Impact of Clinical Reverse Transcriptase Sequences on the Replication Capacity of HIV-1 Drug-Resistant Mutants

ABSTRACT Determining the fitness of drug-resistant human immunodeficiency virus type 1 (HIV-1) strains is necessary for the development of population-based studies of resistance patterns. For this purpose, we have developed a reproducible, systematic assay to determine the competitive fitness of HIV-1 drug-resistant mutants. To demonstrate the applicability of this assay, we tested the fitness of the five most common nevirapine-resistant mutants (103N, 106A, 181C, 188C, and 190A), with mutations in HIV-1 reverse transcriptase (RT), singly and in combination (for a total of 31 variants) in a defined HIV-1 background. For these experiments, the 27 RT variants that produced viable virus were cocultured with wild-type virus without nevirapine. The ratios of the viral species were determined over time by utilization of a quantitative real-time RT-PCR-based assay. These experiments revealed that all of the viable variants were less fit than the wild type and demonstrated that the order of relative fitness of the single mutants tested was as follows: 103N > 181C > 190A > 188C > 106A. This order correlated with the commonality of these mutants as a result of nevirapine monotherapy. These investigations also revealed that, on average, the double mutants were less fit than the single mutants and the triple mutants were less fit than the double mutants. However, the fitness of the single and double mutants was often not predictive of the fitness of the derivative triple mutants, suggesting the presence of complex interactions between the closely aligned residues that confer nevirapine resistance. This complexity was also evident from the observation that all three of the replication-competent quadruple mutants were fitter than most of the triple mutants, and in some cases, even the double mutants. Our data suggest that, in many cases, viral fitness is the determining factor in the evolution of nevirapine-resistant mutants in vivo, that interactions between the residues that confer nevirapine resistance are complex, and that these interactions substantially affect reverse transcriptase structure and/or function.

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(Alkylamino) piperidine bis(heteroaryl)piperizine analogs are potent, broad-spectrum nonnucleoside reverse transcriptase inhibitors of drug-resistant isolates of human immunodeficiency virus type 1 (HIV-1) and select for drug-resistant variants of HIV-1IIIB with reduced replication phenotypes.

Journal of Virology ◽

10.1128/jvi.70.6.3698-3705.1996 ◽

1996 ◽

Vol 70 (6) ◽

pp. 3698-3705 ◽

Cited By ~ 22

Author(s):

R A Olmsted ◽

D E Slade ◽

L A Kopta ◽

S M Poppe ◽

T J Poel ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Reverse Transcriptase ◽

Human Immunodeficiency Virus Type ◽

Broad Spectrum ◽

Drug Resistant ◽

Reverse Transcriptase Inhibitors ◽

Nonnucleoside Reverse Transcriptase Inhibitors ◽

Immunodeficiency Virus ◽

Hiv 1

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Inhibition of multi-drug resistant HIV-1 reverse transcriptase by nucleoside β-triphosphates

Bioorganic & Medicinal Chemistry Letters ◽

10.1016/j.bmcl.2011.05.005 ◽

2011 ◽

Vol 21 (12) ◽

pp. 3519-3522 ◽

Cited By ~ 2

Author(s):

Chandravanu Dash ◽

Yousef Ahmadibeni ◽

Michael J. Hanley ◽

Jui Pandhare ◽

Mathias Gotte ◽

...

Keyword(s):

Reverse Transcriptase ◽

Drug Resistant ◽

Hiv 1

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Novel Single-Cell-Level Phenotypic Assay for Residual Drug Susceptibility and Reduced Replication Capacity of Drug-Resistant Human Immunodeficiency Virus Type 1

Journal of Virology ◽

10.1128/jvi.78.4.1718-1729.2004 ◽

2004 ◽

Vol 78 (4) ◽

pp. 1718-1729 ◽

Cited By ~ 135

Author(s):

Haili Zhang ◽

Yan Zhou ◽

Cecily Alcock ◽

Tara Kiefer ◽

Daphne Monie ◽

...

Keyword(s):

Drug Combination ◽

Wild Type Virus ◽

Replication Capacity ◽

Drug Resistant ◽

Type Virus ◽

Wild Type ◽

Cell Level ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT Human immunodeficiency virus type 1 (HIV-1)-infected individuals who develop drug-resistant virus during antiretroviral therapy may derive benefit from continued treatment for two reasons. First, drug-resistant viruses can retain partial susceptibility to the drug combination. Second, therapy selects for drug-resistant viruses that may have reduced replication capacities relative to archived, drug-sensitive viruses. We developed a novel single-cell-level phenotypic assay that allows these two effects to be distinguished and compared quantitatively. Patient-derived gag-pol sequences were cloned into an HIV-1 reporter virus that expresses an endoplasmic reticulum-retained Env-green fluorescent protein fusion. Flow cytometric analysis of single-round infections allowed a quantitative analysis of viral replication over a 4-log dynamic range. The assay faithfully reproduced known in vivo drug interactions occurring at the level of target cells. Simultaneous analysis of single-round infections by wild-type and resistant viruses in the presence and absence of the relevant drug combination divided the benefit of continued nonsuppressive treatment into two additive components, residual virus susceptibility to the drug combination and selection for drug-resistant variants with diminished replication capacities. In some patients with drug resistance, the dominant circulating viruses retained significant susceptibility to the combination. However, in other cases, the dominant drug-resistant viruses showed no residual susceptibility to the combination but had a reduced replication capacity relative to the wild-type virus. In this case, simplification of the regimen might still allow adequate suppression of the wild-type virus. In a third pattern, the resistant viruses had no residual susceptibility to the relevant drug regimen but nevertheless had a replication capacity equivalent to that of wild-type virus. In such cases, there is no benefit to continued treatment. Thus, the ability to simultaneously analyze residual susceptibility and reduced replication capacity of drug-resistant viruses may provide a basis for rational therapeutic decisions in the setting of treatment failure.

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Reverse transcriptase mutation K65N confers a decreased replication capacity to HIV-1 in comparison to K65R due to a decreased RT processivity

Virology ◽

10.1016/j.virol.2011.03.007 ◽

2011 ◽

Vol 414 (1) ◽

pp. 34-41 ◽

Cited By ~ 5

Author(s):

HimaBindu Chunduri ◽

Clyde Crumpacker ◽

Prem L. Sharma

Keyword(s):

Reverse Transcriptase ◽

Replication Capacity ◽

Hiv 1

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Primary HIV drug resistance among newly HIV type-1 diagnosed patients in St. Petersburg

HIV Infection and Immunosuppressive Disorders ◽

10.22328/2077-9828-2021-13-1-70-79 ◽

2021 ◽

Vol 13 (1) ◽

pp. 70-79

Author(s):

Thierry Ingabire ◽

A. V. Semenov ◽

E. V. Esaulenko ◽

E. B. Zueva ◽

A. N. Schemelev ◽

...

Keyword(s):

Drug Resistance ◽

Reverse Transcriptase ◽

Direct Sequencing ◽

Population Level ◽

Multidrug Resistant ◽

Antiretroviral Drugs ◽

Drug Resistant ◽

Resistant Virus ◽

Primary Drug Resistance ◽

Hiv 1

There is concern that the widespread use of antiretroviral drugs (ARV) to treat human immunodeficiency virus 1 (HIV-1) infection may result in the emergence of transmission of drug-resistant virus among persons newly infected with HIV-1. Russia is one of a growing number of countries in the world where drug-resistant HIV is becoming a serious health problem because it has the potential to compromise the efficacy of antiretroviral therapy (ART) at the population level.Materials and methods. We performed a genetic analysis of the HIV-1 plasma derived pol gene among the newly diagnosed ART-naïve HIV-1 infected patients during the period from November 2018 to October 2019 in the St. Petersburg Clinical Infectious Diseases Hospital named after S.P. Botkin. We used reverse transcriptase polymerase chain reaction (RT-PCR) followed by direct sequencing of PCR products to determine the prevalence of primary drug resistance (PDR) conferring mutations. HIV-1 genotypes were determined by phylogenetic analysis.Results. The predominant HIV-1 subtype was A1 (87.2%), followed by B (11.8%) and CRF06_cpx (1%). The overall prevalence of PDR was 11%. Virus with known resistance-conferring mutations to any nucleoside reverse transcriptase inhibitors (NRTIs) was found in 8 individuals, to any non NRTIs in 5 subjects, and to any protease inhibitors in 1 case. Multidrug-resistant virus was identified in 2 individuals (2%).Conclusion. The distribution of HIV-1 genotypes in St. Petersburg, Russia is diverse. The emerging prevalence of PDR in ART-naïve patients demonstrates the significance of constant monitoring due to the challenges it presents towards treatment.

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