Persistent Production of an Integrase-Deleted HIV-1 Variant with No Resistance Mutation and Wild-Type Proviral DNA in a Treated Patient

HIV-1 resistance to antiretroviral therapy (ART) is a crucial issue, despite various effective drugs are available for the treatment. Although the viral RNA is suppressed below the detection limit (<50 copies/ml) with the use of potent antiviral drugs, the mutation can be archived in the cellular reservoir as proviral DNA. The detection of proviral DNA and mutation screening in HIV 1 RNA for genotypic resistance is the sole basis for monitoring the effectiveness of ART. Our study aim to access the extent of latent HIV infections by detecting env V3 DNA and also testing of M184V (meth184val; ATG - GTG substitution at 184th codon) specific mutations in HIV-1 RT gene to monitor the effectiveness of ART. The HIV-1 env V3 DNA sequence was amplified using multiple upstream and downstream primes to show the latent HIV infections, whereas polymerase chain reaction- restriction fragment digestion assay (PCR-RFDA) was used for testing M184V mutation in HIV-1 RT gene. In the study, out of 15 HIV infected patient blood samples, 12 shows amplification of env V3 DNA, confirming the latent HIV infections while 3 were negative for env V3 DNA. HIV-1 RT gene tested for M184V mutation in all 15 samples showed wild type after analysis using PCR-RFDA. After digestion with CviAII, three bands were observed in wild type whereas in mutant only two bands. Although the study shows negative for the M184V resistance mutation, screening of various panels of drug resistance mutations should be performed in recently infected HIV-1 patients for planning the effective ART strategy. The data is not enough to compare the overall scenario of the Nepal thus warrant urgency for large scale study with standard genotypic tools.

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Improved HIV-1 drug resistance mutation prediction using quasispecies reconstruction supported analysis

10.1101/2021.05.24.445423 ◽

2021 ◽

Author(s):

Jyoti Sutar ◽

Shilpa Bhowmick ◽

Varsha Padwal ◽

Vidya Nagar ◽

Priya Patil ◽

...

Keyword(s):

Drug Resistance ◽

High Throughput Sequencing ◽

Resistance Mutation ◽

Detection Sensitivity ◽

Treatment As Prevention ◽

Reconstruction Algorithms ◽

Resistance Mutations ◽

Proviral Dna ◽

Hiv 1

Accurate and sensitive approaches to detect HIV-1 drug resistance mutations (DRMs) are indispensable for the paradigm of treatment as prevention. While HIV-1 proviral DNA allows sensitive high throughput sequencing (HTS)-based DRM detection, its applicability is limited by presence of defective genomes. This study demonstrates application of quasispecies reconstruction algorithms (QRAs) to improve DRM detection sensitivity from proviral DNA. A robust benchmarking of 5 QRAs was performed with 2 distinct experimental control-datasets including a stringent, novel control: DCPM, simulating in-vivo variant distribution (0.08%-86.5%). Selected QRA was further evaluated for its ability to differentiate DRMs from hypermutated sequences using an in-silico control. PredictHaplo outperformed all others in terms of precision and was selected for further analysis. Near full-genome HTS was performed on proviral DNA from 20 HIV-1C infected individuals, at different stages of ART, from Mumbai, India. DRM detection was performed through residue-wise variation analysis and implementation of QRAs. Both analyses were highly concordant for DRM frequencies >10% (spearman r=0.91, p<0.0001). Phylogenetic association in HTS datasets with shared transmission history could also be demonstrated by PredictHaplo. This study highlights utility of QRAs as an adjunct to traditional residue-wise variation-based DRM detection leading to optimal personalized ART as well as better disease management.

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Maintenance of the Gag/Gag-Pol Ratio Is Important for Human Immunodeficiency Virus Type 1 RNA Dimerization and Viral Infectivity

Journal of Virology ◽

10.1128/jvi.75.4.1834-1841.2001 ◽

2001 ◽

Vol 75 (4) ◽

pp. 1834-1841 ◽

Cited By ~ 147

Author(s):

Miranda Shehu-Xhilaga ◽

Suzanne M. Crowe ◽

Johnson Mak

Keyword(s):

Human Immunodeficiency Virus ◽

Expression Vector ◽

Wild Type ◽

Rna Dimerization ◽

Proviral Dna ◽

Viral Particles ◽

Immunodeficiency Virus ◽

The Impact ◽

Hiv 1

ABSTRACT Production of the human immunodeficiency virus type 1 (HIV-1) Gag-Pol precursor protein results from a −1 ribosomal frameshifting event. In infected cells, this generates Gag and Gag-Pol in a ratio that is estimated to be 20:1, a ratio that is conserved among retroviruses. To examine the impact of this ratio on HIV-1 replication and viral assembly, we altered the Gag/Gag-Pol ratio in virus-producing cells by cotransfecting HIV-1 proviral DNA with an HIV-1 Gag-Pol expression vector. Two versions of the Gag-Pol expression vector were used; one contains an active protease [PR(+)], and the other contains an inactive protease [PR(−)]. In an attempt to produce viral particles with Gag/Gag-Pol ratios ranging from 20:21 to 20:1 (wild type), 293T cells were cotransfected with various ratios of wild-type proviral DNA and proviral DNA from either Gag-Pol expression vector. Viral particles derived from cells with altered Gag/Gag-Pol ratios via overexpression of PR(−) Gag-Pol showed a ratio-dependent defect in their virion protein profiles. However, the defects in virion infectivity were independent of the nature of the Gag-Pol expression vector, i.e., PR(+) or PR(−). Based on equivalent input of reverse transcriptase activity, we estimated that HIV-1 infectivity was reduced 250- to 1,000-fold when the Gag/Gag-Pol ratio in the virion-producing cells was altered from 20:1 to 20:21. Although virion RNA packaging was not affected by altering Gag/Gag-Pol ratios, changing the ratio from 20:1 to 20:21 progressively reduced virion RNA dimer stability. The impact of the Gag/Gag-Pol ratio on virion RNA dimerization was amplified when the Gag-Pol PR(−) expression vector was expressed in virion-producing cells. Virions produced from cells expressing Gag and Gag-Pol PR(−) in a 20:21 ratio contained mainly monomeric RNA. Our observations provide the first direct evidence that, in addition to proteolytic processing, the ratio of Gag/Gag-Pol proteins is also important for RNA dimerization and that stable RNA dimers are not required for encapsidation of genomic RNA in HIV-1.

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the Study to Evaluate the Safety of UB-421 in Combination With Antiretroviral Therapy (ART) and the Efficacy in Reduction of HIV Viral Load and Proviral DNA as Compared to ART Alone in ART-experienced Viremic HIV-1 Patients

Case Medical Research ◽

10.31525/ct1-nct04041362 ◽

2019 ◽

Author(s):

Keyword(s):

Viral Load ◽

Antiretroviral Therapy ◽

Hiv Viral Load ◽

Proviral Dna ◽

Hiv 1

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Faculty Opinions recommendation of HIV-1 proviral DNA excision using an evolved recombinase.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1087695.541782 ◽

2007 ◽

Author(s):

Hanneke Schuitemaker

Keyword(s):

Proviral Dna ◽

Hiv 1

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DEVELOPMENT OF APPROACHES FOR DETECTION OF GENOME-INTEGRATED PROVIRAL DNA OF THE HUMAN IMMUNODEFICIENCY VIRUS (HIV-1) IN ULTRA LOW CONCENTRATIONS USING THE CRISPR/CAS SYSTEM

Molecular Diagnostics and Biosafety – 2020. Russian national scientific and practical conference with international participation (October, 6–8, 2020): Conference Proceedings ◽

10.36233/978-5-9900432-9-9-118 ◽

2020 ◽

Author(s):

M.A. Tyumentseva ◽

◽

A.I. Tyumentsev ◽

V.G. Akimkin ◽

◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Health Monitoring ◽

Biological Samples ◽

Proviral Dna ◽

Guide Rnas ◽

Ribonucleoprotein Complexes ◽

Low Concentrations ◽

Immunodeficiency Virus ◽

Hiv 1

For the effective functioning of supervisory and health monitoring services, it is necessary to introduce modern molecular technologies into their practice. Therefore, the task of developing new effective methods for detecting pathogen, for example HIV, based on CRISPR/CAS genome editing systems, remains urgent. In the present work, guide RNAs and specific oligonucleotides were developed for preliminary amplification of highly conserved regions of the HIV-1 genome. The developed guide RNAs make it possible to detect single copies of HIV-1 proviral DNA in vitro as part of CRISPR/CAS ribonucleoprotein complexes in biological samples after preliminary amplification.

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Molecular and genetic characterization of natural variants of HIV-1 Nef gene from North India and its functional implication in down-regulation of MHC-I and CD-4

Current HIV Research ◽

10.2174/1570162x18666200925160755 ◽

2020 ◽

Vol 18 ◽

Author(s):

J. Singh ◽

L. Ronsard ◽

M. Pandey ◽

R. Kapoor ◽

V.G. Ramachandran ◽

...

Keyword(s):

Biological Activities ◽

Sequence Similarity ◽

Eukaryotic Expression ◽

North India ◽

Cell Surface Expression ◽

Functional Domains ◽

Wild Type ◽

Down Regulation ◽

Subtype B ◽

Hiv 1

Background: HIV-1 Nef is an important accessory protein with multiple effector functions. Genetic studies of HIV-1 Nef gene shows extensive genetic diversity and the functional studies have been carried out mostly with Nef derived from regions dominated by subtype B (North America & Europe). Objective: This study was carried out to characterize genetic variations of the Nef gene from HIV-1 infected individuals from North-India and to find out their functional implications. Methods: The unique representative variants were sub-cloned in eukaryotic expression vector and further characterized with respect to their ability to down regulate cell surface expression of CD4 and MHC-1molecules. Results: The phylogenetic analysis of Nef variants revealed sequence similarity with either consensus subtype B or B/C recombinants. Boot scan analysis of some of our variants showed homology to B/C recombinant and some to wild type Nef B. Extensive variations were observed in most of the variants. The dN/dS ratio revealed 80% purifying selection and 20% diversifying selection implying the importance of mutations in Nef variants. Intracellular stability of Nef variants differed greatly when compared with wild type Nef B and C. There were some variants that possessed mutations in the functional domains of Nef and responsible for its differential CD4 and MHC-1 down regulation activity. Conclusion: We observed enhanced biological activities in some of the variants, perhaps arising out of amino acid substitutions in their functional domains. The CD4 and MHC-1 down-regulation activity of Nef is likely to confer immense survival advantage allowing the most rare genotype in a population to become the most abundant after a single selection event.

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Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

Current Computer - Aided Drug Design ◽

10.2174/1573409916666200628103359 ◽

2020 ◽

Vol 16 ◽

Author(s):

Arash Soltani ◽

Seyed Isaac Hashemy ◽

Farnaz Zahedi Avval ◽

Houshang Rafatpanah ◽

Seyed Abdolrahim Rezaee ◽

...

Keyword(s):

Reverse Transcriptase ◽

Binding Capacity ◽

Binding Pocket ◽

Ligand Docking ◽

Binding Modes ◽

Wild Type ◽

Parent Molecule ◽

Discovery Studio ◽

Approved Drugs ◽

Hiv 1

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. Then the parent molecule and derivatives were docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in druglikeness screening by Swiss-ADME or in docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to -58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

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108. Selective Decay of Intact HIV-1 Proviral DNA on Antiretroviral Therapy

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.418 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S183-S183

Author(s):

Rajesh Gandhi ◽

Joshua Cyktor ◽

Ronald Bosch ◽

Hanna Mar ◽

Gregory Laird ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Panel Member ◽

Plasma Viremia ◽

Research Support ◽

Review Panel ◽

Proviral Dna ◽

Hiv 1 ◽

Over Time ◽

Residual Plasma Viremia ◽

Research Grant

Abstract Background HIV-1 proviruses persist in people on antiretroviral therapy (ART) but most are defective and do not constitute a replication-competent reservoir. The decay of infected cells carrying intact compared with defective HIV-1 proviruses has not been well-defined in people on ART. Methods We separately quantified intact and defective proviruses (using an intact proviral DNA assay), residual plasma viremia, and markers of inflammation and activation in people on long-term ART. Longitudinal measurements were done at three timepoints: timepoint 1 was a median of 7.1 years on ART; timepoint 2 was a median of 3.7 years later; timepoint 3 was a median of 5.5 years after timepoint 1 and a median 12 years after starting ART (Figure 1). Figure 1: Study timepoints Results Among 40 participants tested longitudinally from a median of 7.1 years to 12 years after ART initiation, intact provirus levels declined significantly over time (median half-life 7.1 years; 95% confidence interval [CI], 3.9, 18), whereas defective provirus levels did not decrease. The median half-life of total HIV-1 DNA was 41.6 years (95% CI, 13.6, 75). When we evaluated the change in proviral DNA per year, intact proviral DNA declined significantly more (p< 0.001) than defective proviral DNA (the latter did not change) (Figure 2). The proportion of all proviruses that were intact diminished over time on ART, from about 10% at the first on-ART timepoint to about 5% at the last timepoint (Figure 3). At timepoint 1, intact provirus levels on ART correlated with total HIV-1 DNA and residual plasma viremia, but there was no evidence for associations between intact provirus levels and inflammation or immune activation. Figure 2: Percent change in HIV-1 proviral DNA per year Figure 3: Total HIV-1 proviruses (grey bars) and the percentage of intact proviruses (red lines, displaying median, Q1, Q3) by timepoint. Conclusion Cells containing intact, replication-competent proviruses are selectively lost during suppressive ART. Defining the mechanisms involved should inform strategies to accelerate HIV-1 reservoir depletion. Disclosures Rajesh Gandhi, MD, Merck (Advisor or Review Panel member) Gregory Laird, PhD, Accelevir Diagnostics (Shareholder, Other Financial or Material Support, Employee) Albine Martin, PhD, Accelevir Diagnostics (Shareholder, Other Financial or Material Support, Employee) Bernard Macatangay, MD, Gilead (Grant/Research Support) Joseph J. Eron, MD, Gilead Sciences (Consultant, Research Grant or Support)Janssen (Consultant, Research Grant or Support)Merck (Consultant)ViiV Healthcare (Consultant, Research Grant or Support) Janet Siliciano, PhD, Gilead (Advisor or Review Panel member)US Military HIV Research Program (Advisor or Review Panel member) John Mellors, MD, Abound Bio (Shareholder)Accelevir Diagnostics (Consultant)Co-Crystal Pharmaceuticals (Shareholder)Gilead (Consultant, Grant/Research Support)Merck (Consultant)

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