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Martín V, Perales C, Fernández-Algar M, Dos Santos HG, Garrido P, Pernas M, Parro V, Moreno M, García-Pérez J, Alcamí J, Torán JL, Abia D, Domingo E, Briones C. An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies. PLoS One 2016; 11:e0166902. [PMID: 27959928 PMCID: PMC5154500 DOI: 10.1371/journal.pone.0166902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023] Open
Abstract
The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice. Here we describe the development and testing of a HIV-1 genotyping DNA microarray that detects and quantifies, in majority and minority viral subpopulations, relevant mutations and amino acid insertions in 42 codons of the pol gene associated with drug- and multidrug-resistance to protease (PR) and reverse transcriptase (RT) inhibitors. A customized bioinformatics protocol has been implemented to analyze the microarray hybridization data by including a new normalization procedure and a stepwise filtering algorithm, which resulted in the highly accurate (96.33%) detection of positive/negative signals. This microarray has been tested with 57 subtype B HIV-1 clinical samples extracted from multi-treated patients, showing an overall identification of 95.53% and 89.24% of the queried PR and RT codons, respectively, and enough sensitivity to detect minority subpopulations representing as low as 5–10% of the total quasispecies. The developed genotyping platform represents an efficient diagnostic and prognostic tool useful to personalize antiviral treatments in clinical practice.
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Affiliation(s)
- Verónica Martín
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d’Hebron Institut de Recerca-Hospital Universitari Vall d´Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona. Barcelona, Spain
| | - María Fernández-Algar
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Helena G. Dos Santos
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Patricia Garrido
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - María Pernas
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Miguel Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Javier García-Pérez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - José Alcamí
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - José Luis Torán
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - David Abia
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
- * E-mail:
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HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. Virus Res 2008; 134:104-23. [PMID: 18289713 DOI: 10.1016/j.virusres.2007.12.021] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 12/27/2007] [Accepted: 12/28/2007] [Indexed: 01/04/2023]
Abstract
Genetic diversity plays a key role in human immunodeficiency virus (HIV) adaptation, providing a mechanism to escape host immune responses and develop resistance to antiretroviral drugs. This process is driven by the high-mutation rate during DNA synthesis by reverse transcriptase (RT), by the large viral populations, by rapid viral turnover, and by the high-recombination rate. Drugs targeting HIV RT are included in all regimens of highly active antiretroviral therapy (HAART), which helps to reduce the morbidity and mortality of HIV-infected patients. However, the emergence of resistant viruses is a significant obstacle to effective long-term management of HIV infection and AIDS. The increasing complexity of antiretroviral regimens has favored selection of HIV variants harboring multiple drug resistance mutations. Evolution of drug resistance is characterized by severe fitness losses when the drug is not present, which can be partially overcome by compensatory mutations or other adaptive changes that restore replication capacity. Here, we review the impact of mutations conferring resistance to nucleoside and nonnucleoside RT inhibitors on in vitro and in vivo fitness, their involvement in pathogenesis, persistence upon withdrawal of treatment, and transmission. We describe the techniques used to estimate viral fitness, the molecular mechanisms that help to improve the viral fitness of drug-resistant variants, and the clinical implications of viral fitness data, by exploring the potential relationship between plasma viral load, drug resistance, and disease progression.
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Domingo E, Escarmís C, Menéndez-Arias L, Perales C, Herrera M, Novella IS, Holland JJ. Viral Quasispecies: Dynamics, Interactions, and Pathogenesis *. ORIGIN AND EVOLUTION OF VIRUSES 2008. [PMCID: PMC7149507 DOI: 10.1016/b978-0-12-374153-0.00004-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Quasispecies theory is providing a solid, evolving conceptual framework for insights into virus population dynamics, adaptive potential, and response to lethal mutagenesis. The complexity of mutant spectra can influence disease progression and viral pathogenesis, as demonstrated using virus variants selected for increased replicative fidelity. Complementation and interference exerted among components of a viral quasispecies can either reinforce or limit the replicative capacity and disease potential of the ensemble. In particular, a progressive enrichment of a replicating mutant spectrum with interfering mutant genomes prompted by enhanced mutagenesis may be a key event in the sharp transition of virus populations into error catastrophe that leads to virus extinction. Fitness variations are influenced by the passage regimes to which viral populations are subjected, notably average fitness decreases upon repeated bottleneck events and fitness gains upon competitive optimization of large viral populations. Evolving viral quasispecies respond to selective constraints by replication of subpopulations of variant genomes that display higher fitness than the parental population in the presence of the selective constraint. This has been profusely documented with fitness effects of mutations associated with resistance of pathogenic viruses to antiviral agents. In particular, selection of HIV-1 mutants resistant to one or multiple antiretroviral inhibitors, and the compensatory effect of mutations in the same genome, offers a compendium of the molecular intricacies that a virus can exploit for its survival. This chapter reviews the basic principles of quasispecies dynamics as they can serve to explain the behavior of viruses.
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García-Arriaza J, Domingo E, Briones C. Characterization of minority subpopulations in the mutant spectrum of HIV-1 quasispecies by successive specific amplifications. Virus Res 2007; 129:123-34. [PMID: 17706828 DOI: 10.1016/j.virusres.2007.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 06/29/2007] [Accepted: 07/02/2007] [Indexed: 01/06/2023]
Abstract
RNA viruses do not replicate as defined genomic nucleotide sequences but rather as complex distributions of mutant genomes termed viral quasispecies. Quasispecies dynamics has a number of relevant biological consequences in ribo- and retroviruses, among these the possible presence of memory genomes as minority components of their mutant spectra. Minority memory genomes reflect those viral subpopulations that were dominant at an earlier phase of viral evolution, and can quickly re-emerge to react to certain selective pressures, as it was documented with HIV-1 in vivo. Therefore, an adequate clinical management of HIV-1 requires the development of experimental methods for the detection and quantification of minority viral subpopulations, even at levels of less than 1% of the total quasispecies. We describe a new approach based on successive, highly specific PCR amplifications, which allows the genetic characterization of minority genomes present in increasingly smaller proportion in viral populations. We have coined the term 'quasispecies diving' to reflect the progressive draw on minority or 'deeper' genomes in the mutant spectrum of the quasispecies. In the case of the multidrug-resistant HIV-1 strain analyzed here, quasispecies diving allowed the detection of mutant minority genomes at an unprecedented level of 0.0054% of the amplified viral population. This approach represents a general strategy for the genetic characterization of smaller minority genomes in complex molecular populations.
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Affiliation(s)
- Juan García-Arriaza
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049 Cantoblanco, Madrid, Spain
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Briones C, de Vicente A, Molina-París C, Domingo E. Minority memory genomes can influence the evolution of HIV-1 quasispecies in vivo. Gene 2006; 384:129-38. [PMID: 17059869 DOI: 10.1016/j.gene.2006.07.037] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 07/09/2006] [Accepted: 07/13/2006] [Indexed: 11/13/2022]
Abstract
One of the consequences of viral quasispecies dynamics is the presence, in the mutant spectrum, of minority memory genomes that reflect those variants that were dominant at an earlier phase of the same evolutionary lineage. Replicative and cellular (or anatomical) contributions to quasispecies memory were previously defined during intrahost evolution of human immunodeficiency virus type 1 (HIV-1) [Briones, C., Domingo, E., Molina-París, C., 2003. Memory in retroviral quasispecies: experimental evidence and theoretical model for human immunodeficiency virus. J. Mol. Biol. 331, 213-229.]. However, the effects of replicative memory regarding virus evolution in vivo have not been investigated. Here we document that a multidrug-resistant (MDR) HIV-1, present at memory level, determined the ensuing evolution of the virus in an infected patient. Nucleotide sequencing and detailed phylogenetic analyses of sequential viral populations and individual molecular clones evidenced that the progeny of a minority MDR genome during a treatment interruption contributed the dominant genomes when an antiretroviral treatment was restored. An extension of a mathematical model of establishment and maintenance of memory, based on quasispecies theory, supports the experimental data. Therefore a replicative memory subpopulation, not detectable in a consensus nucleotide sequence, affected decisively subsequent states of viral evolution in vivo.
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Affiliation(s)
- Carlos Briones
- Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir, Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain.
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Domingo E, Martin V, Perales C, Grande-Pérez A, García-Arriaza J, Arias A. Viruses as quasispecies: biological implications. Curr Top Microbiol Immunol 2006; 299:51-82. [PMID: 16568896 PMCID: PMC7120838 DOI: 10.1007/3-540-26397-7_3] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During viral infections, the complex and dynamic distributions of variants, termed viral quasispecies, play a key role in the adaptability of viruses to changing environments and the fate of the population as a whole. Mutant spectra are continuously and avoidably generated during RNA genome replication, and they are not just a by-product of error-prone replication, devoid of biological relevance. On the contrary, current evidence indicates that mutant spectra contribute to viral pathogenesis, can modulate the expression of phenotypic traits by subpopulations of viruses, can include memory genomes that reflect the past evolutionary history of the viral lineage, and, furthermore, can participate in viral extinction through lethal mutagenesis. Also, mutant spectra are the target on which selection and random drift act to shape the long-term evolution of viruses. The biological relevance of mutant spectra is the central topic of this chapter.
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Affiliation(s)
- E Domingo
- Centro de Biologia Molecular, Severo Ochoa, (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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Guerrero A, Cañizares A, Tomás S, Velasco D, Cartelle M. Prevalencia de resistencia a los fármacos antirretrovirales en pacientes españoles infectados por el VIH y sin tratamiento previo. Enferm Infecc Microbiol Clin 2005; 23:605-8. [PMID: 16324550 DOI: 10.1016/s0213-005x(05)75040-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Genotypic resistance was tested to investigate changes in the rates of resistance to antiretroviral drugs in non-treated patients in Spain. MATERIAL AND METHOD A total of 209 HIV-infected patients from different autonomous communities in Spain without prior antiretroviral (AR) drug treatment were studied from 1997 to 2001. Regions of the HIV pol gene coding for protease (PR) and retrotranscriptase (RT) were sequenced in plasma samples by RT PCR amplification and automated PCR sequencing. RESULTS At least one primary RT or PR mutation was detected in 14 patients (6.7%); 11 of them were associated with resistance to RT inhibitors (5.3%) and 3 to PR inhibitors (1.4%). The changes in the resistance rate between March 1997-February 1999 and March 1999-February 2001 were as follows: resistance mutations were detected in 3 of the 111 patients studied in the first period, and in 10 of 98 patients in the second period (2.7% versus 10.2%, P = 0.025). The infection time was less than three months in 1.5% of cases, less than 1 year in 13.4%, more than 1 year in 45.9% and unknown in 39.2%. CONCLUSION The rate of primary resistance in naive patients is low in Spain, although there may be a trend toward an increase. The rising prevalence of resistance is a cause for concern.
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Affiliation(s)
- Antonio Guerrero
- Area de Diagnóstico Biológico, Hospital de la Ribera, Alzira, Valencia, Spain.
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Winters MA, Merigan TC. Insertions in the human immunodeficiency virus type 1 protease and reverse transcriptase genes: clinical impact and molecular mechanisms. Antimicrob Agents Chemother 2005; 49:2575-82. [PMID: 15980322 PMCID: PMC1168704 DOI: 10.1128/aac.49.7.2575-2582.2005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mark A Winters
- Division of Infectious Diseases and Geographic Medicine, Stanford University, 300 Pasteur Drive, Room S-146, Stanford, California 94305-5107, USA.
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Briones C, Bastolla U. Protein evolution in viral quasispecies under selective pressure: A thermodynamic and phylogenetic analysis. Gene 2005; 347:237-46. [PMID: 15725390 DOI: 10.1016/j.gene.2004.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Revised: 11/23/2004] [Accepted: 12/10/2004] [Indexed: 01/21/2023]
Abstract
The evolution of RNA viruses under antiviral pressure is characterized by high mutation rates and strong selective forces that induce extremely rapid changes of protein sequences. This makes the course of molecular evolution directly observable on time scales of months. Here we study the interplay between selection for drug resistance and selection for thermodynamic stability in the protease (PR) and the reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) clones extracted from two patients with complex treatment histories. This analysis shows that folding thermodynamic properties may fluctuate very strongly in the course of quasispecies evolution under selective pressure. For the first case, our data suggest that folding efficiency of the RT is sacrificed at the advantage of drug resistance, while the corresponding PR seems to undergo selection for thermodynamic stability in the absence of substitutions associated to resistance. The PR of the second case is not submitted to antiviral pressure during the period analyzed and seems to initiate random fluctuations that lead to the accidental increase of its folding efficiency. In summary, joint consideration of sequence evolution and thermodynamic parameters can represent a more comprehensive approach for the study of the evolution of RNA viruses.
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Affiliation(s)
- Carlos Briones
- Molecular Evolution Laboratory, Centro de Astrobiología, CSIC-INTA, Carretera de Ajalvir, Km. 4, 28850 Torrejón de Ardoz, Madrid, Spain.
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Prado JG, Franco S, Matamoros T, Ruiz L, Clotet B, Menéndez-Arias L, Martínez MA, Martinez-Picado J. Relative replication fitness of multi-nucleoside analogue-resistant HIV-1 strains bearing a dipeptide insertion in the fingers subdomain of the reverse transcriptase and mutations at codons 67 and 215. Virology 2004; 326:103-12. [PMID: 15262499 DOI: 10.1016/j.virol.2004.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Accepted: 06/03/2004] [Indexed: 10/26/2022]
Abstract
A two-serine insertion at position 69 (i69SS) of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) appears to be critical to enhance multi-nucleoside RT inhibitor resistance (MNR) in the sequence context of multiple zidovudine (AZT) resistance mutations (i.e., M41L, L210W, T215Y). In this study, we measured the replication capacity relative to the wild-type (WT) HIV-1 of a series of recombinant viruses carrying the i69SS in the background of a clinical isolate with MNR in which we introduced mutations D67N, Y215T, Y215S, or Y215N. In vitro measurements included replication kinetics and growth competition assays at different multiplicities of infection (MOI). While the addition of D67N had a minor effect on replication capacity, the reversion of Tyr-215 to Thr, Ser, or Asn was sufficient to increase the virus ability to replicate in a drug-free environment. The same genotypic changes at position 215 rendered the MNR virus susceptible to AZT and stavudine. Interestingly, the presence of the insertion together with mutation T215Y in an otherwise WT sequence background was not sufficient to confer high-level resistance to AZT, although its replication capacity was clearly impaired. Therefore, the RT residue 215 plays a critical role in both replication capacity and drug resistance of multidrug-resistant viruses containing the i69SS.
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Affiliation(s)
- Julia G Prado
- IrsiCaixa Foundation, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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White KL, Chen JM, Margot NA, Wrin T, Petropoulos CJ, Naeger LK, Swaminathan S, Miller MD. Molecular mechanisms of tenofovir resistance conferred by human immunodeficiency virus type 1 reverse transcriptase containing a diserine insertion after residue 69 and multiple thymidine analog-associated mutations. Antimicrob Agents Chemother 2004; 48:992-1003. [PMID: 14982794 PMCID: PMC353090 DOI: 10.1128/aac.48.3.992-1003.2004] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two amino acids inserted between residues 69 and 70 of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) are rare mutations that may develop in viruses containing multiple thymidine analog (zidovudine [AZT], stavudine)-associated mutations and that confer high-level resistance to all currently approved chain-terminating nucleoside and nucleotide RT inhibitors (NRTIs). The two known mechanisms of resistance to NRTIs are decreased incorporation and increased excision. The mechanism used by RT insertion mutants has not been described for tenofovir (TFV), a recently approved agent in this class. A patient-derived HIV-1 strain (strain FS-SSS) that contained an insertion mutation in a background of additional resistance mutations M41L, L74V, L210W, and T215Y was obtained. A second virus (strain FS) was derived from FS-SSS. In strain FS the insertion and T69S were reverted but the other resistance mutations were retained. The FS virus showed strong resistance to AZT but low-level changes in susceptibilities to other NRTIs and TFV. The FS-SSS virus showed reduced susceptibilities to all NRTIs including TFV. Steady-state kinetics demonstrated that the relative binding or incorporation of TFV was slightly decreased for FS-SSS RT compared to those for wild-type RT. However, significant ATP-mediated excision of TFV was detected for both mutant RT enzymes and followed the order FS-SSS RT > FS RT > wild-type RT. The presence of physiological concentrations of the +1 nucleotide inhibited TFV excision by the wild-type RT and slightly inhibited excision by the FS RT, whereas the level of excision by the FS-SSS RT remained high. Computer modeling suggests that the increased mobility of the beta3-beta4 loop may contribute to the high-level and broad NRTI resistance caused by the T69 insertion mutation.
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Matamoros T, Franco S, Vázquez-Alvarez BM, Mas A, Martínez MA, Menéndez-Arias L. Molecular determinants of multi-nucleoside analogue resistance in HIV-1 reverse transcriptases containing a dipeptide insertion in the fingers subdomain: effect of mutations D67N and T215Y on removal of thymidine nucleotide analogues from blocked DNA primers. J Biol Chem 2004; 279:24569-77. [PMID: 15047690 DOI: 10.1074/jbc.m312658200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus type 1 isolates having dipeptide insertions in the fingers subdomain of the reverse transcriptase (RT) show high level resistance to 3 '-azido-3 '-deoxythymidine (AZT) and other nucleoside analogues. Insertions are usually associated with thymidine analogue resistance mutations, such as T215Y. The resistance phenotype correlates with increased ATP-dependent phosphorolytic activity, which facilitates removal of thymidine analogues from inhibitor-terminated primers. In this report, we show that substituting Thr, Ser, or Asn for Tyr-215 in a multidrug-resistant RT, bearing a Ser-Ser insertion between codons 69 and 70, leads to AZT and stavudine resensitization through the loss of the ATP-mediated removal activity. The mutation D67N, which is rarely found in insertion-containing strains, had no effect on excision and a minor influence on resistance. Substituting Tyr-215 had a larger effect than deleting the dipeptide insertion. The presence of both the insertion and mutation T215Y in the wild-type BH10 RT conferred significant ATP-mediated removal activity and moderate resistance to AZT. However, resistance levels and unblocking activities were lower than those observed with the multidrug-resistant enzyme. Removal reactions can be inhibited by the next complementary dNTP. Both Tyr-215 and the dipeptide insertion affect RT-DNA.DNA-dNTP ternary complex formation, an effect that was not detected in the presence of foscarnet. Based on crystal structures of binary and ternary complexes of HIV-1 RT, we propose that Tyr-215 exerts its action by facilitating a proper orientation of the pyrophosphate donor molecule, whereas the effects on dNTP binding are indirect and could be related to significant conformational changes occurring during polymerization.
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Affiliation(s)
- Tania Matamoros
- Centro de Biologìa Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientìficas-Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Bulgheroni E, Croce F, Citterio P, Viganò O, Visonà R, Sala E, Galli M, Rusconi S. Unusual codon 69 insertions: influence on human immunodeficiency virus type 1 reverse transcriptase drug susceptibility. J Clin Virol 2004; 29:27-32. [PMID: 14675866 DOI: 10.1016/s1386-6532(03)00082-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Multiple amino acid changes in the reverse transcriptase (RT) enzyme of the human immunodeficiency virus 1 (HIV-1) confer simultaneous resistance to most nucleoside RT inhibitors (NRTI). It may take place through different pathways: one of these is the codon 69 insertion, which can involve several 2-amino acid patterns. MATERIALS AND METHODS We are reporting the case of three patients treated with various antiretroviral compounds. For these subjects we have conducted both a genotypical and a phenotypical analysis in order to understand what kind of influence these insertions may have on HIV-1 RT drug susceptibility. Plasma samples from these patients have been extracted and the RT region has been amplified, cloned and sequenced; meanwhile their PBMCs have been separated, cultivated and then tested for drug susceptibility. RESULTS Data obtained from the cloning assay showed that the patients had different mutational patterns but constant multiple resistance to NRTI. In particular, they harbored mutations related to Zidovudine (ZDV), 3TC and various NRTIs. Moreover, all three samples had a T69S substitution followed by three different dual amino acid insertions: SG, TG and VG. Several phenotypic experiments revealed that the viruses were resistant to 3TC as well as to ZDV and ABC. Different results were obtained using d4T and ddI. DISCUSSION In our three patients, all mutation inserts impaired the use of NRTI, particularly ZDV and 3TC. Patient 001 presented a pattern that should not cause a high phenotypic resistance to 3TC per se, and so we can argue that the concomitant presence of the insertion T69S (SG) makes this isolate moderately resistant to this drug. We observed a similar phenomenon in subject 003. d4T was less involved in the resistance generation caused by the RT insertion (in one out of three cases). Moreover, we identified a new 2aa insertion (TG) that has, to the best of our knowledge, never been reported before. A careful survey of novel RT genotypic insertion is thus warranted.
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Affiliation(s)
- Elisabetta Bulgheroni
- Istituto di Malattie Infettive e Tropicali, Università degli Studi, Ospedale Luigi Sacco, Via GB Grassi 74, 20157 Milan, Italy
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Emmenegger EJ, Troyer RM, Kurath G. Characterization of the mutant spectra of a fish RNA virus within individual hosts during natural infections. Virus Res 2003; 96:15-25. [PMID: 12951262 DOI: 10.1016/s0168-1702(03)00169-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Infectious hematopoietic necrosis virus (IHNV) is an RNA virus that causes significant mortalities of salmonids in the Pacific Northwest of North America. RNA virus populations typically contain genetic variants that form a heterogeneous virus pool, referred to as a quasispecies or mutant spectrum. This study characterized the mutant spectra of IHNV populations within individual fish reared in different environmental settings by RT-PCR of genomic viral RNA and determination of partial glycoprotein gene sequences of molecular clones. The diversity of the mutant spectra from ten in vivo populations was low and the average mutation frequencies of duplicate populations did not significantly exceed the background mutation level expected from the methodology. In contrast, two in vitro populations contained variants with an identical mutational hot spot. These results indicated that the mutant spectra of natural IHNV populations is very homogeneous, and does not explain the different magnitudes of genetic diversity observed between the different IHNV genogroups. Overall the mutant frequency of IHNV within its host is one of the lowest reported for RNA viruses.
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Briones C, Domingo E, Molina-París C. Memory in retroviral quasispecies: experimental evidence and theoretical model for human immunodeficiency virus. J Mol Biol 2003; 331:213-29. [PMID: 12875847 PMCID: PMC7173031 DOI: 10.1016/s0022-2836(03)00661-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Viral quasispecies may possess a molecular memory of their past evolutionary history, imprinted on minority components of the mutant spectrum. Here we report experimental evidence and a theoretical model for memory in retroviral quasispecies in vivo. Apart from replicative memory associated with quasispecies dynamics, retroviruses may harbour a "cellular" or "anatomical" memory derived from their integrative cycle and the presence of viral reservoirs in body compartments. Three independent sets of data exemplify the two kinds of memory in human immunodeficiency virus type 1 (HIV-1). The data provide evidence of re-emergence of sequences that were hidden in cellular or anatomical compartments for extended periods of infection, and recovery of a quasispecies from pre-existing genomes. We develop a three-component model that incorporates the essential features of the quasispecies dynamics of retroviruses exposed to selective pressures. Significantly, a numerical study based on this model is in agreement with the experimental data, further supporting the existence of both replicative and reservoir memory in retroviral quasispecies.
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Key Words
- quasispecies
- memory
- viral reservoirs
- retroviruses
- human immunodeficiency virus
- hiv-1, human immunodeficiency virus type 1
- fmdv, foot-and-mouth disease virus
- rti, reverse transcriptase inhibitor
- pri, protease inhibitor
- haart, highly active antiretroviral therapy
- azt, zidovudine
- ddi, didanosine
- ddc, zalcitabine
- d4t, stavudine
- 3tc, lamivudine
- rtv, ritonavir
- sqv, saquinavir
- nfv, nelfinavir
- idv, indinavir
- nvp, nevirapine
- hu, hydroxyurea
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Affiliation(s)
- Carlos Briones
- Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir, Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
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Domingo E. Quasispecies and the development of new antiviral strategies. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2003; 60:133-58. [PMID: 12790341 DOI: 10.1007/978-3-0348-8012-1_4] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
RNA virus populations consist of complex and dynamic mutant distributions, rather than defined genomic sequences. This feature confers great adaptability on viruses and is partly responsible for current difficulties of viral disease prevention and control. Mutant distributions, also termed mutant swarms or mutant clouds, were first proposed in a theory of molecular evolution termed quasispecies theory. The theoretical formulation of quasispecies and its links to present day RNA viruses are discussed. The need to accommodate antiviral strategies to the dynamic nature of viral populations is emphasized. In particular, recent results on viral extinction associated with enhanced mutagenesis (virus entry into error catastrophe) are reviewed and presented as an example of how the understanding of viruses as quasispecies could lead to a potential practical application in medicine.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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Meyer PR, Lennerstrand J, Matsuura SE, Larder BA, Scott WA. Effects of dipeptide insertions between codons 69 and 70 of human immunodeficiency virus type 1 reverse transcriptase on primer unblocking, deoxynucleoside triphosphate inhibition, and DNA chain elongation. J Virol 2003; 77:3871-7. [PMID: 12610164 PMCID: PMC149510 DOI: 10.1128/jvi.77.6.3871-3877.2003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Finger insertion mutations of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) (T69S mutations followed by various dipeptide insertions) have a multinucleoside resistance phenotype that can be explained by decreased sensitivity to deoxynucleoside triphosphate (dNTP) inhibition of the nucleotide-dependent unblocking activity of RT. We show that RTs with SG or AG (but not SS) insertions have three- to fourfold-increased unblocking activity and that all three finger insertion mutations have threefold-decreased sensitivity to dNTP inhibition. The additional presence of M41L and T215Y mutations increased unblocking activity for all three insertions, greatly reduced the sensitivity to dNTP inhibition, and resulted in defects in in vitro DNA chain elongation. The DNA chain elongation defects were partially repaired by additional mutations at positions 210, 211, and 214. These results suggest that structural communication between the regions of RT defined by these mutations plays a role in the multinucleoside resistance phenotype.
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Affiliation(s)
- Peter R Meyer
- University of Miami, School of Medicine, Miami, Florida 33101-6129, USA
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Selmi B, Deval J, Boretto J, Canard B. Nucleotide Analogue Binding, Catalysis and Primer Unblocking in the Mechanisms of HIV-1 Reverse Transcriptase-Mediated Resistance to Nucleoside Analogues. Antivir Ther 2003. [DOI: 10.1177/135965350300800209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nucleoside analogues play a key role in the fight against HIV-1. Unfortunately, under therapeutic pressure, HIV-1 inevitably develops resistance to these inhibitors. This resistance correlates with specific pol gene mutations giving rise to specific substitutions in reverse transcriptase that are responsible for the loss of efficacy of the corresponding analogue. This work is an overview of the molecular mechanisms of HIV-1 drug resistance as judged by the analysis of chemical reactions at play at the reverse transcriptase active site. One class of mechanism involves nucleotide analogue discrimination either at the binding step or at the catalytic step, the latter being by far the most common mechanism. The other class of mechanism involves repair of the analogue-terminated DNA chain. The mechanisms were elucidated using purified reverse transcriptase and biochemical assays aimed at correlating resistant HIV-1 phenotypes to enzymatic data. The elucidation of these molecular mechanisms of drug-resistant reverse transcriptase is important for effective and rational combination therapies as well as for the conception of second-generation drugs that do not confer nucleotide resistance to reverse transcriptase or are active against pre-existing resistant viruses.
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Affiliation(s)
- Boulbaba Selmi
- Centre National de la Recherche Scientifique et Université d'Aix-Marseille I and II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, ESIL-Case 925, 163 avenue de Luminy, 13288 Marseille cedex 9, France
| | - Jérôme Deval
- Centre National de la Recherche Scientifique et Université d'Aix-Marseille I and II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, ESIL-Case 925, 163 avenue de Luminy, 13288 Marseille cedex 9, France
| | - Joëlle Boretto
- Centre National de la Recherche Scientifique et Université d'Aix-Marseille I and II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, ESIL-Case 925, 163 avenue de Luminy, 13288 Marseille cedex 9, France
| | - Bruno Canard
- Centre National de la Recherche Scientifique et Université d'Aix-Marseille I and II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, ESIL-Case 925, 163 avenue de Luminy, 13288 Marseille cedex 9, France
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Mas A, Vázquez-Alvarez BM, Domingo E, Menéndez-Arias L. Multidrug-resistant HIV-1 reverse transcriptase: involvement of ribonucleotide-dependent phosphorolysis in cross-resistance to nucleoside analogue inhibitors. J Mol Biol 2002; 323:181-97. [PMID: 12381314 DOI: 10.1016/s0022-2836(02)00911-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) strains having a dipeptide insertion between codons 69 and 70 of the viral reverse transcriptase (RT) have been observed in isolates from patients treated with 3'-azido-3'-deoxythymidine (AZT) and other nucleoside analogues. These viruses contain additional mutations related to drug resistance and display reduced susceptibility to most nucleoside analogue inhibitors, including AZT. The mechanism of AZT resistance implies an increased ability of the multidrug-resistant (SS) RT to remove AZT-monophosphate (AZTMP) from blocked primers through a nucleotide-dependent reaction. We show that its higher ATP-dependent phosphorolytic activity is also detectable with primers terminated with 2',3'-didehydro-3'-deoxythymidine-5'-monophosphate (d4TMP) or 2',3'-dideoxythymidine-5'-monophosphate (ddTMP), but is significantly reduced when the dipeptide insertion is deleted. Removal of AZTMP, d4TMP and ddTMP can be inhibited by the next complementary deoxynucleoside triphosphate (dNTP). AZTMP removal reactions catalysed by SS RT were highly resistant to dNTP inhibition (IC(50)>0.25mM), while unblocking of d4TMP- and ddTMP-terminated primers was around tenfold more sensitive to inhibition by the next complementary dNTP. Both SS and mutant 2S0S RTs were able to unblock and extend primers terminated with 2',3'-dideoxycytidine-5'-monophosphate (ddCMP) in the presence of ATP, albeit very poorly. Under these conditions, none of the RTs was able to remove 2',3'-dideoxy-3'-thiacytidine-5'-monophosphate (3TCMP) from a terminated DNA primer. Resistance mediated by ATP-dependent phosphorolysis depends on the intracellular levels of dNTP. High levels as found in transformed cell lines (i.e. H-9, CEM lymphoblasts, SupT1 cells, etc.) may prevent repair of primers terminated with d4TMP. However, ATP-dependent phosphorolysis could be relevant for d4T resistance in cells having low levels of dNTPs. This proposal could explain why insertion-containing HIV-1 variants have been detected in the absence of AZT, during d4T treatment.
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Affiliation(s)
- Antonio Mas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
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Quiñones-Mateu ME, Tadele M, Parera M, Mas A, Weber J, Rangel HR, Chakraborty B, Clotet B, Domingo E, Menéndez-Arias L, Martínez MA. Insertions in the reverse transcriptase increase both drug resistance and viral fitness in a human immunodeficiency virus type 1 isolate harboring the multi-nucleoside reverse transcriptase inhibitor resistance 69 insertion complex mutation. J Virol 2002; 76:10546-52. [PMID: 12239335 PMCID: PMC136580 DOI: 10.1128/jvi.76.20.10546-10552.2002] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2002] [Accepted: 07/03/2002] [Indexed: 11/20/2022] Open
Abstract
Recent studies have shown that the accumulation of multiple mutations associated with nucleoside reverse transcriptase inhibitor (NRTI) resistance may be grouped as multi-NRTI resistance (MNR) complexes. In this study, we have examined the viral fitness of recombinant viruses carrying the reverse transcriptase (RT) of a human immunodeficiency virus type 1 (HIV-1) primary isolate harboring mutations comprising the MNR 69 insertion complex. Different RT mutants were prepared in the sequence context of either the wild-type RT sequence of the HIV-1(BH10) isolate or the sequence found in a clinical HIV-1 isolate with the MNR 69 insertion mutation. As expected, in the presence of zidovudine, recombinant viruses harboring the MNR RT from the patient were more fit than wild-type viruses. However, in the absence of drug, the virus with the RT from the original clinical isolate (SS) was more fit than (i) the wild-type virus with an engineered serine insertion between residues 69 and 70 (T69SSS) and (ii) the recombinant virus with the MNR RT where the insertion was removed (2S0S). These results suggest that RT insertions, in the right sequence context (i.e., additional mutations contained in the MNR 69 insertion complex), enhance NRTI resistance and may improve viral fitness. Thus, comparing complex mutation patterns with viral fitness may help to elucidate the role of uncharacterized drug resistance mutations in antiretroviral treatment failure.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- Department of Virology/NN10, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
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Domingo E, Mas A, Yuste E, Pariente N, Sierra S, Gutiérrez-Riva M, Menéndez-Arias L. Virus population dynamics, fitness variations and the control of viral disease: an update. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2002; 57:77-115. [PMID: 11728003 DOI: 10.1007/978-3-0348-8308-5_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Viral quasispecies dynamics and variations of viral fitness are reviewed in connection with viral disease control. Emphasis is put on resistance of human immunodeficiency virus and some human DNA viruses to antiviral inhibitors. Future trends in multiple target antiviral therapy and new approaches based on virus entry into error catastrophe (extinction mutagenesis) are discussed.
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Affiliation(s)
- E Domingo
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Spain.
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Domingo E, Ruiz-Jarabo CM, Sierra S, Arias A, Pariente N, Baranowski E, Escarmis C. Emergence and selection of RNA virus variants: memory and extinction. Virus Res 2002; 82:39-44. [PMID: 11885948 DOI: 10.1016/s0168-1702(01)00385-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two features of viral quasispecies are reviewed: the presence of memory genomes as minority components of their mutant spectra, and viral extinction due to enhanced mutagenesis. Memory has been documented with several genetic markers of the important animal picornavirus foot-and-mouth disease virus (FMDV). The presence of memory genomes in viral quasispecies may accelerate their adaptive response whenever a selective constraint has already been experienced by a viral population during previous stages of its evolution. Enhanced mutagenesis has been shown to lead to losses of infectivity of a number of RNA viruses: poliovirus, vesicular stomatitis virus, human immunodeficiency virus type 1 and FMDV. These observations, based on the theoretical prediction of the existence of a copying error-threshold for maintenance of genetic information, may contribute to the development of a new antiviral strategy.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular, Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Spain.
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Kim EY, Winters MA, Kagan RM, Merigan TC. Functional correlates of insertion mutations in the protease gene of human immunodeficiency virus type 1 isolates from patients. J Virol 2001; 75:11227-33. [PMID: 11602763 PMCID: PMC114703 DOI: 10.1128/jvi.75.22.11227-11233.2001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty-four of over 24,000 patients genotyped over the past 3 years were found to have human immunodeficiency virus (HIV) isolates that possess an insert in the protease gene. In this report, we evaluated the spectrum of protease gene insertion mutations in patient isolates and analyzed the effect of these various insertion mutations on viral phenotypes. The inserts were composed of 1, 2, 5, or 6 amino acids that mapped at or between codons 35 and 38, 17 and 18, 21 and 25, or 95 and 96. Reduced susceptibility to protease inhibitors was found in isolates which possess previously reported drug resistance mutations. Fitness assays, including replication and competition experiments, showed that most of the isolates with inserts grew somewhat better than their counterparts with a deletion of the insert. These experiments demonstrate that, rarely, insertion mutations can develop in the HIV type 1 protease gene, are no more resistant than any other sequences which have similar associated resistance mutations, and can provide a borderline advantage in replication.
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Affiliation(s)
- E Y Kim
- Center for AIDS Research, Stanford University, Stanford, California 94305-5107, USA.
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Sato H, Tomita Y, Ebisawa K, Hachiya A, Shibamura K, Shiino T, Yang R, Tatsumi M, Gushi K, Umeyama H, Oka S, Takebe Y, Nagai Y. Augmentation of human immunodeficiency virus type 1 subtype E (CRF01_AE) multiple-drug resistance by insertion of a foreign 11-amino-acid fragment into the reverse transcriptase. J Virol 2001; 75:5604-13. [PMID: 11356968 PMCID: PMC114273 DOI: 10.1128/jvi.75.12.5604-5613.2001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A human immunodeficiency virus type 1 (HIV-1) subtype E (CRF01_AE) variant (99JP-NH3-II) possessing an in-frame 33-nucleotide insertion mutation in the beta3-beta4 loop coding region of the reverse transcriptase (RT) gene was isolated from a patient who had not responded to nucleoside analogue RT inhibitors. This virus exhibited an extremely high level of multiple nucleoside analog resistance (MNR). Neighbor-joining tree analysis of the pol sequences indicated that the 99JP-NH3-II variant had originated from the swarm of drug-sensitive predecessors in the patient. Population-based sequence analyses of 82 independently cloned RT segments from the patient suggested that the variants with the insertion, three or four 3'-azido-3'-deoxythymidine resistance mutations, and a T69I mutation in combination had strong selective advantages during chemotherapy. Consistently, in vitro mutagenesis of a drug-sensitive predecessor virus clone demonstrated that this mutation set functions cooperatively to confer a high level of MNR without deleterious effects on viral replication capability. Homology modeling of the parental RT and its MNR mutant showed that extension of the beta3-beta4 loop by an insertion caused reductions in the distances between the loop and the other subdomains, narrowing the template-primer binding cleft and deoxynucleoside triphosphate-binding pocket in a highly flexible manner. The origin of the insert is elusive, as every effort to find a homologue has been unsuccessful. Taken together, these data suggest that (i) HIV-1 tolerates in vivo insertions as long as 33 nucleotides into the highly conserved enzyme gene to survive multiple anti-HIV-1 inhibitors and (ii) the insertion mutation augments multiple-drug resistance, possibly by reducing the biochemical inaccuracy of substrate-enzyme interactions in the active center.
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Affiliation(s)
- H Sato
- AIDS Research Center, National Institute of Infectious Diseases, Japan.
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Lukashov VV, Huismans R, Jebbink MF, Danner SA, de Boer RJ, Goudsmit J. Selection by AZT and rapid replacement in the absence of drugs of HIV type 1 resistant to multiple nucleoside analogs. AIDS Res Hum Retroviruses 2001; 17:807-18. [PMID: 11429122 DOI: 10.1089/088922201750252007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We studied the intrahost evolution and dynamics of a multidrug-resistant HIV-1, which contains an insertion of two amino acids (aa) and several aa changes within the reverse transcriptase (RT) gene. From an individual receiving intermittent therapy, sequences of 231 full-length molecular clones of HIV-1 RT were obtained from serum-derived viruses at 12 consecutive time points over a period of 6 years, 17 to 20 clones per time point. In the 3.5-year period prior to the first course of therapy, only wild-type (wt) viruses were found. As soon as 6 months after the start of zidovudine (AZT) monotherapy, all viruses contained an insertion of two aa between positions 68 and 69 of the RT and aa changes at positions 67 and 215, a combination conferring resistance to multiple nucleoside analogs. After termination of therapy, the insertion mutants were rapidly and completely replaced by the wt viruses. In turn, the insertion mutants replaced the wt viruses after initiation of therapy with 3TC, d4T, and saquinavir. After termination of triple therapy, the wt viruses completely replaced the mutants within 1 month, which is markedly faster than has been observed earlier for the replacement of AZT-resistant viruses. Fast replacements of the mutant virus populations after termination of therapy indicate gross competitive disadvantage of the insertion mutant in the absence of therapy, which we estimated by using several models. The insertion mutants attained high virus loads, demonstrating that virus load cannot be used as a direct measure of virus fitness.
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Affiliation(s)
- V V Lukashov
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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Primary Genotypic and Phenotypic HIV-1 Drug Resistance in Recent Seroconverters in Madrid. J Acquir Immune Defic Syndr 2001. [DOI: 10.1097/00126334-200102010-00006] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Briones C, Pérez-Olmeda M, Rodríguez C, del Romero J, Hertogs K, Soriano V. Primary genotypic and phenotypic HIV-1 drug resistance in recent seroconverters in Madrid. J Acquir Immune Defic Syndr 2001; 26:145-50. [PMID: 11242181 DOI: 10.1097/00042560-200102010-00006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Transmission of drug-resistant HIV-1 strains is increasing with widespread use of antiretroviral drugs in developed countries. This study examined the prevalence of resistant viruses in recent seroconverters in Madrid, Spain. DESIGN HIV isolates from 30 consecutive participants with positive or indeterminate HIV antibody test results and a negative test result at a mean of 6.6 months earlier were examined for HIV drug resistance. All study subjects admitted to having very recently engaged in high-risk practices. All were therapeutically naive and were recruited between 1997 and 1999 in a referring health care facility for sexually transmitted diseases. METHODS Population-based sequencing of the viral reverse transcriptase (RT) and protease (PR) regions derived from plasma viral RNA was performed. Phenotypic resistance was assessed by a recombinant virus assay. RESULTS Overall prevalence of genotypes associated with reduced susceptibility was 26.7% (8 of 30 participants). Resistance mutations were seen against nucleoside analogues in 7 (23.3%), nonnucleoside reverse transcriptase inhibitors in 1 (3.3%), and protease inhibitors in 2 (6.7%). Zidovudine-resistance mutations M41L and/or T215Y were the commonest, found in 20% (6 of 30 participants). Resistance mutations to at least two antiretroviral families (multidrug-resistance) were detected in 2 (6.7%) study subjects. A median infectious dose (IC50) increase of fourfold for any drug was found in 7 patients, and in 2 was > tenfold for zidovudine (genotype M41L + T215Y) and lamivudine (genotype M184V), respectively. CONCLUSIONS Drug-resistant HIV variants were present in over one quarter of individuals recently diagnosed as infected in Madrid, Spain. Therefore, resistance testing at baseline should be considered for the optimal design of first-line antiretroviral combinations.
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Affiliation(s)
- C Briones
- Service of Infectious Diseases, Hospital Carlos III, Instituto de Salud Carlos III, Madrid, Spain
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Mas A, Parera M, Briones C, Soriano V, Martínez MA, Domingo E, Menéndez-Arias L. Role of a dipeptide insertion between codons 69 and 70 of HIV-1 reverse transcriptase in the mechanism of AZT resistance. EMBO J 2000; 19:5752-61. [PMID: 11060026 PMCID: PMC305792 DOI: 10.1093/emboj/19.21.5752] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 3'-azido-3'-deoxythymidine (AZT)-resistant pheno type of a heavily mutated human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) carrying a dipeptide (Ser-Ser) insertion between codons 69 and 70 as well as other mutations related to resistance to RT inhibitors has been studied. Recombinant virus carrying this variant RT (termed SS RT) showed reduced susceptibility to all nucleoside RT inhibitors in clinical use, particularly to AZT. In the presence of ATP, recombinant SS RT had an increased ability to remove the 3'-terminal nucleotide from AZT- terminated primers and extend the unblocked primer, compared with wild-type HIV-1 RT (BH10 isolate). Insertion of two serines in the sequence context of BH10 RT did not affect the ATP-dependent phosphorolytic activity of the enzyme, and had no influence in resistance to RT inhibitors. However, SS RT mutants lacking the dipeptide insertion or bearing a four-serine insertion showed reduced ATP-dependent phosphorolytic activity that correlated with increased AZT sensitivity, as determined using a recombinant virus assay. Therefore, the insertion appears to be critical to enhance AZT resistance in the sequence context of multidrug-resistant HIV-1 RT.
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Affiliation(s)
- A Mas
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Abstract
Biological adaptive systems share some common features: variation among their constituent elements and continuity of core information. Some of them, such as the immune system, are endowed with memory of past events. In this study we provide direct evidence that evolving viral quasispecies possess a molecular memory in the form of minority components that populate their mutant spectra. The experiments have involved foot-and-mouth disease virus populations with known evolutionary histories. The composition and behavior of the viral population in response to a selective constraint were influenced by past evolutionary history in a way that could not be predicted from examination of consensus nucleotide sequences of the viral populations. The molecular memory of the viral quasispecies influenced both the nature and the intensity of the response of the virus to a selective constraint.
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Affiliation(s)
- C M Ruiz-Jarabo
- Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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