Panel of Prototypical Raltegravir-Resistant Infectious Molecular Clones in a Novel Integrase-Deleted Cloning Vector

BACKGROUND: Antiretroviral therapy containing an integrase strand transfer inhibitor plus two Nucleoside Reverse Transcriptase inhibitors has now been recommended for treatment of HIV-1-infected patients. This thus determined possible pre-existing integrase resistance associated mutations in the integrase gene prior to introduction of integrase inhibitors combination therapy in Kenya.METHODS: Drug experienced HIV patients were enrolled at Kisii Teaching and Referral in Kenya. Blood specimens from (33) patients were collected for direct sequencing of HIV-1 polintegrase genes. Drug resistance mutations were interpreted according to the Stanford algorithm and phylogenetically analysed using insilico tools.RESULTS: From pooled 188 Kenyan HIV integrase sequences that were analysed for drug resistance, no major mutations conferring resistance to integrase inhibitors were detected. However, polymorphic accessory mutations associated with reduced susceptibility of integrase inhibitors were observed in low frequency; M50I (12.2%), T97A (3.7%), S153YG, E92G (1.6%), G140S/A/C (1.1%) and E157Q (0.5%). Phylogenetic analysis (330 sequences revealed that HIV-1 subtype A1 accounted for majority of the infections, 26 (78.8%), followed by D, 5 (15.2%) and C, 2 (6%).CONCLUSION: The integrase inhibitors will be effective in Kenya where HIV-1 subtype A1 is still the most predominant. However, occurring polymorphisms may warrant further investigation among drug experienced individuals on dolutegravir combination or integrase inhibitor treatment.

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Prevalence of Primary Resistance Mutations to Integrase Inhibitors in Treatment-Naïve and -Experienced Patients Infected With B and Non-B HIV-1 Variants

HIV Clinical Trials ◽

10.1310/hct1401-10 ◽

2013 ◽

Vol 14 (1) ◽

pp. 10-16 ◽

Cited By ~ 14

Author(s):

Carolina Gutiérrez ◽

Beatriz Hernández-Novoa ◽

María Jesús Pérez-Elías ◽

Ana María Moreno ◽

África Holguín ◽

...

Keyword(s):

Integrase Inhibitors ◽

Resistance Mutations ◽

Primary Resistance ◽

Treatment Naïve ◽

Hiv 1

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Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities

10.7287/peerj.preprints.27833 ◽

2019 ◽

Author(s):

Lea El Khoury ◽

Krystel El Hage ◽

Jean-Philip Piquemal ◽

Serge Fermandjian ◽

Richard Maroun ◽

...

Keyword(s):

Density Functional ◽

Strand Transfer ◽

Free Energies ◽

Integrase Inhibitors ◽

Resistance Mutations ◽

Viral Dna ◽

Functional Theory ◽

Fluorescence Titrations ◽

Dynamics Simulations ◽

Hiv 1

Three Integrase (IN) strand transfer inhibitors are in intensive clinical use, raltegravir, elvitegravir anddolutegravir. However, the onset of IN resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviralnucleobases, which are little, if at all, mutation-prone. We report experimental results of anisotropy fluorescence titrations of viral DNA by these three drugs . These show that the ranking of their inhibitory activities of the intasome corresponds to that of their free energies of binding, D Gs,to retroviral DNA, and that such a ranking is only governed by the binding enthalpies, D H, the entropy undergoing marginal variations.This ranking can therefore be directly correlated to that of model Quantum Chemistry (QC) calculations of intermolecular interaction energies of the sole halobenzene ring with the highly conserved retroviral nucleobases G4 and C14, using Density Functional Theory. This DE(QC) ranking is in turn reproduced by the corresponding DE tot values computed with a polarizable molecular mechanics/dynamics procedure, SIBFA (Sum of Interactions Between Fragments Ab initio computed). Such validations should enable polarizable molecular dynamics simulations on more potent inhibitors in their complexes with the complete intasome. Such derivatives should principally encompass modified halobenzene rings.

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Absence of Resistance Mutations in the Integrase Coding Region among ART-Experienced Patients in the Republic of the Congo

Microorganisms ◽

10.3390/microorganisms9112355 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2355

Author(s):

Ferdinand Emaniel Brel Got ◽

Patricia Recordon-Pinson ◽

Ghislain Loubano-Voumbi ◽

Dagene Ebourombi ◽

Marie-Lise Blondot ◽

...

Keyword(s):

Drug Resistance ◽

Clinical Signs ◽

University Hospital ◽

Integrase Inhibitors ◽

Resistance Mutations ◽

Drug Resistance Mutations ◽

Republic Of The Congo ◽

The Republic ◽

Hiv 1 ◽

High Diversity

Background: HIV infects around one hundred thousand patients in the Republic of the Congo. Approximately 25% of them receive an antiretroviral treatment; current first-line regimens include two NRTIs and one NNRTI, reverse transcriptase inhibitors. Recently, protease inhibitors (PIs) were also introduced as second-line therapy upon clinical signs of treatment failure. Due to the limited number of molecular characterizations and amount of drug resistance data available in the Republic of the Congo, this study aims to evaluate the prevalence of circulating resistance mutations within the pol region. Methods: HIV-positive, ART-experienced patients have been enrolled in four semi-urban localities in the Republic of the Congo. Plasma samples were collected, and viral RNA was extracted. The viral load for each patient was evaluated by RT-qPCR, following the general diagnostic procedures of the University Hospital of Bordeaux. Finally, drug resistance genotyping and phylogenetic analysis were conducted following Sanger sequencing of the pol region. Results: A high diversity of HIV-1 strains was observed with many recombinant forms. Drug resistance mutations in RT and PR genes were determined and correlated to HAART. Because integrase inhibitors are rarely included in treatments in the Republic of the Congo, the prevalence of integrase drug resistance mutations before treatment was also determined. Interestingly, very few mutations were observed. Conclusions: We confirmed a high diversity of HIV-1 in the Republic of the Congo. Most patients presented an accumulation of mutations conferring resistance against NRTIs, NNRTIs and PIs. Nonetheless, the absence of integrase mutations associated with drug resistance suggests that the introduction of integrase inhibitors into therapy will be highly beneficial to patients in the Republic of the Congo.

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An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors

10.1101/647297 ◽

2019 ◽

Author(s):

Kristof Theys ◽

Pieter Libin ◽

Kristel Van Laethem ◽

Ana B Abecasis

Keyword(s):

Drug Resistance ◽

Antiviral Treatment ◽

Integrase Inhibitors ◽

Resistance Mutations ◽

Genetic Barrier ◽

Viral Pathogens ◽

Subtype B ◽

Genetic Potential ◽

The Impact ◽

Hiv 1

AbstractViral pathogens causing global disease burdens are often characterised by high rates of evolutionary changes, facilitating escape from therapeutic or immune selective pressure. Extensive viral diversity at baseline can shorten the time to resistance emergence and alter mutational pathways, but the impact of genotypic background on the genetic barrier can be difficult to capture, in particular for antivirals in experimental stages, recently approved or expanded into new settings. We developed an evolutionary-based counting method to quantify the population genetic potential to resistance and assess differences between populations. We demonstrate its applicability to HIV-1 integrase inhibitors, as their increasing use globally contrasts with limited availability of non-B subtype resistant sequences and corresponding knowledge gap on drug resistance. A large sequence dataset encompassing most prevailing subtypes and resistance mutations of first- and second-generation inhibitors were investigated. A varying genetic potential for resistance across HIV-1 subtypes was detected for 15 mutations at 12 positions, with notably 140S in subtype B, while 140C was discarded to vary across subtypes. An additional analysis for HIV-1 reverse transcriptase inhibitors identified a higher potential for 65R in subtype C, on the basis of a differential codon usage not reported before. The evolutionary interpretation of genomic differences for antiviral treatment remains challenging. Our framework advances existing counting methods with an increased sensitivity that identified novel subtype dependencies as well as rejected previous statements. Future applications include novel HIV-1 drug classes as well as other viral pathogens.

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Elvitegravir: A New HIV Integrase Inhibitor

Antiviral Chemistry and Chemotherapy ◽

10.3851/imp1397 ◽

2009 ◽

Vol 20 (2) ◽

pp. 79-85 ◽

Cited By ~ 51

Author(s):

Kazuya Shimura ◽

Eiichi N Kodama

Keyword(s):

Antiviral Drug ◽

Integrase Inhibitor ◽

Phase Iii ◽

Hiv Integrase ◽

Integrase Inhibitors ◽

Resistance Mutations ◽

Hiv 1

Integration is a distinctive and essential process in the HIV infection cycle and thus represents an attractive antiviral drug target. Integrase inhibitors combined with other classes of drug might contribute to long-lasting suppression of HIV type-1 (HIV-1) replication for many patients. Of the numerous potential integrase inhibitor leads that have been reported, few have reached clinical trials and only one, raltegravir, has been approved (in late 2007) for the treatment of HIV-1-infected patients. Another integrase inhibitor, elvitegravir, is currently showing promise in Phase III clinical studies. Once-daily administration of elvitegravir has a comparable antiviral activity to twice-daily of raltegravir in HIV-1-infected patients. Here, we highlight the salient features of elvitegravir: its chemical structure compared with representative integrase inhibitors, mechanism of action, in vitro and in vivo activity against HIV and other retroviruses, and the effect of integrase polymorphisms and resistance mutations on its anti-HIV activity.

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Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities

10.7287/peerj.preprints.27833v1 ◽

2019 ◽

Author(s):

Lea El Khoury ◽

Krystel El Hage ◽

Jean-Philip Piquemal ◽

Serge Fermandjian ◽

Richard Maroun ◽

...

Keyword(s):

Density Functional ◽

Strand Transfer ◽

Free Energies ◽

Integrase Inhibitors ◽

Resistance Mutations ◽

Viral Dna ◽

Functional Theory ◽

Fluorescence Titrations ◽

Dynamics Simulations ◽

Hiv 1

Three Integrase (IN) strand transfer inhibitors are in intensive clinical use, raltegravir, elvitegravir anddolutegravir. However, the onset of IN resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviralnucleobases, which are little, if at all, mutation-prone. We report experimental results of anisotropy fluorescence titrations of viral DNA by these three drugs . These show that the ranking of their inhibitory activities of the intasome corresponds to that of their free energies of binding, D Gs,to retroviral DNA, and that such a ranking is only governed by the binding enthalpies, D H, the entropy undergoing marginal variations.This ranking can therefore be directly correlated to that of model Quantum Chemistry (QC) calculations of intermolecular interaction energies of the sole halobenzene ring with the highly conserved retroviral nucleobases G4 and C14, using Density Functional Theory. This DE(QC) ranking is in turn reproduced by the corresponding DE tot values computed with a polarizable molecular mechanics/dynamics procedure, SIBFA (Sum of Interactions Between Fragments Ab initio computed). Such validations should enable polarizable molecular dynamics simulations on more potent inhibitors in their complexes with the complete intasome. Such derivatives should principally encompass modified halobenzene rings.

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M184V/I does not impact the efficacy of abacavir/lamivudine/dolutegravir use as switch therapy in virologically suppressed patients

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa019 ◽

2020 ◽

Vol 75 (5) ◽

pp. 1290-1293 ◽

Cited By ~ 1

Author(s):

Aude Jary ◽

Anne-Geneviève Marcelin ◽

Charlotte Charpentier ◽

Marc Wirden ◽

Minh P Lê ◽

...

Keyword(s):

Resistance Mutation ◽

Integrase Inhibitors ◽

Resistance Mutations ◽

Hiv Viral Load ◽

Genotypic Resistance ◽

Genotypic Resistance Test ◽

Pretreated Patients ◽

Hiv 1 ◽

Residual Viraemia

Abstract Background M184V/I NRTI resistance mutations can be selected by either lamivudine/emtricitabine or abacavir. There are controversies about the use of abacavir/lamivudine/dolutegravir combinations in HIV-1-infected treatment-experienced patients with a fully suppressed HIV viral load (VL) and harbouring M184V/I. Objectives We assessed the efficacy of abacavir/lamivudine/dolutegravir when used in HIV-infected pretreated patients with an undetectable VL who previously harboured M184V/I as a unique NRTI resistance mutation in a genotypic resistance test and had no resistance to integrase inhibitors. Patients and methods A total of 154 patients with a fully suppressed HIV-1 plasma VL (<50 copies/mL) treated with tenofovir disoproxil fumarate/emtricitabine/boosted PI or abacavir/lamivudine/boosted PI who switched to an abacavir/lamivudine/dolutegravir regimen and had M184V/I as a unique NRTI resistance mutation in their therapeutic history were retrospectively analysed up to 12 months after the switch to abacavir/lamivudine/dolutegravir. Assessment of residual viraemia was performed at Months 1, 3, 6 and 12. Plasma VL with undetectable HIV-1 RNA corresponded to an absence of residual viraemia. Results During the 12 months of follow-up, three patients had a blip of VL (53, 62 and 106 copies/mL) at Month 3 followed by a subsequent VL <50 copies/mL. No patient harboured a virological failure during the follow-up. Moreover, there was no change in residual viraemia during the follow-up. Conclusions M184V/I as a unique NRTI resistance mutation, regardless of possible selection by regimens containing lamivudine/emtricitabine or abacavir, does not affect the virological response of well-controlled patients who switched to abacavir/lamivudine/dolutegravir for at least 12 months.

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An HIV-1 integrase genotype assay for the detection of drug resistance mutations

Sexual Health ◽

10.1071/sh09041 ◽

2009 ◽

Vol 6 (4) ◽

pp. 305 ◽

Cited By ~ 3

Author(s):

Anna C. Hearps ◽

Vicki Greengrass ◽

Jennifer Hoy ◽

Suzanne M. Crowe

Keyword(s):

Drug Resistance ◽

Antiretroviral Drugs ◽

Plasma Samples ◽

Integrase Inhibitors ◽

Resistance Mutations ◽

Assay Sensitivity ◽

Integrase Gene ◽

Drug Resistance Mutations ◽

Hiv 1

Background: The integrase inhibitors (e.g. Raltegravir) are a new class of antiretroviral drugs that have recently become available for the treatment of patients with multi-drug resistant HIV-1 within Australia. The emergence of mutations that confer resistance to the integrase inhibitors has been observed in vivo; however, no commercial genotyping assay is currently available to screen for resistance to these drugs. Methods: The HIV-1 integrase gene was amplified from plasma-derived HIV-1 viral RNA via reverse transcription-polymerase chain reaction and genotype determined via population DNA sequencing. Drug resistance mutations and polymorphisms were detected using the Stanford University online HIV database. Assay sensitivity and reproducibility were determined using clinical and laboratory-derived samples. Results: Our in-house assay was capable of genotyping the integrase gene from all samples tested (n = 30) of HIV-1 subtypes B, C, D, F, CFR01_AE and CRF02_AG and can amplify the integrase region from plasma samples containing as few as 50 HIV RNA copies/mL. The assay is highly reproducible (average nucleotide concordance = 99.6%, n = 4) and is capable of detecting resistance-associated mutations. Conclusions:This assay is suitable for routine drug resistance screening of plasma samples from HIV-infected patients receiving integrase inhibitor antiretroviral drugs and also serves as a useful research tool.

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