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Heger E, Theis AA, Remmel K, Walter H, Pironti A, Knops E, Di Cristanziano V, Jensen B, Esser S, Kaiser R, Lübke N. Development of a phenotypic susceptibility assay for HIV-1 integrase inhibitors. J Virol Methods 2016; 238:29-37. [PMID: 27737783 DOI: 10.1016/j.jviromet.2016.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 09/02/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
Abstract
Phenotypic resistance analysis is an indispensable method for determination of HIV-1 resistance and cross-resistance to novel drug compounds. Since integrase inhibitors are essential components of recent antiretroviral combination therapies, phenotypic resistance data, in conjunction with the corresponding genotypes, are needed for improving rules-based and data-driven tools for resistance prediction, such as HIV-Grade and geno2pheno[integrase]. For generation of phenotypic resistance data to recent integrase inhibitors, a recombinant phenotypic integrase susceptibility assay was established. For validation purposes, the phenotypic resistance to raltegravir, elvitegravir and dolutegravir of nine subtype-B virus strains, isolated from integrase inhibitor-naïve and raltegravir-treated patients was determined. Genotypic resistance analysis identified four virus strains harbouring RAL resistance-associated mutations. Phenotypic resistance analysis was performed as follows. The HIV-1 integrase genes were cloned into a modified pNL4-3 vector and transfected into 293T cells for the generation of recombinant virus. The integrase-inhibitor susceptibility of the recombinant viruses was determined via an indicator cell line. While raltegravir resistance profiles presented a high cross-resistance to elvitegravir, dolutegravir maintained in-vitro activity in spite of the Y143R and N155H mutations, confirming the strong activity of dolutegravir against raltegravir-resistant viruses. Solely a Q148H+G140S variant presented reduced susceptibility to dolutegravir. In conclusion, our phenotypic susceptibility assay permits resistance analysis of the integrase gene of patient-derived viruses for integrase inhibitors by replication-competent recombinants. Thus, this assay can be used to analyze phenotypic drug resistance of integrase inhibitors in vitro. It provides the possibility to determine the impact of newly appearing mutational patterns to drug resistance of recent integrase inhibitors.
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Affiliation(s)
- Eva Heger
- Institute of Virology, University of Cologne, Germany
| | | | - Klaus Remmel
- Institute of Virology, University of Cologne, Germany
| | - Hauke Walter
- Medical Center for Infectiology, Berlin, and Medical Laboratory Stendal, Stendal, Germany
| | - Alejandro Pironti
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Elena Knops
- Institute of Virology, University of Cologne, Germany
| | | | - Björn Jensen
- Department of Gastroenterology, Hepatology and Infectiology, Heinrich-Heine-University, University Hospital Düsseldorf, Germany
| | - Stefan Esser
- Department of Dermatology and Venerology, University Hospital Duisburg-Essen, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Germany
| | - Nadine Lübke
- Institute of Virology, University of Cologne, Germany.
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2
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Chen I, Khaki L, Lindsey JC, Fry C, Cousins MM, Siliciano RF, Violari A, Palumbo P, Eshleman SH. Association of pol diversity with antiretroviral treatment outcomes among HIV-infected African children. PLoS One 2013; 8:e81213. [PMID: 24312277 PMCID: PMC3842253 DOI: 10.1371/journal.pone.0081213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/09/2013] [Indexed: 01/02/2023] Open
Abstract
Background In HIV-infected children, viral diversity tends to increase with age in the absence of antiretroviral treatment (ART). We measured HIV diversity in African children (ages 6–36 months) enrolled in a randomized clinical trial comparing two ART regimens (Cohort I of the P1060 trial). Children in this cohort were exposed to single dose nevirapine (sdNVP) at birth. Methods HIV diversity was measured retrospectively using a high resolution melting (HRM) diversity assay. Samples were obtained from 139 children at the enrollment visit prior to ART initiation. Six regions of the HIV genome were analyzed: two in gag, one in pol, and three in env. A single numeric HRM score that reflects HIV diversity was generated for each region; composite HRM scores were also calculated (mean and median for all six regions). Results In multivariable median regression models using backwards selection that started with demographic and clinical variables, older age was associated with higher HRM scores (higher HIV diversity) in pol (P = 0.005) and with higher mean (P = 0.014) and median (P<0.001) HRM scores. In multivariable models adjusted for age, pre-treatment HIV viral load, pre-treatment CD4%, and randomized treatment regimen, higher HRM scores in pol were associated with shorter time to virologic suppression (P = 0.016) and longer time to study endpoints (virologic failure [VF], VF/death, and VF/off study treatment; P<0.001 for all measures). Conclusions In this cohort of sdNVP-exposed, ART-naïve African children, higher levels of HIV diversity in the HIV pol region prior to ART initiation were associated with better treatment outcomes.
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Affiliation(s)
- Iris Chen
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (SHE); (IC)
| | - Leila Khaki
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jane C. Lindsey
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Carrie Fry
- Frontier Science and Technology Research Foundation, Amherst, New York, United States of America
| | - Matthew M. Cousins
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Robert F. Siliciano
- Dept. of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Avy Violari
- PHRU, Chris Baragwanath Hospital, Soweto, South Africa
| | - Paul Palumbo
- Depts. of Pediatrics and Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Susan H. Eshleman
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (SHE); (IC)
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3
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Hsieh SM, Pan SC, Chang SY, Hung CC, Sheng WH, Chen MY, Chang SC. Differential impact of resistance-associated mutations to protease inhibitors and nonnucleoside reverse transcriptase inhibitors on HIV-1 replication capacity. AIDS Res Hum Retroviruses 2013; 29:1117-22. [PMID: 23594266 DOI: 10.1089/aid.2013.0038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effects of drug resistance on HIV-1 replication capacity have been studied, but data from clinical isolates are few. We accessed the patients with HIV-1 infection at the National Taiwan University Hospital who experienced virological failure. Genotypic susceptibility and replication capacity of clinical HIV-1 isolates were measured. There were 80 patients enrolled between September 2007 and August 2010. The HIV-1 replication capacity declined significantly with the increasing number of major resistance-associated mutations (RAMs) to protease inhibitors (PIs) (p<0.001); however, it did not decline significantly with the increasing RAMs to first-line nonnucleoside analogue reverse transcriptase inhibitors (NNRTIs) (p=0.098). Regarding the effects of resistance to antiretroviral drugs in salvage therapy, decreased replication capacity was noted with the increasing RAMs to darunavir/ritonavir (p<0.001) and specific RAMs (L100I, K101P, and Y181C/I/V) to etravirine (p<0.001). Although NNRTI-related RAMs have less remarkable effects, both PI- and NNRTI-related RAMs reduced replication capacity, especially RAMs to darunavir/ritonavir and etravirine, which are commonly used in salvage therapy for treatment of patients infected with highly resistant HIV. Thus, decreased viral fitness during the emergence of RAMs suggests the importance of continued optimal antiretroviral treatment even when virological failure was noted.
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Affiliation(s)
- Szu-Min Hsieh
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sung-Ching Pan
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Ching Hung
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wang-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mao-Yuan Chen
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shan-Chwen Chang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
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4
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Theys K, Deforche K, Vercauteren J, Libin P, van de Vijver DAMC, Albert J, Åsjö B, Balotta C, Bruckova M, Camacho RJ, Clotet B, Coughlan S, Grossman Z, Hamouda O, Horban A, Korn K, Kostrikis LG, Kücherer C, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stockl E, Riva C, Ruiz L, Liitsola K, Schmit JC, Schuurman R, Sönnerborg A, Stanekova D, Stanojevic M, Struck D, Van Laethem K, Wensing AMJ, Boucher CAB, Vandamme AM. Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients. Retrovirology 2012; 9:81. [PMID: 23031662 PMCID: PMC3487874 DOI: 10.1186/1742-4690-9-81] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The effect of drug resistance transmission on disease progression in the newly infected patient is not well understood. Major drug resistance mutations severely impair viral fitness in a drug free environment, and therefore are expected to revert quickly. Compensatory mutations, often already polymorphic in wild-type viruses, do not tend to revert after transmission. While compensatory mutations increase fitness during treatment, their presence may also modulate viral fitness and virulence in absence of therapy and major resistance mutations. We previously designed a modeling technique that quantifies genotypic footprints of in vivo treatment selective pressure, including both drug resistance mutations and polymorphic compensatory mutations, through the quantitative description of a fitness landscape from virus genetic sequences. RESULTS Genotypic correlates of viral load and CD4 cell count were evaluated in subtype B sequences from recently diagnosed treatment-naive patients enrolled in the SPREAD programme. The association of surveillance drug resistance mutations, reported compensatory mutations and fitness estimated from drug selective pressure fitness landscapes with baseline viral load and CD4 cell count was evaluated using regression techniques. Protease genotypic variability estimated to increase fitness during treatment was associated with higher viral load and lower CD4 cell counts also in treatment-naive patients, which could primarily be attributed to well-known compensatory mutations at highly polymorphic positions. By contrast, treatment-related mutations in reverse transcriptase could not explain viral load or CD4 cell count variability. CONCLUSIONS These results suggest that polymorphic compensatory mutations in protease, reported to be selected during treatment, may improve the replicative capacity of HIV-1 even in absence of drug selective pressure or major resistance mutations. The presence of this polymorphic variation may either reflect a history of drug selective pressure, i.e. transmission from a treated patient, or merely be a result of diversity in wild-type virus. Our findings suggest that transmitted drug resistance has the potential to contribute to faster disease progression in the newly infected host and to shape the HIV-1 epidemic at a population level.
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Affiliation(s)
- Kristof Theys
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Jurgen Vercauteren
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Jan Albert
- Clinical Microbiology, Karolinska University Hospital and Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Birgitta Åsjö
- Section for Microbiology and Immunology, Gade institute, University of Bergen, Bergen, Norway
| | | | - Marie Bruckova
- National Institute of Public Health, Prague, Czech Republic
| | - Ricardo J Camacho
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
- Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Bonaventura Clotet
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari “Germans Trias i Pujol”, Badalona, Spain
| | | | - Zehava Grossman
- Sheba Medical Center, Tel-Hashomer, and School of Public Health, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Andrzei Horban
- Warsaw Medical University and Hospital for Infectious Diseases, Warsaw, Poland
| | - Klaus Korn
- Institut für Klinische und Molekulare Virologie, University of Erlangen, Erlangen, Germany
| | | | | | | | - Dimitrios Paraskevis
- National Retrovirus Reference Center, Department of Hygiene Epidemiology of Medical Statistics, University of Athens, Medical School, Athens, Greece
| | | | | | | | - Lidia Ruiz
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari “Germans Trias i Pujol”, Badalona, Spain
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Jean-Claude Schmit
- Centre Hospitalier de Luxembourg and Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Anders Sönnerborg
- Divisions of Infectious Diseases and Clinical Virology, Karolinska Institutet, Stockholm, Sweden
| | | | - Maja Stanojevic
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Daniel Struck
- Centre Hospitalier de Luxembourg and Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Kristel Van Laethem
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Annemarie MJ Wensing
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Charles AB Boucher
- Department of Virology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Anne-Mieke Vandamme
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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Bedimo R, Kyriakides T, Brown S, Weidler J, Lie Y, Coakley E, Holodniy M. Predictive value of HIV-1 replication capacity and phenotypic susceptibility scores in antiretroviral treatment-experienced patients. HIV Med 2012; 13:345-51. [PMID: 22276745 DOI: 10.1111/j.1468-1293.2011.00981.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2011] [Indexed: 11/26/2022]
Abstract
OBJECTIVES The aim of the study was to determine the prognostic value of HIV replication capacity (RC) for subsequent antiretroviral (ARV) treatment response in ARV-experienced patients. METHODS RC and phenotypic resistance testing were performed at baseline and week 12 on plasma samples from patients randomized to undergo a 12-week ARV drug-free period (ARDFP) or initiate immediate salvage therapy (no-ARDFP group) in the Options in Management with Antiretrovirals (OPTIMA) trial. Dichotomous and incremental phenotypic susceptibility scores (dPSSs and iPSSs, respectively) were calculated. The predictive value of RC and PSS for ARV therapy response and/or ARDFP was evaluated using multivariate regression analysis and Pearson correlations. RESULTS In 146 no-ARDFP subjects, baseline RC (50.8%) did not change at week 12 and was not correlated with CD4 cell count or viral load changes at week 12 (P=0.33 and P=0.79, respectively) or at week 24 (P=0.96 and P=0.14, respectively). dPSS predicted virological but not CD4 cell count response to ARV therapy at weeks 12, 24 and 48 (P=0.002, P<0.001 and P=0.005, respectively). RC was significantly correlated with dPSS and iPSS at baseline, but did not increase their predictive value. In the 137 ARDFP patients, RC increased significantly (from 52.4 to 85.8%), but did not predict CD4 cell count and viral load changes during ARDFP (P=0.92 and P=0.26, respectively). RC after ARDFP did not predict subsequent CD4 cell count and viral load changes 12 weeks following ARV treatment reinitiation (P=0.90 and P=0.29, respectively). CONCLUSIONS We found no additional predictive value of replication capacity for virological or immunological responses (above what PSS provides) in patients undergoing salvage ARV treatment.
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Affiliation(s)
- R Bedimo
- Veterans Affairs North Texas Health Care System, Dallas, TX 75216, USA.
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Schapiro JM, Boucher CAB, Kuritzkes DR, van de Vijver DA, Llibre JM, Lewis M, Simpson P, Delogne C, McFadyen L, Chapman D, Perros M, Valdez H, van der Ryst E, Westby M. Baseline CD4(+) T-cell counts and weighted background susceptibility scores strongly predict response to maraviroc regimens in treatment-experienced patients. Antivir Ther 2011; 16:395-404. [PMID: 21555822 DOI: 10.3851/imp1759] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Maraviroc-containing regimens are known to achieve virological suppression in many treatment-experienced patients. This study aimed to evaluate a more rigorous methodological approach to resistance-response analysis in large clinical studies and to better establish which subpopulations of patients were most likely to benefit from maraviroc by refining and extending previous subgroup analyses from the MOTIVATE studies. METHODS Individual weighted optimized background therapy (OBT) susceptibility scores were calculated by combining genotypic or phenotypic resistance testing with prior drug use information. Virological response (HIV-1 RNA<50 copies/ml at week 48) using each of these methods was compared with a commonly used method of counting active drugs. Baseline predictors of virological response, including weighted or unweighted scoring, maraviroc use, baseline CD4(+) T-cell count, HIV-1 plasma viral load and tropism, were assessed by logistic regression modelling. RESULTS Genotypic or phenotypic weighted methods were similarly predictive of virological response and better than counting active drugs. Weighted scoring and baseline CD4(+) T-cell count were the strongest predictors of virological response (P<0.0001): ≈70% of maraviroc patients with a weighted score ≥2 had a virological response, rising to ≈80% when the baseline CD4(+) T-cell count was ≥50 cells/mm(3). CONCLUSIONS Approximately 80% of patients with a CD4(+) T-cell count ≥50 cells/mm(3) receiving maraviroc with the equivalent of at least two fully active agents achieved HIV-1 RNA<50 copies/ml at week 48 in the MOTIVATE studies. Genotypic and phenotypic weighted scores were similarly predictive of virological response.
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Flor-Parra F, Pérez-Pulido AJ, Pachón J, Pérez-Romero P. The HIV type 1 protease L10I minor mutation decreases replication capacity and confers resistance to protease inhibitors. AIDS Res Hum Retroviruses 2011; 27:65-70. [PMID: 21142921 DOI: 10.1089/aid.2010.0072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effect of minor mutations in PR on treatment outcome has not been well established. We characterized the HIV protease minor mutations, L10I, compared to the minor mutation, L63P, and the major mutation D30N and their impact on viral fitness and resistance to protease inhibitors. Mutations were introduced individually and in combination by site-directed mutagenesis into the provirus pNL4.3ren and constructs used for replication capacity (RC) and resistance assays. A structure prediction of the protease carrying the L10I mutation was determined. The prevalence of the minor mutation L10I had a pattern similar to that found for major mutations D30N, with a low prevalence (4.9%) in naive patients and significantly higher prevalence in treated patients. Furthermore, viruses carrying the major mutation D30N or the minor mutation L10I showed a significant decrease in RC (p-value <0.05), whereas viruses carrying the minor mutation L63P had RC similar to wild-type virus. In addition, the L10I mutation conferred resistance to saquinavir, which was supported by the higher prevalence in the cohort of the L10I mutation among patients with SQV resistance. The molecular modeling suggests that L10I may affect the conformation of Leu-23, a critical residue in the substrate binding site. In conclusion, the L10I mutation impairs RC and confers resistance to SQV, similarly to other major mutations, which may be related with changes in the conformation in the protease binding site. The presence of this mutation in the genotype of HIV from patients should be taken into consideration when designing new optimize treatments.
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Affiliation(s)
- Fernando Flor-Parra
- Institute of Biomedicine of Sevilla, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Spain
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Human immunodeficiency virus type 1 protease inhibitor drug-resistant mutants give discordant results when compared in single-cycle and multiple-cycle fitness assays. J Clin Microbiol 2010; 48:4035-43. [PMID: 20826651 DOI: 10.1128/jcm.00605-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The replication fitness of HIV-1 drug-resistant mutants has been measured using either multiple-cycle or single-cycle assays (MCAs or SCAs); these assays have not been systematically compared. We developed an MCA and an SCA that utilized either intact or env-deleted recombinant viral vectors, respectively, in which virus-infected cells were detected by flow cytometry of a reporter gene product. Fitness was measured using each assay for 11 protease mutants, 9 reverse transcriptase mutants, and two mutants with mutations in gag p6, which is important for the release of virus particles from the cell membrane. In the SCA, fitness (replication capacity [RC]) was defined as the proportion of cells infected by the mutant compared to the wild type 40 h after infection. MCA fitness (1+s) was determined by comparing the changes in the relative proportions of cells infected by the mutant and the wild type between 3 and 5 days after infection. Five protease mutants showed statistically different fitness values by the MCA versus the SCA: the D30N, G48V, I50V, I54L, and I54M mutants. When all the mutants were ranked in order from most to least fit for both assays, 4 protease mutants moved more than 5 positions in rank: the D30N, I54L, I54M, and V82A mutants. There were no significant differences in fitness for the gag p6 or reverse transcriptase mutants. We propose that discordant results in the MCA and SCA are due to alterations in late events in the virus life cycle that are not captured in an SCA, such as burst size, cell-to-cell transmission, or infected-cell life span.
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Bonura F, Tramuto F, Vitale F, Perna AM, Viviano E, Romano N. Transmission of drug-resistant HIV type 1 strains in HAART-naive patients: a 5-year retrospective study in Sicily, Italy. AIDS Res Hum Retroviruses 2010; 26:961-5. [PMID: 20707733 DOI: 10.1089/aid.2009.0250] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The transmission of drug-resistant HIV-1 strains might compromise the efficacy of current first-line antiretroviral (ARV) regimens. Between 2004 and 2008, HIV-1 reverse transcriptase (RT) and protease (PR) genes of 108 ARV-naive Sicilian patients were amplified and sequenced to describe the prevalence of ARV resistance mutations among HAART-naive HIV-1-infected individuals. The frequency of transmitted drug resistance mutations (DRAMs) was determined by using genotypic interpretation algorithms. The proportion of HAART-naive HIV-1-infected patients in Sicily increased from 18.4% to 23.5% during 2004-2008. Among naive patients, the overall prevalence of DRAMs was 15.7% [17/108; 95% CI: 9.4-24.0]. DRAMs to nonnucleoside reverse transcriptase inhibitors (nNRTI) were detected most frequently [11/108 (10.2%)], of which K103N was the most prevalent (4.6%), whereas the prevalence of DRAMs was lowest for protease inhibitors (PI) [3/108 (2.8%)]. Drug resistance substitutions associated with two or three drug classes were rarely observed. The prevalence of HIV-1 DRAMs in Sicily was relatively higher than that observed in Italy and other European geographic areas and much higher than in resource-limited countries. However, the possible clinical role played by DRAMs in HAART-naive HIV-1-infected individuals will require further assessment.
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Affiliation(s)
- Filippa Bonura
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Scienze per la Promozione della Salute, Università degli Studi di Palermo, Palermo, Italy
| | - Fabio Tramuto
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Scienze per la Promozione della Salute, Università degli Studi di Palermo, Palermo, Italy
| | - Francesco Vitale
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Scienze per la Promozione della Salute, Università degli Studi di Palermo, Palermo, Italy
| | - Anna Maria Perna
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Scienze per la Promozione della Salute, Università degli Studi di Palermo, Palermo, Italy
| | - Enza Viviano
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Scienze per la Promozione della Salute, Università degli Studi di Palermo, Palermo, Italy
| | - Nino Romano
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Scienze per la Promozione della Salute, Università degli Studi di Palermo, Palermo, Italy
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Weisser H, Altmann A, Sierra S, Incardona F, Struck D, Sönnerborg A, Kaiser R, Zazzi M, Tschochner M, Walter H, Lengauer T. Only slight impact of predicted replicative capacity for therapy response prediction. PLoS One 2010; 5:e9044. [PMID: 20140263 PMCID: PMC2815793 DOI: 10.1371/journal.pone.0009044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 01/15/2010] [Indexed: 12/23/2022] Open
Abstract
Background Replication capacity (RC) of specific HIV isolates is occasionally blamed for unexpected treatment responses. However, the role of viral RC in response to antiretroviral therapy is not yet fully understood. Materials and Methods We developed a method for predicting RC from genotype using support vector machines (SVMs) trained on about 300 genotype-RC pairs. Next, we studied the impact of predicted viral RC (pRC) on the change of viral load (VL) and CD4+ T-cell count (CD4) during the course of therapy on about 3,000 treatment change episodes (TCEs) extracted from the EuResist integrated database. Specifically, linear regression models using either treatment activity scores (TAS), the drug combination, or pRC or any combination of these covariates were trained to predict change in VL and CD4, respectively. Results The SVM models achieved a Spearman correlation (ρ) of 0.54 between measured RC and pRC. The prediction of change in VL (CD4) was best at 180 (360) days, reaching a correlation of ρ = 0.45 (ρ = 0.27). In general, pRC was inversely correlated to drug resistance at treatment start (on average ρ = −0.38). Inclusion of pRC in the linear regression models significantly improved prediction of virological response to treatment based either on the drug combination or on the TAS (t-test; p-values range from 0.0247 to 4 10−6) but not for the model using both TAS and drug combination. For predicting the change in CD4 the improvement derived from inclusion of pRC was not significant. Conclusion Viral RC could be predicted from genotype with moderate accuracy and could slightly improve prediction of virological treatment response. However, the observed improvement could simply be a consequence of the significant correlation between pRC and drug resistance.
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Affiliation(s)
- Hendrik Weisser
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - André Altmann
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
- * E-mail:
| | - Saleta Sierra
- Institute of Virology, University of Cologne, Cologne, Germany
| | | | - Daniel Struck
- Retrovirology Laboratory, CRP-Santé, Strassen, Luxembourg
| | - Anders Sönnerborg
- Department of Medicine, Division of Infectious Diseases, Karolinska Institute, Stockholm, Sweden
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Maurizio Zazzi
- Department of Molecular Biology, University of Siena, Siena, Italy
| | - Monika Tschochner
- Institute of Clinical and Molecular Virology, University of Erlangen, Erlangen, Germany
| | - Hauke Walter
- Institute of Clinical and Molecular Virology, University of Erlangen, Erlangen, Germany
| | - Thomas Lengauer
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
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Mata RC, Flor-Parra F, Viciana P, López-Cortés LF, Pérez-Romero P. Virological and immunological stability in HIV infected patients undergoing partial-treatment interruption. J Clin Virol 2009; 45:362-6. [PMID: 19539522 DOI: 10.1016/j.jcv.2009.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 05/04/2009] [Accepted: 05/06/2009] [Indexed: 10/20/2022]
Abstract
BACKGROUND Partial-treatment interruption in patients with drug-resistant viremia has been associated with stable HIV RNA levels suggesting that interruption of protease inhibitors may be an effective strategy for patients without other therapeutic options while waiting for the development of new drugs. OBJECTIVE Our goal was to maintain virological and immunological stability in patients experiencing virologic failure with multiresistant HIV to allow access to newly developed antiretroviral drugs, and to characterize the impact of partial-treatment interruption on replication capacity and resistance profile. STUDY DESIGN From 2003 to 2004, a group of 12 heavily treated patients was studied. Protease inhibitor treatment was interrupted and patients were treated with nucleoside analog retrotranscriptase inhibitors (Trizivir) and the fusion inhibitor Enfurvirtide to establish the therapeutic benefit and the virologic response. RESULTS Both, CD4 T-cell counts and viral load remained stable for a period of time that enabled all the patients to access rescue treatments (median=13.5 months; IQR: 9-19). The replication capacity of the patient-derived viruses significantly decreased or remained stable during the partial-treatment interruption. The decrease in replication capacity was mainly attributable to the selection of viruses carrying at least two fewer minor mutations in the protease. As of December 2008 10 of 12 patients maintained undetectable HIV RNA levels. CONCLUSIONS Study results indicate that a partial-treatment interruption regimen based on Trizivir with Enfurvirtide augmentation allows for a loss of protease inhibitor resistance mutations as well as for a decrease in the replication capacity of patient-derive HIV protease gene recombinants.
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Affiliation(s)
- Rosario C Mata
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
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Skowron G, Spritzler JG, Weidler J, Robbins GK, Johnson VA, Chan ES, Asmuth DM, Gandhi RT, Lie Y, Bates M, Pollard RB. Replication capacity in relation to immunologic and virologic outcomes in HIV-1-infected treatment-naive subjects. J Acquir Immune Defic Syndr 2009; 50:250-8. [PMID: 19194319 PMCID: PMC3482469 DOI: 10.1097/qai.0b013e3181938faf] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To evaluate the association between baseline (BL) replication capacity (RC) (RCBL) and immunologic/virologic parameters (at BL and after 48 weeks on therapy) in HIV-1-infected subjects initiating antiretroviral therapy. METHODS RCBL was determined using a modified Monogram PhenoSense HIV drug susceptibility assay on plasma HIV-1 from 321 treatment-naive subjects from AIDS Clinical Trials Group 384. Univariate and multivariable analyses were performed to determine the association of RCBL with BL and on-therapy virologic and immunologic outcomes. RESULTS Higher RCBL was associated with lower baseline CD4 (CD4BL) (r = -0.23, P < 0.0001), higher baseline HIV-1 RNA (r = 0.25, P < 0.0001), higher CD4BL activation percent (r = 0.23, P < 0.0001), and lower CD4BL memory count (r = -0.21, P = 0.0002). In a multivariable model, week 48 CD4 increase (DeltaCD448) was associated with lower CD4BL memory count and higher CD4BL-naive percent (P = 0.004, P = 0.015, respectively). The interaction between CD4BL and RCBL was significant (P = 0.018), with a positive association between RCBL and DeltaCD448 in subjects with higher CD4BL and a negative association at lower absCD4BL. CONCLUSIONS At baseline, higher RC was significantly associated with higher HIV-1 RNA, higher CD4 cell activation, lower CD4 cell count, and lower CD4 memory cell count. These factors may interact, directly or indirectly, to modify the extent to which CD4 recovery occurs in patients starting antiretroviral therapy at different CD4BL counts.
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Affiliation(s)
- Gail Skowron
- Division of Infectious Diseases, Roger Williams Medical Center, Providence, RI 02908, USA.
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Apisarnthanarak A, Jirayasethpong T, Sa-nguansilp C, Thongprapai H, Kittihanukul C, Kamudamas A, Tungsathapornpong A, Mundy LM. Antiretroviral drug resistance among antiretroviral-naïve persons with recent HIV infection in Thailand. HIV Med 2008; 9:322-5. [PMID: 18400079 DOI: 10.1111/j.1468-1293.2008.00562.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To evaluate the prevalence and patterns of antiretroviral (ARV) drug resistance (ARV-DR) among ARV drug-naïve, recently infected persons with HIV in the 4-year interval (2003-2006) after the inception of the National Access to ARV Programme for People who have AIDS in Thailand. METHODS Cross-sectional study of patients with recent HIV infection for HIV risks, ARV-DR risks and baseline ARV-DR. RESULTS Seven of the 305 patients (2%) had baseline ARV-DR. Via contract tracing, all seven patients with transmitted ARV-DR identified sexual partners with prior ARV treatment failure and had documented low (<75%) ARV adherence. Annual ARV-DR increased from 0 to 5.2% (P=0.06) between 2003 and 2006. CONCLUSIONS Report of sexual partners with potential HIV and ARV drug exposures can prompt baseline ARV-DR testing of at-risk individuals, while behavioural interventions for adherence and safer sex are refined to minimize the emergence of resistance to generic, fixed-dose combination stavudine, lamivudine and nevirapine (GPO-VIR) therapy.
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Affiliation(s)
- A Apisarnthanarak
- Department of Medicine, Division of Infectious Diseases, Thammasat University Hospital, Pratumthani, Thailand.
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