Transmission of HIV-1 Drug-Resistant Variants: Prevalence and Effect on Treatment Outcome

Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark.
Clinical Infectious Diseases (Impact Factor: 8.89). 02/2010; 50(4):566-73. DOI: 10.1086/650001
Source: PubMed


Human immunodeficiency virus type 1 (HIV-1) drug resistance is an important threat to the overall success of antiretroviral therapy (ART). Because of the limited sensitivity of commercial assays, transmitted drug resistance (TDR) may be underestimated; thus, the effect that TDR has on treatment outcome needs to be investigated. The objective of this study was to investigate the prevalence of TDR in HIV-infected patients and to evaluate the significance of TDR with respect to treatment outcome by analyzing plasma viral RNA and peripheral blood mononuclear cell proviral DNA for the presence of drug resistance mutations.
In a prospective study, we investigated the level of TDR in 61 patients by comparing the results of a sensitive multiplex-primer-extension approach (termed HIV-SNaPshot) that is capable of screening for 9 common nucleoside reverse-transcriptase inhibitor and nonnucleotide reverse-transcriptase inhibitor mutations with those of a commercial genotyping kit, ViroSeq (Abbott).
Twenty-two patients were found to carry mutations. More patients with TDR were identified by the HIV-SNaPshot assay than by ViroSeq analysis (33% vs 13%; [P=.015). There was no significant difference in the time from initiation of ART to virological suppression between susceptible patients and those carrying low- or high-level resistance mutations (mean +/- standard deviation, 128 +/- 59.1 vs 164.9 +/- 120.4; P=.147). Furthermore, analyses of CD4 cell counts showed no significant difference between these 2 groups 1 year after the initiation of ART (mean, 184 vs 219 cells/microL; P=.267).
We found the prevalence of TDR in recently infected ART-naive patients to be higher than that estimated by ViroSeq genotyping alone. Follow-up of patients after treatment initiation showed a trend toward there being more clinical complications for patients carrying TDR, although a significant effect on treatment outcome could not be demonstrated. Therefore, the clinical relevance of low-abundance resistant quasispecies in early infection is still in question.

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    • "Prevalence in the treatment-naı¨ve patients was assessed for the 16 RPV-associated RAMs listed in the IAS-USA recommendations: K101E/P, E138A/G/ K/Q/R, V179L, Y181C/I/V, Y188L, H221Y, F227C, and M230I/L. For first-generation NNRTIs, the substitutions K103N, Y181C, G190A/S/E were chosen as herald of RAMs for this class [Jakobsen et al., 2010]. Prevalence of any NNRTIs-related RAMs was compared to any RPV-related (and to the main substitutions , K101E and E138K). "
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    ABSTRACT: Rilpivirine (RPV) is a novel NNRTI with a mutational pattern different from first-generation drugs of the same class: 16 resistance-associated mutations (RAM) are listed, but the combination E138K + M184I seems to be the most important. Aims of the present study were to evaluate the prevalence of these RAMs in Italian HIV-1 infected patients and to assess if previous drug history could represent a risk to develop RPV-related RAMs. The analysis was performed using the ARCA database, which contains data on resistance and therapy from subjects throughout Italy. Prevalence of RPV-associated and first-generation NNRTI-associated RAMs was evaluated. Linear regression model, odds ratio and 95% Confidence Interval were used to assess factors associated with the development of RPV RAMs, substitutions at position 184 and their combinations. A total of 8,067 tests were selected within the database. In Italian HIV-positive HAART-naïve patients, prevalence of the main RAMs for RPV is low except for E138A (present in 5.1% of subjects). The combination E138K + M184I is absent in both naïve and experienced subjects. A previous exposure to NVP might increase the risk to develop RPV-associated RAMs. TDF, EFV, and possibly FTC may predispose to the selection for M184I. Among Italian patients the susceptibility to RPV is widespread since some severe substitutions (e.g., E138K are rare), whereas issues exist for others (i.e., E138A, Y181C) which are more frequent. Appropriate use of RPV within a therapeutic sequencing might be controversial. J. Med. Virol. 9999: XX–XX, 2014. © 2014 Wiley Periodicals, Inc.
    Journal of Medical Virology 09/2014; 86(9). DOI:10.1002/jmv.23978 · 2.35 Impact Factor
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    • "The impact of minor variants on disease progression and HIV evolution is controversial. In drug resistance studies, some have reported an association between minor variants and poor clinical outcome [35-40], while others have found no such association [41-44]. Another important application of MPS is for the detection of minor variants in acute HIV infection, and possibility of early evolution resulting from immune selection pressure as detectable viremia emerges [27]. "
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    ABSTRACT: 454 pyrosequencing, a massively parallel sequencing (MPS) technology, is often used to study HIV genetic variation. However, the substantial mismatch error rate of the PCR required to prepare HIV-containing samples for pyrosequencing has limited the detection of rare variants within viral populations to those present above ~1%. To improve detection of rare variants, we varied PCR enzymes and conditions to identify those that combined high sensitivity with a low error rate. Substitution errors were found to vary up to 3-fold between the different enzymes tested. The sensitivity of each enzyme, which impacts the number of templates amplified for pyrosequencing, was shown to vary, although not consistently across genes and different samples. We also describe an amplicon-based method to improve the consistency of read coverage over stretches of the HIV-1 genome. Twenty-two primers were designed to amplify 11 overlapping amplicons in the HIV-1 clade B gag-pol and env gp120 coding regions to encompass 4.7 kb of the viral genome per sample at sensitivities as low as 0.01-0.2%.
    PLoS ONE 10/2013; 8(10):e76502. DOI:10.1371/journal.pone.0076502 · 3.23 Impact Factor
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    • "The advent of next generation sequencing platforms means that clinically relevant low abundance drug resistant HIV variants can be detected to prevalences as low as 1% of the viral population [10-16]. While several studies have found correlations between the presence of low abundance drug resistant viruses and clinical outcomes this has not always been the case [17,18]. To our knowledge, no studies have been undertaken to use ultra deep pyrosequencing (UDPS) to quantify the prevalence of low abundance drug resistant viral variants in the proviral DNA. "
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    ABSTRACT: Background The role of HIV-1 RNA in the emergence of resistance to antiretroviral therapies (ARTs) is well documented while less is known about the role of historical viruses stored in the proviral DNA. The primary focus of this work was to characterize the genetic diversity and evolution of HIV drug resistant variants in an individual’s provirus during antiretroviral therapy using next generation sequencing. Methods Blood samples were collected prior to antiretroviral therapy exposure and during the course of treatment from five patients in whom drug resistance mutations had previously been identified using consensus sequencing. The spectrum of viral variants present in the provirus at each sampling time-point were characterized using 454 pyrosequencing from multiple combined PCR products. The prevalence of viral variants containing drug resistant mutations (DRMs) was characterized at each time-point. Results Low abundance drug resistant viruses were identified in 14 of 15 sampling time-points from the five patients. In all individuals DRMs against current therapy were identified at one or more of the sampling time-points. In two of the five individuals studied these DRMs were present prior to treatment exposure and were present at high prevalence within the amplified and sequenced viral population. DRMs to drugs other than those being currently used were identified in four of the five individuals. Conclusion The presence of DRMs in the provirus, regardless of their observed prevalence did not appear to have an effect on clinical outcomes in the short term suggesting that the drug resistant viral variants present in the proviral DNA do not appear to play a role in the short term in facilitating the emergence of drug resistance.
    BMC Infectious Diseases 01/2013; 13(1):52. DOI:10.1186/1471-2334-13-52 · 2.61 Impact Factor
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