scholarly journals Impact of Novel Resistance Profiles in HIV-1 Reverse Transcriptase on Phenotypic Resistance to NVP

2012 ◽  
Vol 2012 ◽  
pp. 1-8
Author(s):  
Liyan Jiao ◽  
Hanping Li ◽  
Lin Li ◽  
Daomin Zhuang ◽  
Yongjian Liu ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Site Directed Mutagenesis ◽  
Drug Resistant ◽  
Wild Type ◽  
Phenotypic Resistance ◽  
Drug Resistant Mutation ◽  
The Impact ◽  
Hiv 1 ◽  
Resistant Mutation ◽  
Phenotypic Drug Resistance

Objective. To clarify the impact of H221Y mutation on drug resistance to NVP.Methods. 646 bp HIV-1polgene fragments (from 592 to 1237 nucleotide) with different NNRTIs mutation profiles from AIDS patients receiving antiretroviral therapy containing NVP regimens were introduced into pNL4-3 backbone plasmid. H221Y and (or) Y181C mutations were reverted to wild type amino acids by site-directed mutagenesis, then strains containing various mutation patterns were packaged. Phenotypic drug resistance was analyzed on TZM-bl cells.Results. 12 strains containing different drug-resistant mutation profiles were constructed, including the K101Q series (K101Q/Y181C/H221Y, K101Q/Y181C, K101Q/H221Y, and K101Q), the V179D series (V179D/Y181C/H221Y, V179D/Y181C, V179D/H221Y, and V179D), and the K103N series (K103N/Y181C/H221Y, K103N/Y181C, K103N/H221Y, K103N). For strains containing the mutation profiles (K101Q/Y181C, K101Q, V179D/Y181C, V179D, K103N/Y181C, and K103N), the presence of H221Y reduced NVP susceptibility by2.1±0.5to3.6±0.5fold. To the mutation profiles K101Q/H221Y, K101Q, V179D/H221Y, V179D, K103N/H221Y, and K103N, the presence of Y181C reduced NVP susceptibility by41.9±8.4to1297.0±289.1fold. For the strains containing K101Q, V179D, and K103N, the presence of Y181C/H221Y combination decreased NVP susceptibility by100.6±32.5to3444.6±834.5fold.Conclusion. On the bases of various NNRTIs mutation profiles, Y181C remarkably improved the IC50to NVP, although H221Ymutation alone just increases 2.1 ∼ 3.6-fold resistance to NVP, the mutation could improve 100.6 ∼ 3444.6-fold resistance to NVP when it copresent with Y181C, the phenotypic drug resistance fold was improved extremely. For strains containing the mutation profiles (K101Q/Y181C, K101Q, V179D/Y181C, V179D, K103N/Y181C, and K103N), the presence of H221Y reduced NVP susceptibility by2.1±0.5to3.6±0.5fold.

scholarly journals Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals

2020 ◽  
Vol 75 (11) ◽  
pp. 3319-3326
Author(s):  
Benjamin Chimukangara ◽  
Jennifer Giandhari ◽  
Richard Lessells ◽  
Nonhlanhla Yende-Zuma ◽  
Benn Sartorius ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Virological Failure ◽  
Statistical Significance ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
The Impact ◽  
Hiv 1 ◽  
Control Study

Abstract Objectives To determine the impact of pretreatment low-abundance HIV-1 drug-resistant variants (LA-DRVs) on virological failure (VF) among HIV-1/TB-co-infected individuals treated with NNRTI first-line ART. Methods We conducted a case–control study of 170 adults with HIV-1/TB co-infection. Cases had at least one viral load (VL) ≥1000 RNA copies/mL after ≥6 months on NNRTI-based ART, and controls had sustained VLs <1000 copies/mL. We sequenced plasma viruses by Sanger and MiSeq next-generation sequencing (NGS). We assessed drug resistance mutations (DRMs) using the Stanford drug resistance database, and analysed NGS data for DRMs at ≥20%, 10%, 5% and 2% thresholds. We assessed the effect of pretreatment drug resistance (PDR) on VF. Results We analysed sequences from 45 cases and 125 controls. Overall prevalence of PDR detected at a ≥20% threshold was 4.7% (8/170) and was higher in cases than in controls (8.9% versus 3.2%), P = 0.210. Participants with PDR at ≥20% had almost 4-fold higher odds of VF (adjusted OR 3.7, 95% CI 0.8–18.3) compared with those without, P = 0.104. PDR prevalence increased to 18.2% (31/170) when LA-DRVs at ≥2% were included. Participants with pretreatment LA-DRVs only had 1.6-fold higher odds of VF (adjusted OR 1.6, 95% CI 0.6–4.3) compared with those without, P = 0.398. Conclusions Pretreatment DRMs and LA-DRVs increased the odds of developing VF on NNRTI-based ART, although without statistical significance. NGS increased detection of DRMs but provided no additional benefit in identifying participants at risk of VF at lower thresholds. More studies assessing mutation thresholds predictive of VF are required to inform use of NGS in treatment decisions.

scholarly journals The S68G polymorphism is a compensatory mutation associated with the drug resistance mutation K65R in CRF01_AE strains

2019 ◽  
Author(s):  
Shengjia Li ◽  
Jinming Ouyang ◽  
Bin Zhao ◽  
Minghui An ◽  
Lin Wang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Treatment Failure ◽  
Reverse Transcriptase ◽  
Temporal Association ◽  
Compensatory Mutation ◽  
Double Mutation ◽  
Phenotypic Resistance ◽  
K65r Mutation ◽  
The Impact ◽  
Hiv 1

Abstract Background: The rate of S68G mutation in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase has increased and is closely related to the K65R mutation among treatment-failure CRF01_AE-infected patients. We aim to explore the temporal association of S68G and K65R mutations among treatment-failure CRF01_AE-infected patients and disclose the role of the S68G mutation on nucleotide/nucleoside reverse transcriptase inhibitor (NRTI) susceptibility and viral replication with the K65R double mutation. Methods: Occurrence of S68G and K65R mutations was evaluated among HIV-1 of various subtypes in the global HIV Drug Resistance Database. The temporal association of S68G and K65R mutations was analyzed by next-generation sequencing (NGS). The impact of the S68G mutation on NRTI susceptibility and replication adaptability was analyzed with pseudovirus phenotypic resistance assays and growth competition assays, respectively. Results: The frequency of the S68G mutation increased significantly in all HIV subtypes and circulating recombinant forms in treatment-experienced patients (except for subtype F), as did the frequency of the K65R/S68G double mutation. NGS revealed that the S68G mutation occurred following K65R mutation among three out of four patients. No significant difference in fold-change for tenofovir, lamivudine or efavirenz was detected between K65R and K65R/S68G mutations in phenotypic resistance assays. The K65R/S68G double mutant outgrew the K65R mutant within 13 days of co-culture for any input ratio among all patients. Conclusions: S68G might be a natural polymorphism and compensatory mutation of K65R selected by NRTIs among the CRF01_AE strain of HIV-1, which does not affect NRTI susceptibility, but improves the replication adaptability on K65R mutants.

A structural and thermodynamic escape mechanism from a drug resistant mutation of the HIV-1 protease

2004 ◽  
Vol 55 (3) ◽  
pp. 594-602 ◽  
Author(s):  
Sonia Vega ◽  
Lin-Woo Kang ◽  
Adrian Velazquez-Campoy ◽  
Yoshiaki Kiso ◽  
L. Mario Amzel ◽  
...  
Keyword(s):  
Drug Resistant ◽  
Escape Mechanism ◽  
Drug Resistant Mutation ◽  
Hiv 1 ◽  
Resistant Mutation

scholarly journals Contribution of Gag and Protease to HIV-1 Phenotypic Drug Resistance in Pediatric Patients Failing Protease Inhibitor-Based Therapy

2016 ◽  
Vol 60 (4) ◽  
pp. 2248-2256 ◽  
Author(s):  
Jennifer Giandhari ◽  
Adriaan E. Basson ◽  
Katherine Sutherland ◽  
Chris M. Parry ◽  
Patricia A. Cane ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Amino Acid ◽  
Pediatric Patients ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Amino Acid Substitutions ◽  
Resistance Mutations ◽  
Phenotypic Resistance ◽  
Protease Resistance ◽  
Hiv 1

ABSTRACTProtease inhibitors (PIs) are used as a first-line regimen in HIV-1-infected children. Here we investigated the phenotypic consequences of amino acid changes in Gag and protease on lopinavir (LPV) and ritonavir (RTV) susceptibility among pediatric patients failing PI therapy. The Gag-protease from isolates from 20 HIV-1 subtype C-infected pediatric patients failing an LPV and/or RTV-based regimen was phenotyped using a nonreplicativein vitroassay. Changes in sensitivity to LPV and RTV relative to that of the matched baseline (pretherapy) sample were calculated. Gag and protease amino acid substitutions associated with PI failure were created in a reference clone by site-directed mutagenesis and assessed. Predicted phenotypes were determined using the Stanford drug resistance algorithm. Phenotypic resistance or reduced susceptibility to RTV and/or LPV was observed in isolates from 10 (50%) patients, all of whom had been treated with RTV. In most cases, this was associated with protease resistance mutations, but substitutions at Gag cleavage and noncleavage sites were also detected. Gag amino acid substitutions were also found in isolates from three patients with reduced drug susceptibilities who had wild-type protease. Site-directed mutagenesis confirmed that some amino acid changes in Gag contributed to PI resistance but only in the presence of major protease resistance-associated substitutions. The isolates from all patients who received LPV exclusively were phenotypically susceptible. Baseline isolates from the 20 patients showed a large (47-fold) range in the 50% effective concentration of LPV, which accounted for most of the discordance seen between the experimentally determined and the predicted phenotypes. Overall, the inclusion of thegaggene and the use of matched baseline samples provided a more comprehensive assessment of the effect of PI-induced amino acid changes on PI resistance. The lack of phenotypic resistance to LPV supports the continued use of this drug in pediatric patients.

scholarly journals Replication and drug resistant mutation of HIV-1 subtype B' (Thailand B) variants isolated from HAART treatment individuals in China

2009 ◽  
Vol 6 (1) ◽  
pp. 201 ◽  
Author(s):  
Jianping Sun ◽  
Liying Ma ◽  
Xiaoling Yu ◽  
Yang Huang ◽  
Lin Yuan ◽  
...  
Keyword(s):  
Drug Resistant ◽  
Subtype B ◽  
Drug Resistant Mutation ◽  
Hiv 1 ◽  
Resistant Mutation

scholarly journals PANDAA-monium: Intentional violations of conventional qPCR design enables rapid, HIV-1 subtype-independent drug resistance SNP detection

2019 ◽  
Author(s):  
Iain J. MacLeod ◽  
Christopher F. Rowley ◽  
M. Essex
Keyword(s):  
Drug Resistance ◽  
Large Scale ◽  
Clinical Decision Making ◽  
Site Directed Mutagenesis ◽  
Resistance Mutations ◽  
Degenerate Primers ◽  
Genotypic Resistance ◽  
Infected People ◽  
The Impact ◽  
Hiv 1

ABSTRACTGlobal efforts to ensure that 90% of all HIV-infected people receiving antiretroviral therapy (ART) will be virally suppressed by 2020 could be crippled by increases in acquired and transmitted HIV drug resistance (HIVDR), which challenge ART efficacy. The long-term sustainability of ART treatment programs is contingent on effective HIVDR monitoring yet current Sanger sequencing genotypic resistance tests are inadequate for large-scale implementation in low- and middle-income countries (LMICs). A simple, rapid, affordable HIVDR diagnostic would radically improve the treatment paradigm in LMICs by facilitating informed clinical decision-making upon ART failure. Although point mutation assays can be broadly deployed in this context, the primary challenge arises from extensive sequence variation surrounding targeted drug resistance mutations (DRMs). Here, we systematically and intentionally violate the canonical principles of qPCR design to develop a novel assay, Pan-Degenerate Amplification and Adaptation (PANDAA), that mitigates the impact of DRM-proximal secondary polymorphisms on probe-based qPCR performance to enable subtype-independent, focused resistance genotyping. Using extremely degenerate primers with 3’ termini overlapping the probe-binding site, the HIV-1 genome is adapted through site-directed mutagenesis to replace secondary polymorphisms flanking the target DRM during the initial qPCR cycles. We show that PANDAA can quantify key HIV DRMs present at ≥5% and has diagnostic sensitivity and specificity of 96.9% and 97.5%, respectively, to detect DRMs associated with ART failure. PANDAA is an innovative solution for HIVDR genotyping and is an advancement in qPCR technology that could be applicable to any scenario where target-proximal genetic variability has been a roadblock in diagnostic development.

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