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Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK. HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy. mBio 2022; 13:e0026922. [PMID: 35446121 PMCID: PMC9239331 DOI: 10.1128/mbio.00269-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 12/19/2022] Open
Abstract
Prolonged virologic failure on 2nd-line protease inhibitor (PI)-based antiretroviral therapy (ART) without emergence of major protease mutations is well recognized and provides an opportunity to study within-host evolution in long-term viremic individuals. Using next-generation sequencing and in silico haplotype reconstruction, we analyzed whole-genome sequences from longitudinal plasma samples of eight chronically infected HIV-1-positive individuals failing 2nd-line regimens from the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) trial. On nonsuppressive ART, there were large fluctuations in synonymous and nonsynonymous variant frequencies despite stable viremia. Reconstructed haplotypes provided evidence for selective sweeps during periods of partial adherence, and viral haplotype competition, during periods of low drug exposure. Drug resistance mutations in reverse transcriptase (RT) were used as markers of viral haplotypes in the reservoir, and their distribution over time indicated recombination. We independently observed linkage disequilibrium decay, indicative of recombination. These data highlight dramatic changes in virus population structure that occur during stable viremia under nonsuppressive ART. IMPORTANCE HIV-1 infections are most commonly initiated with a single founder virus and are characterized by extensive inter- and intraparticipant genetic diversity. However, existing literature on HIV-1 intrahost population dynamics is largely limited to untreated infections, predominantly in subtype B-infected individuals. The manuscript characterizes viral population dynamics in long-term viremic treatment-experienced individuals, which has not been previously characterized. These data are particularly relevant for understanding HIV dynamics but can also be applied to other RNA viruses. With this unique data set we propose that the virus is highly unstable, and we have found compelling evidence of HIV-1 within-host viral diversification, recombination, and haplotype competition during nonsuppressive ART.
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Affiliation(s)
- Steven A. Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
| | - Oscar J. Charles
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, Durban, South Africa
| | - Werner Smidt
- Africa Health Research Institute, Durban, South Africa
| | - Darren P. Martin
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Collins Iwuji
- Africa Health Research Institute, Durban, South Africa
- Research Department of Infection and Population Health, University College London, United Kingdom
| | - John Adamson
- Africa Health Research Institute, Durban, South Africa
| | | | - Tulio de Oliveira
- Africa Health Research Institute, Durban, South Africa
- KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa
| | - Francois Dabis
- INSERM U1219-Centre Inserm Bordeaux Population Health, Université de Bordeaux, France
- Université de Bordeaux, ISPED, Centre INSERM U1219-Bordeaux Population Health, France
| | - Deenan Pillay
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Richard A. Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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2
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Delaugerre C, Nere ML, Eymard-Duvernay S, Armero A, Ciaffi L, Koulla-Shiro S, Sawadogo A, Ngom Gueye NF, Ndour CT, Mpoudi Ngolle M, Amara A, Chaix ML, Reynes J. Deep sequencing analysis of M184V/I mutation at the switch and at the time of virological failure of boosted protease inhibitor plus lamivudine or boosted protease inhibitor maintenance strategy (substudy of the ANRS-MOBIDIP trial). J Antimicrob Chemother 2021; 76:1286-1293. [PMID: 33624081 DOI: 10.1093/jac/dkab002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The ANRS12286/MOBIDIP trial showed that boosted protease inhibitor (bPI) plus lamivudine dual therapy was superior to bPI monotherapy as maintenance treatment in subjects with a history of M184V mutation. OBJECTIVES We aimed to deep analyse the detection of M184V/I variants at time of switch and at the time of virological failure (VF). METHODS Ultra-deep sequencing (UDS) was performed on proviral HIV-DNA at inclusion among 265 patients enrolled in the ANRS 12026/MOBIDIP trial, and on plasma from 31 patients experiencing VF. The proportion of M184V/I variants was described and the association between the M184V/I mutation at 1% of threshold and VF was explored with logistic regression models. RESULTS M184V and I mutations were detected in HIV-DNA for 173/252 (69%) and 31/252 (12%) of participants, respectively. Longer duration of first-line treatment, higher plasma viral load at first-line treatment failure and higher baseline HIV-DNA load were associated with the archived M184V. M184I mutation was always associated with a STOP codon, suggesting defective virus. The 48 week estimated probability of remaining free from VF was comparable with or without the M184V/I mutation for dual therapy. At failure, M184V and major PI mutations were detected in 1/17 and 5/15 patients in the bPI arm and in 2/2 and 0/3 in the bPI+lamivudine arm, respectively. CONCLUSIONS Using UDS evidenced that archiving of M184V in HIV-DNA is heterogeneous despite past historical M184V in 96% of cases. The antiviral efficacy of lamivudine-based dual therapy regimens is mainly due to the residual lamivudine activity.
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Affiliation(s)
- Constance Delaugerre
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM U944, University of Paris, Paris, France
| | - Marie-Laure Nere
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sabrina Eymard-Duvernay
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France
| | - Alix Armero
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laura Ciaffi
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France
| | - Sinata Koulla-Shiro
- Department of Infectious Diseases, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Adrien Sawadogo
- Day Care Center, University Hospital Souro Sanou, Bobo Dioulasso, Burkina Faso
| | | | | | | | - Ali Amara
- INSERM U944, University of Paris, Paris, France
| | - Marie-Laure Chaix
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM U944, University of Paris, Paris, France
| | - Jacques Reynes
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France.,Department of Infectious Diseases, Montpellier University Hospital, Montpellier, France
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3
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Blanch-Lombarte O, Santos JR, Peña R, Jiménez-Moyano E, Clotet B, Paredes R, Prado JG. HIV-1 Gag mutations alone are sufficient to reduce darunavir susceptibility during virological failure to boosted PI therapy. J Antimicrob Chemother 2021; 75:2535-2546. [PMID: 32556165 PMCID: PMC7443716 DOI: 10.1093/jac/dkaa228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/21/2020] [Accepted: 05/03/2020] [Indexed: 01/01/2023] Open
Abstract
Background Virological failure (VF) to boosted PIs with a high genetic barrier is not usually linked to the development of resistance-associated mutations in the protease gene. Methods From a cohort of 520 HIV-infected subjects treated with lopinavir/ritonavir or darunavir/ritonavir monotherapy, we retrospectively identified nine patients with VF. We sequenced the HIV-1 Gag-protease region and generated clonal virus from plasma samples. We characterized phenotypically clonal variants in terms of replicative capacity and susceptibility to PIs. Also, we used VESPA to identify signature mutations and 3D molecular modelling information to detect conformational changes in the Gag region. Results All subjects analysed harboured Gag-associated polymorphisms in the absence of resistance mutations in the protease gene. Most Gag changes occurred outside Gag cleavage sites. VESPA analyses identified K95R and R286K (P < 0.01) as signature mutations in Gag present at VF. In one out of four patients with clonal analysis available, we identified clonal variants with high replicative capacity and 8- to 13-fold reduction in darunavir susceptibility. These clonal variants harboured K95R, R286K and additional mutations in Gag. Low susceptibility to darunavir was dependent on the Gag sequence context. All other clonal variants analysed preserved drug susceptibility and virus replicative capacity. Conclusions Gag mutations may reduce darunavir susceptibility in the absence of protease mutations while preserving viral fitness. This effect is Gag-sequence context dependent and may occur during boosted PI failure.
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Affiliation(s)
- Oscar Blanch-Lombarte
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain and Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - José R Santos
- Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Ruth Peña
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | | | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Faculty of Medicine, University of Vic - Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Faculty of Medicine, University of Vic - Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Julia G Prado
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain and Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Datir R, Kemp S, El Bouzidi K, Mlchocova P, Goldstein R, Breuer J, Towers GJ, Jolly C, Quiñones-Mateu ME, Dakum PS, Ndembi N, Gupta RK. In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix. mBio 2020; 11:e02036-20. [PMID: 33144375 PMCID: PMC7642677 DOI: 10.1128/mbio.02036-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
Protease inhibitors (PIs) are the second- and last-line therapy for the majority of HIV-infected patients worldwide. Only around 20% of individuals who fail PI regimens develop major resistance mutations in protease. We sought to explore the role of mutations in gag-pro genotypic and phenotypic changes in viruses from six Nigerian patients who failed PI-based regimens without known drug resistance-associated protease mutations in order to identify novel determinants of PI resistance. Target enrichment and next-generation sequencing (NGS) with the Illumina MiSeq system were followed by haplotype reconstruction. Full-length Gag-protease gene regions were amplified from baseline (pre-PI) and virologic failure (VF) samples, sequenced, and used to construct gag-pro-pseudotyped viruses. Phylogenetic analysis was performed using maximum-likelihood methods. Susceptibility to lopinavir (LPV) and darunavir (DRV) was measured using a single-cycle replication assay. Western blotting was used to analyze Gag cleavage. In one of six participants (subtype CRF02_AG), we found 4-fold-lower LPV susceptibility in viral clones during failure of second-line treatment. A combination of four mutations (S126del, H127del, T122A, and G123E) in the p17 matrix of baseline virus generated a similar 4-fold decrease in susceptibility to LPV but not darunavir. These four amino acid changes were also able to confer LPV resistance to a subtype B Gag-protease backbone. Western blotting demonstrated significant Gag cleavage differences between sensitive and resistant isolates in the presence of drug. Resistant viruses had around 2-fold-lower infectivity than sensitive clones in the absence of drug. NGS combined with haplotype reconstruction revealed that resistant, less fit clones emerged from a minority population at baseline and thereafter persisted alongside sensitive fitter viruses. We used a multipronged genotypic and phenotypic approach to document emergence and temporal dynamics of a novel protease inhibitor resistance signature in HIV-1 matrix, revealing the interplay between Gag-associated resistance and fitness.
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Affiliation(s)
| | - Steven Kemp
- University College London, London, United Kingdom
| | | | - Petra Mlchocova
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Judy Breuer
- University College London, London, United Kingdom
| | | | - Clare Jolly
- University College London, London, United Kingdom
| | | | - Patrick S Dakum
- Institute for Human Virology, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nicaise Ndembi
- Institute for Human Virology, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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5
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Datir R, El Bouzidi K, Dakum P, Ndembi N, Gupta RK. Baseline PI susceptibility by HIV-1 Gag-protease phenotyping and subsequent virological suppression with PI-based second-line ART in Nigeria. J Antimicrob Chemother 2020; 74:1402-1407. [PMID: 30726945 PMCID: PMC6477990 DOI: 10.1093/jac/dkz005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/14/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022] Open
Abstract
Objectives Previous work showed that gag-protease-derived phenotypic susceptibility to PIs differed between HIV-1 subtype CRF02_AG/subtype G-infected patients who went on to successfully suppress viral replication versus those who experienced virological failure of lopinavir/ritonavir monotherapy as first-line treatment in a clinical trial. We analysed the relationship between PI susceptibility and outcome of second-line ART in Nigeria, where subtypes CRF02_AG/G dominate the epidemic. Methods Individuals who experienced second-line failure with ritonavir-boosted PI-based ART were matched (by subtype, sex, age, viral load, duration of treatment and baseline CD4 count) to those who achieved virological response (‘successes’). Successes were defined by viral load <400 copies of HIV-1 RNA/mL by week 48. Full-length Gag-protease was amplified from patient samples for in vitro phenotypic susceptibility testing, with PI susceptibility expressed as IC50 fold change (FC) relative to a subtype B reference strain. Results The median (IQR) lopinavir IC50 FC was 4.04 (2.49–7.89) for virological failures and 4.13 (3.14–8.17) for virological successes (P = 0.94). One patient had an FC >10 for lopinavir at baseline and experienced subsequent virological failure with ritonavir-boosted lopinavir as the PI. There was no statistically significant difference in single-round replication efficiency between the two groups (P = 0.93). There was a moderate correlation between single-round replication efficiency and FC for lopinavir (correlation coefficient 0.32). Conclusions We found no impact of baseline HIV-1 Gag-protease-derived phenotypic susceptibility on outcomes of PI-based second-line ART in Nigeria.
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Affiliation(s)
- R Datir
- Division of Infection and Immunity, University College London, London, UK
| | - K El Bouzidi
- Division of Infection and Immunity, University College London, London, UK
| | - P Dakum
- Institute of Human Virology, Abuja, Nigeria
| | - N Ndembi
- Institute of Human Virology, Abuja, Nigeria
| | - R K Gupta
- Division of Infection and Immunity, University College London, London, UK.,Africa Health Research Institute, Durban, South Africa
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6
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Ferretti F, Mackie NE, Singh GKJ, Fox J, Kaye S, McClure MO, Taylor G, Boffito M. Characterization of low level viraemia in HIV-infected patients receiving boosted protease inhibitor-based antiretroviral regimens. HIV Res Clin Pract 2020; 20:107-110. [DOI: 10.1080/25787489.2020.1716159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Francesca Ferretti
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Nicola E. Mackie
- Department of HIV, Sexual Health and Infections, Imperial College Healthcare NHS Trust, London, UK
| | - Gurmit Kaur Jagjit Singh
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Julie Fox
- Guy’s and St Thomas Hospital NHS Foundation Trust, London, UK
| | - Steve Kaye
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Myra O. McClure
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Graham Taylor
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Marta Boffito
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
- Division of Infectious Diseases, Imperial College London, London, UK
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7
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Inzaule SC, Hamers RL, Bertagnolio S, Siedner MJ, Rinke de Wit TF, Gupta RK. Pretreatment HIV drug resistance in low- and middle-income countries. Future Virol 2019. [DOI: 10.2217/fvl-2018-0208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pretreatment HIV drug resistance (PDR) has been increasing with scale-up of antiretroviral therapy (ART) in low- and middle-income countries. Delay in responding to rising levels of PDR is projected to fuel a worldwide increase in mortality, HIV incidence and ART costs. Strategies to curb the rise in PDR include using antiretrovirals (ARVs) with high-genetic barrier to resistance in first-line therapy and for prophylaxis in HIV exposed infants, enhancing HIV drug resistance surveillance in populations initiating, receiving ART, and in those on pre-exposure prophylaxis, universal access and effective use of viral-load tests, improving adherence and retention and minimizing ART programmatic quality gaps. In this review, we assess the drivers of PDR, and potential strategies to mitigate its rise in prevalence and impact in low- and middle-income countries.
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Affiliation(s)
- Seth C Inzaule
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
| | - Raph L Hamers
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
- Eijkman-Oxford Clinical Research Unit, and Faculty of Medicine Universitas Indonesia, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Nuffield Department of Medicine, Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Silvia Bertagnolio
- HIV/AIDS Department & Global Hepatitis Programme, World Health Organization, 20 avenue Appia, 1211 Geneva, 27, Switzerland
| | - Mark J Siedner
- Massachusetts General Hospital, Harvard University, 02114 Boston, MA, USA
- Department of Medicine, University of Cambridge, Cambridge, CB2 OXY, UK
| | - Tobias F Rinke de Wit
- Amsterdam Institute for Global Health & Development, Department of Global Health and Development, Amsterdam UMC, University of Amsterdam, 1105 BM, North Holland, The Netherlands
- Joep Lange Institute, 1105 BM, North Holland, The Netherlands
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, CB2 OXY, UK
- Africa Health Research Institute, 719 Umbilo Road, Durban, KZN, South Africa
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8
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Manasa J, Varghese V, Pond SLK, Rhee SY, Tzou PL, Fessel WJ, Jang KS, White E, Rögnvaldsson T, Katzenstein DA, Shafer RW. Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors. Sci Rep 2017; 7:11559. [PMID: 28912582 PMCID: PMC5599673 DOI: 10.1038/s41598-017-11893-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/31/2017] [Indexed: 11/15/2022] Open
Abstract
Several groups have proposed that genotypic determinants in gag and the gp41 cytoplasmic domain (gp41-CD) reduce protease inhibitor (PI) susceptibility without PI-resistance mutations in protease. However, no gag and gp41-CD mutations definitively responsible for reduced PI susceptibility have been identified in individuals with virological failure (VF) while receiving a boosted PI (PI/r)-containing regimen. To identify gag and gp41 mutations under selective PI pressure, we sequenced gag and/or gp41 in 61 individuals with VF on a PI/r (n = 40) or NNRTI (n = 20) containing regimen. We quantified nonsynonymous and synonymous changes in both genes and identified sites exhibiting signal for directional or diversifying selection. We also used published gag and gp41 polymorphism data to highlight mutations displaying a high selection index, defined as changing from a conserved to an uncommon amino acid. Many amino acid mutations developed in gag and in gp41-CD in both the PI- and NNRTI-treated groups. However, in neither gene, were there discernable differences between the two groups in overall numbers of mutations, mutations displaying evidence of diversifying or directional selection, or mutations with a high selection index. If gag and/or gp41 encode PI-resistance mutations, they may not be confined to consistent mutations at a few sites.
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Affiliation(s)
- Justen Manasa
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - Vici Varghese
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | | | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - W Jeffrey Fessel
- Department of Internal Medicine, Kaiser Permanente Medical Care Program - Northern California, San Francisco, CA, United States
| | - Karen S Jang
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - Elizabeth White
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | | | - David A Katzenstein
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA.
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9
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Collier D, Iwuji C, Derache A, de Oliveira T, Okesola N, Calmy A, Dabis F, Pillay D, Gupta RK. Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis. Clin Infect Dis 2017; 64:1006-1016. [PMID: 28329393 PMCID: PMC5439490 DOI: 10.1093/cid/cix015] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/12/2017] [Indexed: 11/20/2022] Open
Abstract
Background Second-line antiretroviral therapy (ART) based on ritonavir-boosted protease inhibitors (bPIs) represents the only available option after first-line failure for the majority of individuals living with human immunodeficiency virus (HIV) worldwide. Maximizing their effectiveness is imperative. Methods This cohort study was nested within the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) cluster-randomized trial in rural KwaZulu-Natal, South Africa. We prospectively investigated risk factors for virological failure (VF) of bPI-based ART in the combined study arms. VF was defined by a plasma viral load >1000 copies/mL ≥6 months after initiating bPI-based ART. Cumulative incidence of VF was estimated and competing risk regression was used to derive the subdistribution hazard ratio (SHR) of the associations between VF and patient clinical and demographic factors, taking into account death and loss to follow-up. Results One hundred one participants contributed 178.7 person-years of follow-up. Sixty-five percent were female; the median age was 37.4 years. Second-line ART regimens were based on ritonavir-boosted lopinavir, combined with zidovudine or tenofovir plus lamivudine or emtricitabine. The incidence of VF on second-line ART was 12.9 per 100 person-years (n = 23), and prevalence of VF at censoring was 17.8%. Thirteen of these 23 (56.5%) virologic failures resuppressed after a median of 8.0 months (interquartile range, 2.8-16.8 months) in this setting where viral load monitoring was available. Tuberculosis treatment was associated with VF (SHR, 11.50 [95% confidence interval, 3.92-33.74]; P < .001). Conclusions Second-line VF was frequent in this setting. Resuppression occurred in more than half of failures, highlighting the value of viral load monitoring of second-line ART. Tuberculosis was associated with VF; therefore, novel approaches to optimize the effectiveness of PI-based ART in high-tuberculosis-burden settings are needed. Clinical Trials Registration NCT01509508.
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Affiliation(s)
- Dami Collier
- Department of Infection and Immunity, University College London, United Kingdom
| | - Collins Iwuji
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- Research Department of Infection and Population Health, University College London, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- Sorbonne Universités, University Pierre and Marie Curie Université Paris 06, Inserm, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Tulio de Oliveira
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- University of KwaZulu-Natal, Durban, South Africa
| | | | - Alexandra Calmy
- Geneva University Hospital, HIV Unit, Department of Internal Medicine, Switzerland
| | - Francois Dabis
- INSERM U1219-Centre Inserm Bordeaux Population Health, Université de Bordeaux, France
- Université de Bordeaux, ISPED, Centre INSERM U1219-Bordeaux Population Health, France
| | - Deenan Pillay
- Department of Infection and Immunity, University College London, United Kingdom
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Ravindra K Gupta
- Department of Infection and Immunity, University College London, United Kingdom
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
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10
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Saladini F, Vicenti I. Role of phenotypic investigation in the era of routine genotypic HIV-1 drug resistance testing. Future Virol 2016. [DOI: 10.2217/fvl-2016-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of drug resistance can seriously compromise HIV type-1 therapy and decrease therapeutic options. Resistance testing is highly recommended to guide treatment decisions and drug activity can be accurately predicted in the clinical setting through genotypic assays. While phenotypic systems are not suitable for monitoring drug resistance in routine laboratory practice, genotyping can misclassify unusual or complex mutational patterns, particularly with recently approved antivirals. In addition, phenotypic assays remain fundamental for characterizing candidate antiretroviral compounds. This review aims to discuss how phenotypic assays contributed to and still play a role in understanding the mechanisms of resistance of both licensed and investigational HIV type-1 inhibitors.
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Affiliation(s)
- Francesco Saladini
- Department of Medical Biotechnologies, University of Siena Italy, Policlinico Le Scotte, Viale Bracci 16 53100 Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena Italy, Policlinico Le Scotte, Viale Bracci 16 53100 Siena, Italy
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Vardhanabhuti S, Katzenstein D, Bartlett J, Kumarasamy N, Wallis CL. Human Immunodeficiency Virus-1 Sequence Changes and Drug Resistance Mutation Among Virologic Failures of Lopinavir/Ritonavir Monotherapy: AIDS Clinical Trials Group Protocol A5230. Open Forum Infect Dis 2016; 3:ofw154. [PMID: 27704010 PMCID: PMC5047431 DOI: 10.1093/ofid/ofw154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/17/2016] [Indexed: 12/12/2022] Open
Abstract
Background. The mechanism of virologic failure (VF) of lopinavir/ritonavir (LPV/r) monotherapy is not well understood. We assessed sequence changes in human immunodeficiency virus-1 reverse-transcriptase (RT) and protease (PR) regions. Methods. Human immunodeficiency virus-1 pol sequences from 34 participants who failed second-line LPV/r monotherapy were obtained at study entry (SE) and VF. Sequence changes were evaluated using phylogenetic analysis and hamming distance. Results. Human immunodeficiency virus-1 sequence change was higher over drug resistance mutation (DRM) sites (median genetic distance, 2.2%; Q1 to Q3, 2.1%–2.5%) from SE to VF compared with non-DRM sites (median genetic distance, 1.3%; Q1 to Q3, 1.0%–1.4%; P < .0001). Evolution over DRM sites was mainly driven by changes in the RT (median genetic distance, 2.7%; Q1 to Q3, 2.2%–3.2%) compared with PR (median genetic distance, 1.1%; Q1 to Q3, 0.0%–1.1%; P < .0001). Most RT DRMs present at SE were lost at VF. At VF, 19 (56%) and 26 (76%) were susceptible to efavirenz/nevirapine and etravirine (ETV)/rilpivirine (RPV), respectively, compared with 1 (3%) and 12 (35%) at SE. Participants who retained nonnucleoside reverse-transcriptase inhibitor (NNRTI) DRMs and those without evolution of LPV/r DRMs had significantly shorter time to VF. Conclusions. The selection of LPV/r DRMs in participants with longer time to VF suggests better adherence and more selective pressure. Fading NNRTI mutations and an increase in genotypic susceptibility to ETV and RPV could allow for the reuse of NNRTI. Further studies are warranted to understand mechanisms of PR failure.
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Affiliation(s)
| | | | - John Bartlett
- Duke University Medical Center , Durham, North Carolina
| | | | - Carole L Wallis
- Department of Molecular Pathology , Lancet Laboratories and BARC-SA , Johannesburg , South Africa
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Contribution of Gag and Protease to HIV-1 Phenotypic Drug Resistance in Pediatric Patients Failing Protease Inhibitor-Based Therapy. Antimicrob Agents Chemother 2016; 60:2248-56. [PMID: 26833162 DOI: 10.1128/aac.02682-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/17/2016] [Indexed: 12/15/2022] Open
Abstract
Protease inhibitors (PIs) are used as a first-line regimen in HIV-1-infected children. Here we investigated the phenotypic consequences of amino acid changes in Gag and protease on lopinavir (LPV) and ritonavir (RTV) susceptibility among pediatric patients failing PI therapy. The Gag-protease from isolates from 20 HIV-1 subtype C-infected pediatric patients failing an LPV and/or RTV-based regimen was phenotyped using a nonreplicativein vitroassay. Changes in sensitivity to LPV and RTV relative to that of the matched baseline (pretherapy) sample were calculated. Gag and protease amino acid substitutions associated with PI failure were created in a reference clone by site-directed mutagenesis and assessed. Predicted phenotypes were determined using the Stanford drug resistance algorithm. Phenotypic resistance or reduced susceptibility to RTV and/or LPV was observed in isolates from 10 (50%) patients, all of whom had been treated with RTV. In most cases, this was associated with protease resistance mutations, but substitutions at Gag cleavage and noncleavage sites were also detected. Gag amino acid substitutions were also found in isolates from three patients with reduced drug susceptibilities who had wild-type protease. Site-directed mutagenesis confirmed that some amino acid changes in Gag contributed to PI resistance but only in the presence of major protease resistance-associated substitutions. The isolates from all patients who received LPV exclusively were phenotypically susceptible. Baseline isolates from the 20 patients showed a large (47-fold) range in the 50% effective concentration of LPV, which accounted for most of the discordance seen between the experimentally determined and the predicted phenotypes. Overall, the inclusion of thegaggene and the use of matched baseline samples provided a more comprehensive assessment of the effect of PI-induced amino acid changes on PI resistance. The lack of phenotypic resistance to LPV supports the continued use of this drug in pediatric patients.
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Sutherland KA, Parry CM, McCormick A, Kapaata A, Lyagoba F, Kaleebu P, Gilks CF, Goodall R, Spyer M, Kityo C, Pillay D, Gupta RK. Evidence for Reduced Drug Susceptibility without Emergence of Major Protease Mutations following Protease Inhibitor Monotherapy Failure in the SARA Trial. PLoS One 2015; 10:e0137834. [PMID: 26382239 PMCID: PMC4575205 DOI: 10.1371/journal.pone.0137834] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/23/2015] [Indexed: 12/11/2022] Open
Abstract
Background Major protease mutations are rarely observed following failure with protease inhibitors (PI), and other viral determinants of failure to PI are poorly understood. We therefore characterized Gag-Protease phenotypic susceptibility in subtype A and D viruses circulating in East Africa following viral rebound on PIs. Methods Samples from baseline and treatment failure in patients enrolled in the second line LPV/r trial SARA underwent phenotypic susceptibility testing. Data were expressed as fold-change in susceptibility relative to a LPV-susceptible reference strain. Results We cloned 48 Gag-Protease containing sequences from seven individuals and performed drug resistance phenotyping from pre-PI and treatment failure timepoints in seven patients. For the six patients where major protease inhibitor resistance mutations did not emerge, mean fold-change EC50 to LPV was 4.07 fold (95% CI, 2.08–6.07) at the pre-PI timepoint. Following viral failure the mean fold-change in EC50 to LPV was 4.25 fold (95% CI, 1.39–7.11, p = 0.91). All viruses remained susceptible to DRV. In our assay system, the major PI resistance mutation I84V, which emerged in one individual, conferred a 10.5-fold reduction in LPV susceptibility. One of the six patients exhibited a significant reduction in susceptibility between pre-PI and failure timepoints (from 4.7 fold to 9.6 fold) in the absence of known major mutations in protease, but associated with changes in Gag: V7I, G49D, R69Q, A120D, Q127K, N375S and I462S. Phylogenetic analysis provided evidence of the emergence of genetically distinct viruses at the time of treatment failure, indicating ongoing viral evolution in Gag-protease under PI pressure. Conclusions Here we observe in one patient the development of significantly reduced susceptibility conferred by changes in Gag which may have contributed to treatment failure on a protease inhibitor containing regimen. Further phenotype-genotype studies are required to elucidate genetic determinants of protease inhibitor failure in those who fail without traditional resistance mutations whilst PI use is being scaled up globally.
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Affiliation(s)
| | - Chris M. Parry
- Uganda Research Unit on AIDS, Medical Research Council (MRC), Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Anne Kapaata
- Uganda Research Unit on AIDS, Medical Research Council (MRC), Uganda Virus Research Institute, Entebbe, Uganda
| | - Fred Lyagoba
- Uganda Research Unit on AIDS, Medical Research Council (MRC), Uganda Virus Research Institute, Entebbe, Uganda
| | - Pontiano Kaleebu
- Uganda Research Unit on AIDS, Medical Research Council (MRC), Uganda Virus Research Institute, Entebbe, Uganda
| | - Charles F. Gilks
- School of Population Health, University of Queensland, Brisbane, Australia
| | - Ruth Goodall
- MRC Clinical Trials Unit at UCL, London, United Kingdom
| | - Moira Spyer
- MRC Clinical Trials Unit at UCL, London, United Kingdom
| | - Cissy Kityo
- Joint Clinical Research Centre, Kampala, Uganda
| | - Deenan Pillay
- University College London, London, United Kingdom
- Wellcome Trust Africa Centre for Health and Population Sciences, University of KwaZulu Natal, Mtubatuba, South Africa
- * E-mail: (DP); (RKG)
| | - Ravindra K. Gupta
- University College London, London, United Kingdom
- * E-mail: (DP); (RKG)
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Sutherland KA, Ghosn J, Gregson J, Mbisa JL, Chaix ML, Cohen Codar I, Delfraissy JF, Delaugerre C, Gupta RK. HIV-1 subtype influences susceptibility and response to monotherapy with the protease inhibitor lopinavir/ritonavir. J Antimicrob Chemother 2014; 70:243-8. [PMID: 25228587 PMCID: PMC4267506 DOI: 10.1093/jac/dku365] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE PI susceptibility results from a complex interplay between protease and Gag proteins, with Gag showing wide variation across HIV-1 subtypes. We explored the impact of pre-treatment susceptibility on the outcome of lopinavir/ritonavir monotherapy. METHODS Treatment-naive individuals who experienced lopinavir/ritonavir monotherapy failure from the MONARK study were matched (by subtype, viral load and baseline CD4 count) with those who achieved virological response ('successes'). Successes were defined by viral load <400 copies/mL after week 24 and <50 copies/mL from week 48 to week 96. Full-length Gag-protease was amplified from patient samples for in vitro phenotypic susceptibility testing, with susceptibility expressed as fold change (FC) relative to a subtype B reference strain. RESULTS Baseline lopinavir susceptibility was lower in viral failures compared with viral successes, but the differences were not statistically significant (median lopinavir susceptibility: 4.4 versus 8.5, respectively, P = 0.17). Among CRF02_AG/G patients, there was a significant difference in lopinavir susceptibility between the two groups (7.1 versus 10.4, P = 0.047), while in subtype B the difference was not significant (2.7 versus 3.4, P = 0.13). Subtype CRF02_AG/G viruses had a median lopinavir FC of 8.7 compared with 3.1 for subtype B (P = 0.001). CONCLUSIONS We report an association between reduced PI susceptibility (using full-length Gag-protease sequences) at baseline and subsequent virological failure on lopinavir/ritonavir monotherapy in antiretroviral-naive patients harbouring subtype CRF02_AG/G viruses. We speculate that this may be important in the context of suboptimal adherence in determining viral failure.
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Affiliation(s)
- K A Sutherland
- Virus Reference Department, Public Health England, London, UK Department of Infection, University College London, London, UK
| | - J Ghosn
- Université Paris Descartes, EA 7327, Faculté de Médecine site Necker, Paris, France APHP, UF de thérapeutique en Immuno Infectiologie, CHU Hotel Dieu, Paris, France
| | - J Gregson
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, UK
| | - J L Mbisa
- Virus Reference Department, Public Health England, London, UK
| | - M L Chaix
- Université Paris Descartes, EA 7327, Faculté de Médecine site Necker, Paris, France
| | | | - J F Delfraissy
- AP-HP, Department of Internal Medicine, Bicetre University Hospital, Le Kremlin-Bicetre, France
| | - C Delaugerre
- Virology, U941 INSERM Paris Diderot University, St Louis Hospital-APHP, Paris, France
| | - R K Gupta
- Department of Infection, University College London, London, UK
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