with clinical samples, several human plasma samples of unknown and known HIV-1 subtypes were tested. The SPPA is highly specific and unambiguously identify the major subtypes of the HIV-1 M and O groups. This assay could be a useful method for subtyping samples of HIV-1 infected individuals and for disease management.

Virus phenotype switching and disease progression in HIV-1 infection

One of the phenotypic distinctions between different strains of human immunodeficiency virus type 1 (HIV-1) has to do with the ability to cause target cells to form large multinucleate bodies known as syncytia. There are two phenotypes according to this characterization: syncytium-inducing (SI) and non-syncytium-inducing (NSI). NSI strains are usually present throughout infection, while SI strains are typically seen at the beginning of the infection and near the onset of AIDS. The late emergence of SI strains is referred to as phenotype switching. In this paper we analyse the factors that lead to phenotype switching and contribute to the dynamics of disease progression. We show that a strong immune system selects for NSI strains while a weak immune system favours SI strains. The model explicitly accounts for the fact that CD4+ cells are both targets of HIV infection and crucial for activating immune responses against HIV In such a model, SI strains can emerge after a long and variable period of NSI dominated infection. Furthermore, versions of the model which do not explicitly account for HIV-specific, activated CD4+ cells do not exhibit phenotype switching, emphasizing the critical importance of this pool of cells.

Use of recombinant viruses to assess the pattern of early human immunodeficiency virus breakthrough infection in the presence of stavudine

A variety of cell lines were infected with replication-defective recombinant retroviruses in the presence of stavudine (d4T). Cells which were infected despite the presence of d4T were isolated and subjected to infection with other retroviruses [replication-competent human immunodeficiency virus (HIV), replication-defective HIV or replication-defective recombinant murine retroviruses]. Each of the host cell types tested had a small subset of cells that were infected with HIV or murine retroviruses in the presence of d4T. Some of these infected cells could be infected repeatedly at high efficiency in the presence of d4T. This phenotype of 'persistent refractoriness' to the antiviral effects of d4T could be overcome by the addition of 5-fluoro-2-deoxyuridine (floxuridine) to d4T. The d4T-floxuridine combination also had potent antiretroviral effects in primary blood mononuclear cells.

Antiretroviral Drug Resistance in HIV-1

Progress in understanding antiretroviral resistance has evolved rapidly in recent years. Specific resistance mutations have been associated with virologic failure of different nucleoside reverse transcriptase inhibitors (NRTIs). These mutations vary in the extent of cross resistance they confer to other drugs in the same class. In addition, two novel mutational patterns conferring resistance to multiple NRTIs have been recognized. Considerable class-specific cross resistance also exists among viruses with reduced susceptibility to nonnucleoside reverse transcriptase inhibitors (NNRTIs). Among protease inhibitors, low level resistance that arises early during virologic failure may be drug specific in some situations, but high level resistance seen later during suboptimal therapy is likely to confer cross resistance to the entire class. Prevalence of drug resistance in infected patients appears to be considerable, and transmission of multidrug-resistant virus has been documented. Current methods of testing for resistance are promising, but they have significant limitations and require further clinical validation. The best approach to prevent resistance is to start treatment early during infection with a regimen that engenders good compliance and is potent enough to decrease viral load to below detection limits of the most sensitive assay available. Once resistance arises, salvage regimens in general have compromised efficacy and should be planned with attention to the patient's prior drug treatment history and the viruses' suspected or demonstrated resistance patterns.

Resistance mutations selected in vivo under therapy with anti-HIV drug HBY 097 differ from resistance pattern selected in vitro

The quinoxaline derivative HBY 097, an orally active nonnucleoside inhibitor of HIV-1 reverse transcriptase (NNRTI), showed an efficient suppression of viral load in a dose-escalating phase I study with mean trough concentrations increasing from 137-1299 ug/l [Rübsamen-Waigmann et al., Lancet 349:1517]. Half-maximal inhibitory concentrations (IC50) for viruses grown from the patients at entry of the study were 0.1-3 nM, except for one patient who had a virus with reduced susceptibility to HBY 097 at entry (IC50: 160 nM). During therapy, only two patients developed a virus with a moderately increased IC50 (2.2 and 15 nM). This reduced susceptibility was associated with the known NNRTI-resistance mutation K ==> N at position 103, in contrast to resistance selection in vitro, which had yielded predominant mutations at positions 179 and 190. The Tyr mutation at position 181, inducing high resistance for other NNRTIs, was never observed. The resistant virus at study entry (IC50 = 160 nM) had a mutation at position 103 as well, combined with an AZT resistance mutation (K ==> R) at position 70, suggesting that nucleoside-resistance mutations may help increasing resistance to HBY 097. This is in line with our in vitro selection studies, where resistance mutations at the 'nucleoside sites' 74 and 75 increased the resistance phenotype of NNRTI mutations. Our findings highlight the crucial importance of IC50 determinations from cultured virus for determination of phenotypic resistance development during therapy and demonstrate that in vivo resistance development cannot be predicted from in vitro selection.

Comparison of human immunodeficiency virus type 1 (HIV-1) protease mutations in HIV-1 genomes detected in plasma and in peripheral blood mononuclear cells from patients receiving combination drug therapy

Detections of mutations in the protease gene of human immunodeficiency virus type 1 in plasma and peripheral blood mononuclear cells (PBMC) were sought in two matched populations of 23 individuals receiving combination drug therapy with or without protease inhibitors. In the control group (23 patients not receiving protease inhibitors), no primary resistance mutations were found. In contrast, primary resistance mutations (especially at codons M46, V82, and L90) were found in 16 of 23 patients (70%) treated with protease inhibitors. In 30% of the cases, these mutations were detected in plasma but not in PBMC.

Evolutionary dynamics of HIV-induced subversion of the immune response

Human immunodeficiency virus (HIV) disease progression is characterized by a slow but steady decline in the number of CD4+ T cells. It results in the development of AIDS when the immune response collapses and the virus grows uncontrolled. Pathogenicity of HIV may be due to viral escape from cellular immune responses as well as virus-induced immune impairment. Here we discuss how the dynamic interactions between the virus population and the immune response may lead to the development of AIDS. In particular we argue that in vivo evolution of HIV may be the driving force successively weakening the immune system. This may lead to increased levels of viraemia as well as to the evolution of more virulent phenotypes which indicate progression to AIDS. These insights are important for understanding the disease process itself and for designing effective treatment regimes.

Managing resistance to anti-HIV drugs: an important consideration for effective disease management

Current recommendations for the treatment of HIV-infected patients advise highly active antiretroviral therapy (HAART) consisting of combinations of 3 or more drugs to provide long-term clinical benefit. This is because only a complete suppression of virus replication will be able to prevent virus drug resistance, the main cause of drug failure. Virus drug resistance may remain a cause of concern in patients who have already received suboptimal mono- or bitherapy, or for patients who do not experience complete shut-down of virus replication under HAART. For these patients, replacement of one combination therapy regimen by another at drug failure, taking into account the existing resistance profile, will be needed. The development of new drugs will remain necessary for those patients who have failed to respond to all currently available drugs, as will be the institution of more effective and less toxic HAART regimens.

Mother-to-child transmission of HIV: implications of variation in maternal infectivity

OBJECTIVES

To examine the implications of variation in maternal infectivity on the timing of mother-to-child HIV transmission through breastfeeding.

DESIGN AND METHODS

A mathematical model of mother-to-child HIV transmission was developed that incorporates two main features: (i) the fetus/child potentially experiences a series of exposures (in utero, intrapartum, and via breastmilk) to HIV; and (ii) variation in maternal infectivity. The model was estimated from different sources of epidemiological data: a retrospective cohort study of children born to HIV-1-infected women in Sao Paulo State, Brazil, the International Registry of HIV-Exposed Twins, and the AIDS Clinical Trials Group 076 trial, which assessed the effectiveness of zidovudine in preventing mother-to-child HIV transmission.

RESULTS

Variation in maternal infectivity results in higher average risk of breastfeeding-related transmission in the early stages of breastfeeding than in the late stages, even in the absence of a direct relationship between transmission risk and the age of the child. However, the available data were unable to resolve the quantitative importance of this mechanism.

CONCLUSIONS

Our model has helped identify a previously unrecognized determinant of the timing of breastfeeding-related HIV transmission, which may have adverse implications for the effectiveness of certain interventions to reduce mother-to-child HIV transmission such as maternal antiretroviral therapy in breastfeeding populations and the early cessation of breastfeeding.

Quantitative differences in the distribution of zidovudine resistance mutations in multiple post-mortem tissues from AIDS patients

Replication of HIV introduces errors into the genome which are responsible for conferring a growth advantage over wildtype virus when drugs such as zidovudine (ZDV) exert a selective pressure. The molecular basis for HIV-1 resistance to ZDV has been mapped to codons 41, 67, 70, 215 and 219 of the reverse transcriptase gene both in vitro and in clinical samples of blood. This study has investigated the relationship between the quantitative prevalence of ZDV resistance in multiple organs of the same individual. Proviral HIV-1 load was measured by quantitative-competitive PCR in 90 samples from organs of 11 patients dying with AIDS. Nine of these patients had been prescribed zidovudine. The distribution of wildtype and mutant sequences at the positions 41, 67, 70, 215 and 219 of the reverse transcriptase was assessed using a point mutation assay. The results showed that the highest proviral loads were predominately found in lymph node, spleen and lung and there was a significant association between viral load and resistance to ZDV (P=0.008). Inter-organ distribution of wildtype and mutant sequences at codons 41, 67, 70, 215 and 219 was frequently not uniform and in some patients differed markedly between the lymphoreticular system and other organs. These results demonstrate that treatment of HIV-1 infection with zidovudine does not exert uniform selective pressures in multiple organs. These findings have implications for the interpretation of resistance data and design of treatment strategies for HIV, arguing in particular that alterations in therapeutic regimens should consider the likelihood of different resistance patterns being present in multiple sites within the same individual.

Comparison of culture- and non-culture-based methods for quantification of viral load and resistance to antiretroviral drugs in patients given zidovudine monotherapy

Virological assays for human immunodeficiency virus type 1 load and drug resistance can broadly be divided into culture-based and molecular biology-based methods. Culture-based methods give a direct measure of infectious virus load and phenotypic drug resistance, whereas molecular biology-based methods are indirect, assaying nucleic acid levels to determine virus load and point mutations associated with drug resistance. We have compared culture-based and non-culture-based methods for patients enrolled in a placebo-controlled trial of zidovudine (the Concorde Trial). Virus loads were assayed by culture of peripheral blood mononuclear cells (PBMCs) or quantitative PCR, and drug resistance was assayed in culture or in a quantitative, PCR-based point mutation assay. The rates of detection of viremia and drug resistance were higher by PCR than by culture for this population of subjects. Comparison of the virus loads by the two measures showed a good correlation for virus loads in PBMCs but a poor correlation for virus loads in plasma. The latter result probably reflected the inaccuracies of culture in assaying plasma with the low infectious virus titers seen in the study population. The concordance of phenotypic and genotypic drug resistance methods was high, with all phenotypically resistant isolates having at least one resistance-associated mutation and with no mutations being found in a drug-sensitive isolate. Genomic resistance scores (weighted sums of levels of resistance mutations) showed good correlations with the levels of phenotypic resistance, and both resistance measures were observed to increase as the duration of exposure to drug increased. Overall, non-culture-based methods were shown to correlate well with culture-based methods and offer a low-cost, high-throughput alternative. However, culture-based methods remain the final arbiters of infectious virus load and phenotypic drug resistance and are unlikely to be superseded entirely.

Characterization and use of a recombinant retroviral system for the analysis of drug resistant HIV

A recombinant retroviral system was used for the analysis of early HIV breakthrough infection in the presence of antiviral drugs. The use of replication-defective HIV allowed a quantitative analysis of a single cycle of infection. This report characterizes this recombinant HIV system and demonstrates it's validity in comparison to standard assays. It is demonstrated that the protease inhibitor XM323 inhibits both early and late events in the HIV life-cycle, while dextran sulphate inhibits only early events. In addition, it is shown that this system can be used for detecting and quantitating drug resistant HIV. Thus, the use of this system may provide both novel information about the stage of the viral life-cycle inhibited and a preliminary assessment of the mechanism(s) responsible for breakthrough infection in the presence of antiretroviral drugs.

The frequency of resistant mutant virus before antiviral therapy

OBJECTIVE

To calculate the expected prevalence of resistant HIV mutants before antiviral therapy.

DESIGN

HIV replication generates virus mutants. The prevalence of these mutants is determined by mutation and selection/fitness. Some mutations will confer drug resistance and it is crucial for the success of antiviral drug therapy to determine whether these resistant viruses are present before the initiation of therapy.

METHODS

A quasispecies equation was used to calculate the expected frequency of drug-resistant virus prior to therapy.

RESULTS AND CONCLUSIONS

We show how the pretreatment frequency of resistant virus depends on the number of point mutations between wild-type and mutant virus, the selective disadvantage of the resistant mutant and the intermediate mutants, and the mutation rate.

Proton MRS and quantitative MRI assessment of the short term neurological response to antiretroviral therapy in AIDS

OBJECTIVE

To investigate MRI and proton spectroscopy changes in five patients with HIV associated dementia complex (HADC) treated with antiretroviral therapy.

METHODS

Three markers were evaluated: (1) CSF/intracranial volume ratio; (2) T2 weighted signal ratio between parieto-occipital white and subcortical grey matter; and (3) metabolite ratios from long echo time (TE=135 ms) single voxel proton spectra of parieto-occipital white matter.

RESULTS

Spectroscopic changes indicated initial increases in N-acetyl/(N-acetyl + choline + creatine) ratio (NA/(NA+ Cho+Cr)) and progression of atrophy after initiation of antiretroviral therapy in four of five patients. When the neurological status of the patients subsequently deteriorated (two of five patients), the NA/(NA+Cho+Cr) ratio also declined.

CONCLUSIONS

Spectroscopic changes mirror reversible neuronal dysfunction. These objective, non-invasive techniques may be used for monitoring the neurological effects of antiretroviral drug therapy in patients with HADC.

Understanding drug resistance for monotherapy treatment of HIV infection

The purpose of this study was to investigate strategies in the monotherapy treatment of HIV infection in the presence of drug-resistant (mutant) strains. A mathematical system is developed to model resistance in HIV chemotherapy. It includes the key players in the immune response to HIV infection: virus and both uninfected CD4+ and infected CD4+ T-cell populations. We model the latent and progressive stages of the disease, and then introduce monotherapy treatment. The model is a system of differential equations describing the interaction of two distinct classes of HIV--drug-sensitive (wild type) and drug-resistant (mutant)--with lymphocytes in the peripheral blood. We then introduce chemotherapy effects. In the absence of treatment, the model produces the three types of qualitative clinical behavior--an uninfected steady state, an infected steady state (latency), and progression to AIDS. Simulation of treatment is provided for monotherapy, during the progression to AIDS state, in the consideration of resistance effects. Treatment benefit is based on an increase or retention in CD4+ T-cell counts together with a low viral titer. We explore the following treatment approaches: an antiviral drug which reduces viral infectivity that is administered early--when the CD4+ T-cell count is > or = 300/mm3, and the late--when the CD4+ T-cell count is less than 300/mm3. We compare all results with data. When treatment is initiated during the progression to AIDS state, treatment prevents T-cell collapse, but gradually loses effectiveness due to drug resistance. We hypothesize that it is the careful balance of mutant and wild-type HIV strains which provides the greatest prolonged benefit from treatment. This is best achieved when treatment is initiated when the CD4+ T-cell counts are greater than 250/mm3, but less than 400/mm3 in this model (i.e. not too early, not too late). These results are supported by clinical data. The work is novel in that it is the first model to accurately simulate data before, during and after monotherapy treatment. Our model also provides insight into recent clinical results, as well as suggests plausible guidelines for clinical testing in the monotherapy of HIV infection.

Virus dynamics and drug therapy

The recent development of potent antiviral drugs not only has raised hopes for effective treatment of infections with HIV or the hepatitis B virus, but also has led to important quantitative insights into viral dynamics in vivo. Interpretation of the experimental data depends upon mathematical models that describe the nonlinear interaction between virus and host cell populations. Here we discuss the emerging understanding of virus population dynamics, the role of the immune system in limiting virus abundance, the dynamics of viral drug resistance, and the question of whether virus infection can be eliminated from individual patients by drug treatment.

Antiretroviral resistance and HIV vertical transmission

The author reviews the current and potential problem of antiviral resistance in the prevention of vertical transmission of human immunodeficiency virus (HIV) from mother to child. The paper addresses five questions: (i) How often does antiretroviral resistance occur? While this does not appear to be an important problem now, low levels of resistance are probably common, and resistance can be expected to increase in frequency; (ii) Does resistance influence the rate of vertical transmission? The answer is likely to be yes if the drug in question is used in an effort to prevent or reduce transmission; (iii) What are the consequences for the mother? These are certainly not good and might, if the drug in question is important for the mother's health, be bad; (iv) What are the consequences for the baby? The answer to this question is similar, with the additional concern that resistance might make preventive measures less effective and thus increase the chance of transmission; (v) What can be done about it? Combination treatment may be effective in minimizing the development of resistance. As with other antimicrobials, selective and rational use of drugs for specific purposes will minimize the problem. The conclusion of the discussion is that resistance is likely to emerge as an important problem over time and should be addressed in strategies for prevention.

Simple monitoring of antiretroviral therapy with a signal-amplification-boosted HIV-1 p24 antigen assay with heat-denatured plasma

OBJECTIVE

Virus load determination has become indispensable for the management of HIV patients, but depends on expensive assays of a low throughput. We evaluated whether a highly improved HIV-1 p24 antigen detection procedure which involves heat-mediated immune complex dissociation and signal-amplification-boosted enzyme-linked immunosorbent assay (ELISA) was suitable for antiretroviral treatment monitoring.

DESIGN AND METHODS

Virus load in plasma was determined for 127 plasma samples taken at 0, 2, 6, 12, 18, 24, 30 and 36 weeks from 23 patients with CD4+ T cells < 50 x 10(6)/l who received indinavir 800 mg three times daily in addition to prior antiretroviral treatment. Tests included polymerase chain reaction (PCR) for viral RNA, measured prospectively with the Roche Amplicor kit, and retrospective batch testing of heat-denatured samples for p24 antigen by the DuPont HIV-1 p24 Core Profile ELISA linked with a tyramide signal amplification step. Particle-associated reverse transcriptase (RT) by the product-enhanced RT (PERT) assay was determined as an independent third-opinion viral load marker.

RESULTS

p24 antigen was detected as sensitively as viral RNA. Overall detection during a median observation time of 25 weeks (range, 0-39) amounted to 75.6% for antigen and 73.6% for RNA. The antigen detection limit was 0.2 pg/ml. Antigen was detectable in all 23 baseline samples, whereas RNA was undetectable in one. Antigen and RNA levels in 79 samples positive for both markers correlated with r = 0.714 (P < 0.0001). Average changes in levels of p24 antigen and RNA at eight timepoints correlated with r = 0.982 (P < 0.0001). In individual patients, the two parameters behaved similarly, and in certain cases virtually identically. RT activity was measurable in all samples.

CONCLUSIONS

The performance of this antigen detection procedure is comparable to RNA PCR, thus providing a simple, high throughput alternative in monitoring the efficacy of antiretroviral treatment.

Prospective longitudinal analysis of viral load and surrogate markers in relation to clinical progression in HIV type 1-infected persons

The temporal relationship between viral and surrogate markers and clinical status was analyzed prospectively every 8 weeks in 34 asymptomatic HIV-1-infected persons. After 3 years, 25 persons remained clinically healthy whereas 9 persons showed clinical progression. In accordance with other reports we found that at study entry HIV-RNA load was predictive of clinical progression. All markers tested evolved significantly in time in both progressors and nonprogressors. The HIV RNA load in plasma and HIV DNA load in T cells were linearly related only in nonprogressors. In addition, the RNA/DNA ratio during follow-up was significantly higher in progressors, indicating a higher replication rate in progressors. The HIV DNA load correlated inversely with CD4+ T cell counts and positively with p24 antigenemia in both nonprogressors and progressors. A significant correlation of HIV DNA load with SI phenotype occurred in progressors only. HIV RNA levels correlated with beta 2-microglobulin level and with p24 antigenemia but not with SI phenotype. These three markers can all routinely be measured in plasma; however, only the HIV RNA levels appear to be informative for clinical progression. Six to 8 months before clinical progression, an SI phenotype switch, increased HIV RNA in plasma, and decreased CD4+ T cell counts were all indicative of an impending clinical event.

Clinical data sets of human immunodeficiency virus type 1 reverse transcriptase-resistant mutants explained by a mathematical model

Treatment of human immunodeficiency virus type 1 (HIV-1) infection during the clinical latency phase with drugs inhibiting reverse transcriptase (RT) reduces the HIV-1 RNA load and increases the CD4+ T-cell count. Typically, however, the virus evolves mutations in the RT gene that circumvent the drugs. We develop a mathematical model for this situation. The model distinguishes quiescent from activated CD4+ T cells, incorporates the fact that only activated cells can become productively infected by HIV-1, embodies empirical estimates for the drug resistance and the mutation frequency for each of the HIV-1 drug-resistant mutants, and assumes the antiviral immune response to remain constant over the course of the experiments. We analyze clinical data on the evolution of drug-resistant mutants for the RT inhibitors lamivudine and zidovudine. The results show that the evolutionary sequence of the drug-resistant mutants in both data sets is accounted for by our model, given that lamivudine is more effective than zidovudine. Thus, current empirical estimates of the mutation frequencies and the drug resistances of the mutants suffice for explaining the data. We derive a critical treatment level below which the wild-type HIV-1 RNA load can rebound before the first drug-resistant mutant appears. Our zidovudine data confirm this to be the case. Thus, we demonstrate in the model and the data that the rebound of the HIV-1 RNA load in the case of zidovudine is due to the outgrowth of wild-type virus and the first drug-resistant mutant, whereas that in the case of lamivudine can only be due to the drug-resistant mutants. The evolution of drug resistance proceeds slower in the case of zidovudine because (i) zidovudine is not as effective as lamivudine and (ii) the first zidovudine drug-resistant mutant is competing with the rebounding wild-type virus.

Comparative evaluation of three assays for the quantitation of human immunodeficiency virus type 1 RNA in plasma

Reverse transcriptase-coupled polymerase chain reaction (Amplicor HIV-1 Monitor), the branched DNA (bDNA) method (Quantiplex HIV-1 RNA) and the nucleic acid sequence-based assay (NASBA HIV-1 RNA QT) were comparatively evaluated for the quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in plasma. Among 60 plasma specimens from HIV-1 infected patients, HIV-1 RNA was detected in 56 by Amplicor (sensitivity, 93.3%), in 41 by bDNA (sensitivity, 68.3%), and in 60 by NASBA (sensitivity, 100%). HIV-1 RNA was not detected by any of these methods in 34/34 plasma specimens from HIV-1-seronegative blood donors (specificity, 100%). The HIV-1 RNA levels as determined by the different methods were correlated significantly. The frequency of concordant results (log difference < 0.50) was 80.4% between Amplicor and NASBA, 77.5% between Amplicor and bDNA, and 58.6% between bDNA and NASBA. After initiation of antiviral therapy, HIV-1 RNA level variations observed with the three methods were similar. HIV-1 RNA levels were inversely correlated with the CD4+ T cell counts, whereas no correlation was found with HIV-1 p24-antigen levels. When the methods were evaluated for reproducibility, coefficients of variation ranged from 11% to 40% for Amplicor, from 6% to 35% for bDNA, and from 13% to 62% for NASBA. Quantitation of HIV-1 RNA in culture supernatants from HIV-1 subtype A to H strains showed that bDNA can be used to quantitate RNA from all HIV-1 subtypes, whereas Amplicor failed to detect RNA from subtype A strains and NASBA subtype G strains.

The human immunodeficiency virus

There indeed seems to be a new mood of optimism in researchers and clinicians studying HIVs and patients infected with these viruses. A new understanding of the virology, biology, and therapy of HIV-1 includes the following: (1) The level of HIV-1 viremia, as measured by the HIV-1 plasma RNA, is a critical determinant of the time to development of AIDS and death. (2) Lessons from nonprogressors or long-term survivors, who do not develop AIDS or immune impairment despite their long-term infection, show clearly that the HIV-1 replication is significantly lower (4 to 20 times) than in people with progressive disease, and there is a vigorous and specific immune response against HIV-1. (3) Reducing viremia with antiretroviral drugs can delay the onset of AIDS and prolong survival. (4) Combination drug therapies, including an RT inhibitor and a PR inhibitor, can lower viremia to undetectable levels and delay the development of drug-resistant HIV-1. (5) HIV-1 subgroups have marked geographically distinct distributions, which may specify the routes of infection in different populations at risk.

Nevirapine-resistant human immunodeficiency virus: kinetics of replication and estimated prevalence in untreated patients

The nonnucleoside reverse transcriptase inhibitor nevirapine rapidly selects for mutant human immunodeficiency virus (HIV) in vivo. The most common mutation occurs at amino acid residue 181 in patients receiving monotherapy. After the initiation of nevirapine therapy, plasma and peripheral blood mononuclear cell samples were collected at frequent intervals and assayed for HIV RNA levels and the proportion of virus containing a mutation at residue 181. HIV RNA levels remained stable for the first 24 h after initiation of therapy and rapidly declined between 1 and 7 days. There was a consistent maximum decrease of 2 log10 HIV RNA copies per ml of plasma (range, 1.96 to 2.43) from baseline after 2 weeks in all monotherapy subjects. The estimated median half-life of HIV RNA was 1.11 days (range, 0.63 to 1.61). After 14 days of therapy, HIV RNA levels began to increase and 181 mutant virus was detected. The estimated doubling time of the emerging virus population ranged from 1.80 to 5.73 days. Viral DNA in peripheral blood mononuclear cells turned over from wild type to the mutant with a mutation at residue 181 significantly more slowly than did HIV RNA in plasma. In two subjects, the calculated prevalence of the 181 mutant virus prior to treatment was 7 and 133 per 10,000 copies of plasma HIV RNA.

Viral load, CD4 percentage, and delayed-type hypersensitivity in subjects receiving the HIV-1 immunogen and antiviral drug therapy

Two trials of subjects inoculated with the inactivated, gp120-depleted HIV-1 Immunogen are reported. In one study, in which 19 subjects received ZDV and 8 subjects received ddI, treatment with the HIV-1 Immunogen did not affect the pharmacokinetic parameters of the antiviral drugs. In another study, 65 subjects who were previously immunized with the HIV-1 Immunogen over a mean period of 4.0 years (range, 1.2-5.4 years) received inoculations at 0 and 6 months. At some point during this 48-week study, 72% of the subjects (47/65) were receiving antiviral drug therapy. The HIV-1 DNA load in CD4 cells and CD4 percentage were found to be stable over the 48-week period. Delayed-type hypersensitivity to HIV-1 antigens increased after two inoculations with the HIV-1 Immunogen. In these two trials, no serious treatment-related adverse events were documented in the subjects. The two studies presented herein are the first to suggest that an immune-based therapy such as the HIV-1 Immunogen can be combined safely with antiviral drugs, supporting further study to evaluate the clinical utility of this approach.

Use of viral resistance patterns to antiretroviral drugs in optimising selection of drug combinations and sequences

High rates of viral replication throughout HIV infection, and the frequency of mutation occurring during each replication cycle due to the inaccuracy of reverse transcriptase, drive the potential for drug-resistant viral variants to appear under the selective pressure of antiretroviral therapy. Loss of antiviral effect with a variety of antiretroviral agents has been reported to coincide with the appearance of viral mutants with reduced drug sensitivity. Additionally, the presence of both phenotypic and genotypic zidovudine resistance is associated with an increased risk of clinical disease progression and death, independent of a change of therapy to didanosine. The patterns of resistance to and cross-resistance between antiretroviral agents are increasingly well characterised, and represent an important consideration when deciding how to combine and/or sequence antiretrovirals to achieve optimal antiviral effects. Given the limited number of antiretrovirals currently available or in advanced development, it is important not to potentially limit future therapeutic options by using, early in the treatment sequence, therapies which may select for cross-resistant viral variants and hence potentially reduce the additional therapeutic response when treatment is changed to another member of that drug class.

Fluctuations in steady state level of genomic HIV-1 RNA and replication intermediates related to disease progression rate

Steady state levels of HIV-1 genomic RNA and unintegrated circular DNA fluctuate in the course of HIV-1 infection. Genomic RNA in serum was detected using the NASBA technique and the amount of circular DNA was assessed by PCR. Quantification was done by competitive techniques using co-amplification of internal standards. Within the Amsterdam Cohort Studies it was possible to distinguish rapid progressors, intermediate progressors, slow progressors and non-progressors. Rapid progressors show persistently high viral RNA loads from seroconversion on, while all other HIV-1-infected individuals show a steady decline after seroconversion. Subsequent rises in viral RNA levels herald disease progression in later stages of infection. Unintegrated circular DNA shows similar, but somewhat delayed kinetics. These results indicate that the distribution of AIDS and the average length of the symptom-free period in an HIV-1-infected host population is determined by the steady state levels of genomic RNA and of replication intermediates that are produced by a particular HIV-1 virus population in the average seropositive individual.

Host-parasite dynamics and outgrowth of virus containing a single K70R amino acid change in reverse transcriptase are responsible for the loss of human immunodeficiency virus type 1 RNA load suppression by zidovudine

The association between human immunodeficiency virus type I (HIV-1) RNA load changes and the emergence of resistant virus variants was investigated in 24 HIV-1-infected asymptomatic persons during 2 years of treatment with zidovudine by sequentially measuring serum HIV-1 RNA load and the relative amounts of HIV-1 RNA containing mutations at reverse transcriptase (RT) codons 70 (K-->R), 41 (M-->L), and 215 (T-->Y/F). A mean maximum decline in RNA load occurred during the first month, followed by a resurgence between 1 and 3 months, which appeared independent of drug-resistance. Mathematical modeling suggests that this resurgence is caused by host-parasite dynamics, and thus reflects infection of the transiently increased numbers of CD4+ lymphocytes. Between 3 and 6 months of treatment, the RNA load returned to baseline values, which was associated with the emergence of virus containing a single lysine to arginine amino acid change at RT codon 70, only conferring an 8-fold reduction in susceptibility. Despite the relative loss of RNA load suppression, selection toward mutations at RT codons 215 and 41 continued. Identical patterns were observed in the mathematical model. While host-parasite dynamics and outgrowth of low-level resistant virus thus appear responsible for the loss of HIV-1 RNA load suppression, zidovudine continues to select for alternative mutations, conferring increasing levels of resistance.

Controlling HIV pathogenesis: the role of the noncytotoxic anti-HIV response of CD8+ T cells

Noncytotoxic CD8+ T cells may play a critical role in preventing progression to disease following human immunodeficiency virus (HIV) infection. This antiviral response, mediated by a novel CD8+ T-cell antiviral factor (CAF), occurs soon after infection and is maintained in asymptomatic individuals. Here, Jay Levy and colleagues propose that this antiviral activity represents a natural cellular immune reaction that controls HIV production and protects the host from potential harmful effects of cytotoxic T lymphocytes.

Evolution of zidovudine resistance-associated genotypes in human immunodeficiency virus type 1-infected patients

Substantial differences have been described in the response of individual patients to zidovudine (ZDV) therapy, both in the clinical impact and in virus load. Genotypic changes associated with the appearance of drug resistance may also be different or occur at different rates. We have obtained the nucleotide sequence of the RT domain of individual HIV-1 genomes extracted from 10 plasma and peripheral blood mononuclear cell (PBMC) samples donated by two haemophiliac patients before, during, and after long-term ZDV therapy. Although the plasma virus load was similar throughout, the order and timing of appearance of resistance-associated substitutions differed in the two patients. In patient p74, K70R appeared after 4 months, T215Y at 5.5 months, and M41L at 13 months. In p87, K70R also appeared at 4 months, but T215Y and K219Q were not observed until 18 months and M41L not at all. Much greater sequence change overall occurred in p74. The evolution of the viral population in that patient was dominated by the unique appearance of T215Y and subsequently M41L, with all sequences from the last time point being descended by a single path from the pretreatment samples. However, in p87, several different lineages of RT sequences were found to persist throughout treatment. We propose that these differences in outcome may be determined by differences in genetic background at sites other than the five generally considered to be associated with ZDV sensitivity.

Comparative evaluation of NASBA HIV-1 RNA QT, AMPLICOR-HIV monitor, and QUANTIPLEX HIV RNA assay, three methods for quantification of human immunodeficiency virus type 1 RNA in plasma

Three commercial assays for quantifying plasma human immunodeficiency virus type 1 (HIV-1) RNA were evaluated. The assays differed in their sample volumes, the means of preparing samples, and methods of amplification and detection. Plasma samples were obtained from 36 HIV-1-infected patients representing all stages of HIV-1 infection and were analyzed as coded specimens. Measurement of HIV-1 RNA baseline levels revealed no significant difference in sensitivity between the three assays. The assays were also applied to the quantitation of HIV-1 RNA levels in the plasma of patients who were changing their antiretroviral therapy. The changes measured in HIV-1 RNA levels in plasma in response to therapy were comparable by the three assays. No close correlation was found between the amount of HIV-1 RNA and the CD4 T-cell count; HIV-1 RNA assays were more sensitive than p24 antigen assays as an indicator of plasma viremia. Overall, the study demonstrates that all three quantitative assays for HIV-1 RNA can be used to measure the HIV-1 RNA copy number representing the HIV-1 viremia status in patients with HIV-1 infection. Since this copy number is likely to be useful in monitoring the effectiveness of antiviral therapy, these quantitative assays for HIV-1 RNA are ready to be built into clinical trials.

Kinetics of appearance of neutralizing antibodies in 12 patients with primary or recent HIV-1 infection and relationship with plasma and cellular viral loads

HIV-1 primary infection is characterized by a short high titer viremia, which rapidly declines as the immune response emerges. The role of autologous neutralizing antibodies in the decline of viral replication was evaluated in 12 patients with primary or recent HIV-1 infection. Neutralizing antibodies detected for each patient could not generally be observed before several months after isolation of the first obtained HIV isolate. The plasma viral load, as measured by quantitation of the HIV-1 RNA, underwent a global decrease during the first 6 months of the infection, but this decrease did not seem to be associated with the emergence of neutralizing antibodies. The proviral load in peripheral blood mononuclear cells, which was studied by quantitative DNA polymerase chain reaction, exhibited fluctuations and was not as well curtailed as the plasma viremia in the majority of patients.

Effects of zidovudine-selected human immunodeficiency virus type 1 reverse transcriptase amino acid substitutions on processive DNA synthesis and viral replication

Certain amino acid substitutions in the reverse transcriptase (RT), including D67N, K70R, T215Y, and K219Q, cause high-level resistance of human immunodeficiency virus type 1 (HIV-1) to zidovudine (3'-azidothymidine; AZT) and appear to approximate the template strand of the enzyme-template-primer complex in structural models. We studied whether this set of mutations altered RT-template-primer interaction as well as their effect on virus replication in the absence of inhibitor. When in vitro polymerization was limited to a single association of an RT with an oligodeoxynucleotide-primed heteropolymeric RNA template (a single processive cycle), recombinant-expressed mutant 67/70/215/219 RT synthesized 5- to 10-fold more high-molecular-weight DNA products (>200 nucleotides in length) than wild-type RT. This advantage was maintained as deoxynucleoside triphosphate (dNTP) concentrations were decreased to limiting levels. In contrast, no difference was seen between wild-type and mutant RTs under conditions allowing repeated associations of enzyme with template-primer. Because intracellular dNTP concentrations are low prior to mitogenic stimulation, we compared replication of mutant 67/70/215/219 virus and wild-type virus in peripheral blood mononuclear cells (PBMC) stimulated before and after infection. In the absence of inhibitor, mutant 67/70/215/219 virus had a replication advantage in PBMC stimulated with phytohemagglutinin and interleukin-2 after infection, but virus replication was similar in PBMC stimulated before infection in vitro. The results confirm that RT mutations D67N, K70R, T215Y, and K219Q affect an enzyme-template-primer interaction in vitro and suggest that such substitutions may affect HIV-1 pathogenesis during therapy by increasing viral replication capacity in cells stimulated after infection.

Detection of unintegrated HIV type 1 DNA in cell culture and clinical peripheral blood mononuclear cell samples: correlation to disease stage

This article reports on the development of PCR as a sensitive method of detecting both linear and circular forms of HIV-1 unintegrated viral DNA (UVD). The method was developed in a cell line study designed to follow the sequential synthesis of these forms over time. In all T lymphoid lineage cell lines, the full-length linear UVD (LUVD) was synthesized prior to both 1 and 2 LTR forms of circular UVD (CUVD), although all forms were detected by 12 hr postinoculation. Analysis of unstimulated PBMC samples from HIV-positive patients showed a significant difference in the presence of detectable CUVD forms and CDC groups II and IV (p < 0.001) and CDC groups III and IV (p < 0.001). No significance was demonstrated between CDC groups II and III (p > 0.5), linking the presence of CUVD forms to clinical disease and immunodeficiency. We propose that circular unintegrated forms of HIV-1 DNA may play a role in the development of acquired immunodeficiency syndrome.

Dynamics of viral replication in infants with vertically acquired human immunodeficiency virus type 1 infection

About one-third of vertically HIV-1 infected infants develop AIDS within the first months of life; the remainder show slower disease progression. We investigated the relationship between the pattern of HIV-1 replication early in life and disease outcome in eleven infected infants sequentially studied from birth. Viral load in cells and plasma was measured by highly sensitive competitive PCR-based methods. Although all infants showed an increase in the indices of viral replication within their first weeks of life, three distinct patterns emerged: (a) a rapid increase in plasma viral RNA and cell-associated proviral DNA during the first 4-6 wk, reaching high steady state levels (> 1,000 HIV-1 copies/10(5) PBMC and > 1,000,000 RNA copies/ml plasma) within 2-3 mo of age; (b) a similar initial rapid increase in viral load, followed by a 2.5-50-fold decline in viral levels; (c) a significantly lower (> 10-fold) viral increase during the first 4-6 wk of age. All infants displaying the first pattern developed early AIDS, while infants with slower clinical progression exhibited the second or third pattern. These findings demonstrate that the pattern of viral replication and clearance in the first 2-3 mo of life is strictly correlated with, and predictive of disease evolution in vertically infected infants.

Human immunodeficiency virus replication in the presence of antiretroviral drugs: analogies to antineoplastic drug resistance

There are many analogies between antineoplastic therapy and antiviral therapy. For each there may be sanctuary sites in which the drug is ineffective because of decreased accumulation of the active form of the drug or increased competition by naturally occurring inhibitors. These sanctuaries may be restricted to anatomic or biochemical subsets of the population. A knowledge of these sanctuaries is essential to an understanding of the failure of therapy and for the design of more effective treatments. Eradication of these sanctuary sites may be important because they may be responsible for the viral replication or tumor cell division that continues to generate the diversity that drives clonal evolution. Ultimately, diversity as a consequence of the accumulation of mutations results in the selection of resistant viral or tumor cell variants and the failure of drug therapy. Maximizing therapy in an attempt to diminish the rate of generation of this diversity may result in better clinical outcomes, including a delay in the generation of variants with genetic drug resistance.