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Burdorf RM, Zhou S, Amon C, Long N, Hill CS, Adams L, Tegha G, Chagomerana MB, Jumbe A, Maliwichi M, Wallie S, Li Y, Swanstrom R, Hosseinipour MC. Impact of Low-Frequency Human Immunodeficiency Virus Type 1 Drug Resistance Mutations on Antiretroviral Therapy Outcomes. J Infect Dis 2024; 230:86-94. [PMID: 39052733 PMCID: PMC11272071 DOI: 10.1093/infdis/jiae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND The association between low-frequency human immunodeficiency virus type 1 (HIV-1) drug resistance mutations (DRMs) and treatment failure (TF) is controversial. We explore this association using next-generation sequencing (NGS) methods that accurately sample low-frequency DRMs. METHODS We enrolled women with HIV-1 in Malawi who were either antiretroviral therapy (ART) naive (cohort A), had ART failure (cohort B), or had discontinued ART (cohort C). At entry, cohorts A and C began a nonnucleoside reverse transcriptase inhibitor-based regimen and cohort B started a protease inhibitor-based regimen. We used Primer ID MiSeq to identify regimen-relevant DRMs in entry and TF plasma samples, and a Cox proportional hazards model to calculate hazard ratios (HRs) for entry DRMs. Low-frequency DRMs were defined as ≤20%. RESULTS We sequenced 360 participants. Cohort B and C participants were more likely to have TF than cohort A participants. The presence of K103N at entry significantly increased TF risk among A and C participants at both high and low frequency, with HRs of 3.12 (95% confidence interval [CI], 1.58-6.18) and 2.38 (95% CI, 1.00-5.67), respectively. At TF, 45% of participants showed selection of DRMs while in the remaining participants there was an apparent lack of selective pressure from ART. CONCLUSIONS Using accurate NGS for DRM detection may benefit an additional 10% of patients by identifying low-frequency K103N mutations.
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Affiliation(s)
- Rachel M Burdorf
- Lineberger Comprehensive Cancer Center
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | | | - Nathan Long
- Lineberger Comprehensive Cancer Center
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | | | - Lily Adams
- Lineberger Comprehensive Cancer Center
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | | | - Maganizo B Chagomerana
- UNC Project–Malawi, Lilongwe
- Department of Medicine, University of North Carolina at Chapel Hill
| | | | | | | | - Yijia Li
- Department of Medicine, University of Pittsburgh Medical Center, Pennsylvania
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill
| | - Mina C Hosseinipour
- UNC Project–Malawi, Lilongwe
- Department of Medicine, University of North Carolina at Chapel Hill
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2
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Hake A, Germann A, de Beer C, Thielen A, Däumer M, Preiser W, von Briesen H, Pfeifer N. Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models. PLoS Comput Biol 2023; 19:e1010355. [PMID: 38127856 PMCID: PMC10769057 DOI: 10.1371/journal.pcbi.1010355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/05/2024] [Accepted: 11/06/2023] [Indexed: 12/23/2023] Open
Abstract
The mechanisms triggering the human immunodeficiency virus type I (HIV-1) to switch the coreceptor usage from CCR5 to CXCR4 during the course of infection are not entirely understood. While low CD4+ T cell counts are associated with CXCR4 usage, a predominance of CXCR4 usage with still high CD4+ T cell counts remains puzzling. Here, we explore the hypothesis that viral adaptation to the human leukocyte antigen (HLA) complex, especially to the HLA class II alleles, contributes to the coreceptor switch. To this end, we sequence the viral gag and env protein with corresponding HLA class I and II alleles of a new cohort of 312 treatment-naive, subtype C, chronically-infected HIV-1 patients from South Africa. To estimate HLA adaptation, we develop a novel computational approach using Bayesian generalized linear mixed models (GLMMs). Our model allows to consider the entire HLA repertoire without restricting the model to pre-learned HLA-polymorphisms. In addition, we correct for phylogenetic relatedness of the viruses within the model itself to account for founder effects. Using our model, we observe that CXCR4-using variants are more adapted than CCR5-using variants (p-value = 1.34e-2). Additionally, adapted CCR5-using variants have a significantly lower predicted false positive rate (FPR) by the geno2pheno[coreceptor] tool compared to the non-adapted CCR5-using variants (p-value = 2.21e-2), where a low FPR is associated with CXCR4 usage. Consequently, estimating HLA adaptation can be an asset in predicting not only coreceptor usage, but also an approaching coreceptor switch in CCR5-using variants. We propose the usage of Bayesian GLMMs for modeling virus-host adaptation in general.
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Affiliation(s)
- Anna Hake
- Research Group Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Anja Germann
- Main Department Medical Biotechnology, Fraunhofer Institute for Biomedical Engineering, Sulzbach, Germany
| | - Corena de Beer
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | | | - Martin Däumer
- Institute of Immunology and Genetics, Kaiserslautern, Germany
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Hagen von Briesen
- Main Department Medical Biotechnology, Fraunhofer Institute for Biomedical Engineering, Sulzbach, Germany
| | - Nico Pfeifer
- Research Group Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
- German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
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3
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Gaitan NC, D’Antoni ML, Acosta RK, Gianella S, Little SJ, Chaillon A. Brief Report: Comparative Analysis of Pre-existing HIV Drug Resistance Mutations in Proviral DNA Using Next-Generation Sequencing and Routine HIV RNA Genotyping. J Acquir Immune Defic Syndr 2023; 93:213-218. [PMID: 36961945 PMCID: PMC10272101 DOI: 10.1097/qai.0000000000003195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/06/2023] [Indexed: 03/26/2023]
Abstract
BACKGROUND We investigated whether deep sequencing of archived HIV DNA of antiretroviral-naive persons with acute/early HIV infection could identify transmitted drug resistance mutations (DRM), per the IAS drug resistance algorithm, which are not detected by routine bulk (consensus) sequencing. METHODS Deep sequencing of HIV DNA from peripheral blood mononuclear cells and consensus sequencing from concurrent blood plasma (BP) was performed from antiretroviral (ART)-naive adults with recent infection. We compared the prevalence of low-frequency (2%-20%) and high-frequency (>20%) nonnucleoside reverse transcriptase inhibitor (NNRTI), nucleoside reverse transcriptase inhibitor (NRTI), and protease inhibitor (PI) DRM. RESULTS Overall, 190 individuals were included, 72 (37.9%) with acute, 20 (10.5%) with very early, and 98 (51.6%) with recent HIV infection. Although all DRM detected in plasma appeared in archived proviral DNA, 9 high-frequency mutations were only detected in HIV DNA. These included 3 NRTI mutations, 4 NNRTI mutations, 1 PI mutation, and 1 H221Y (associated rilpivirine resistance) mutation. When considering DRM <20%, 11 NNRTI, 7 NRTI, 6 PI, and 3 F227L (associated doravirine resistance) mutations were found exclusively in HIV DNA. Interestingly, although 2 high-frequency M184V appeared in both DNA and RNA, low-frequency M184I were exclusive to HIV DNA (n = 6). No participants experienced virologic failure after initiating ART during the median 25.39 ± 3.13 months of follow-up on treatment. CONCLUSION Although most high-frequency DRMs were consistently detected in HIV RNA and HIV DNA, the presence of low-frequency DRM in proviral DNA may be relevant for clinicians because these mutations could become dominant under drug selection pressure.
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Affiliation(s)
- Noah C Gaitan
- Division of Infectious Diseases & Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | | | | | - Sara Gianella
- Division of Infectious Diseases & Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Susan J Little
- Division of Infectious Diseases & Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Antoine Chaillon
- Division of Infectious Diseases & Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA, USA
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4
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Jensen BEO, Knops E, Cords L, Lübke N, Salgado M, Busman-Sahay K, Estes JD, Huyveneers LEP, Perdomo-Celis F, Wittner M, Gálvez C, Mummert C, Passaes C, Eberhard JM, Münk C, Hauber I, Hauber J, Heger E, De Clercq J, Vandekerckhove L, Bergmann S, Dunay GA, Klein F, Häussinger D, Fischer JC, Nachtkamp K, Timm J, Kaiser R, Harrer T, Luedde T, Nijhuis M, Sáez-Cirión A, Schulze Zur Wiesch J, Wensing AMJ, Martinez-Picado J, Kobbe G. In-depth virological and immunological characterization of HIV-1 cure after CCR5Δ32/Δ32 allogeneic hematopoietic stem cell transplantation. Nat Med 2023; 29:583-587. [PMID: 36807684 PMCID: PMC10033413 DOI: 10.1038/s41591-023-02213-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/09/2023] [Indexed: 02/22/2023]
Abstract
Despite scientific evidence originating from two patients published to date that CCR5Δ32/Δ32 hematopoietic stem cell transplantation (HSCT) can cure human immunodeficiency virus type 1 (HIV-1), the knowledge of immunological and virological correlates of cure is limited. Here we characterize a case of long-term HIV-1 remission of a 53-year-old male who was carefully monitored for more than 9 years after allogeneic CCR5Δ32/Δ32 HSCT performed for acute myeloid leukemia. Despite sporadic traces of HIV-1 DNA detected by droplet digital PCR and in situ hybridization assays in peripheral T cell subsets and tissue-derived samples, repeated ex vivo quantitative and in vivo outgrowth assays in humanized mice did not reveal replication-competent virus. Low levels of immune activation and waning HIV-1-specific humoral and cellular immune responses indicated a lack of ongoing antigen production. Four years after analytical treatment interruption, the absence of a viral rebound and the lack of immunological correlates of HIV-1 antigen persistence are strong evidence for HIV-1 cure after CCR5Δ32/Δ32 HSCT.
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Affiliation(s)
- Björn-Erik Ole Jensen
- Department of Gastroenterology, Hepatology and Infectious Diseases, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
| | - Elena Knops
- Institute of Virology, University and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Leon Cords
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nadine Lübke
- Institute of Virology, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Maria Salgado
- IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Center for Biomedical Research in Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
- Germans Trias i Pujol Research Institute, Barcelona, Spain
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Laura E P Huyveneers
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Federico Perdomo-Celis
- Institut Pasteur, Paris Cité University, HIV Inflammation and Persistence, Paris, France
| | - Melanie Wittner
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | | | - Christiane Mummert
- Infectious Diseases and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Bavarian Nordic, Martinsried, Germany
| | - Caroline Passaes
- Institut Pasteur, Paris Cité University, HIV Inflammation and Persistence, Paris, France
| | - Johanna M Eberhard
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Helmholtz Center for Infection Research, Helmholtz Institute for One Health, Greifswald, Germany
| | - Carsten Münk
- Department of Gastroenterology, Hepatology and Infectious Diseases, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | | | - Joachim Hauber
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Eva Heger
- Institute of Virology, University and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Jozefien De Clercq
- HIV Cure Research Center and Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center and Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Silke Bergmann
- Infectious Diseases and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gábor A Dunay
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- University Children's Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Klein
- Institute of Virology, University and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Dieter Häussinger
- Department of Gastroenterology, Hepatology and Infectious Diseases, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Johannes C Fischer
- Institute for Transplant Diagnostics and Cell Therapeutics, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Kathrin Nachtkamp
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Düsseldorf University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Joerg Timm
- Institute of Virology, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Rolf Kaiser
- Institute of Virology, University and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Thomas Harrer
- Infectious Diseases and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Monique Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Asier Sáez-Cirión
- Institut Pasteur, Paris Cité University, HIV Inflammation and Persistence, Paris, France
| | - Julian Schulze Zur Wiesch
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
| | - Annemarie M J Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
- Ezintsha, University of the Witwatersrand, Johannesburg, South Africa
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Center for Biomedical Research in Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
- University of Vic-Central University of Catalonia, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Guido Kobbe
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Düsseldorf University Hospital, Heinrich Heine University, Düsseldorf, Germany
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5
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Cozzi-Lepri A, Peters L, Pelchen-Matthews A, Neesgaard B, De Wit S, Johansen IS, Edwards S, Stephan C, Adamis G, Staub T, Zagalo A, Domingo P, Elbirt D, Kusejko K, Brännström J, Paduta D, Trofimova T, Szlavik J, Zilmer K, Losso M, Van Eygen V, Pai H, Lundgren J, Mocroft A. Observational cohort study of rilpivirine (RPV) utilization in Europe. AIDS Res Ther 2022; 19:38. [PMID: 35933352 PMCID: PMC9357334 DOI: 10.1186/s12981-022-00457-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Data on safety and effectiveness of RPV from the real-world setting as well as comparisons with other NNRTIs such as efavirenz (EFV) remain scarce. METHODS Participants of EuroSIDA were included if they had started a RPV- or an EFV-containing regimen over November 2011-December 2017. Statistical testing was conducted using non-parametric Mann-Whitney U test and Chi-square test. A logistic regression model was used to compare participants' characteristics by treatment group. Kaplan-Meier analysis was used to estimate the cumulative risk of virological failure (VF, two consecutive values > 50 copies/mL). RESULTS 1,355 PLWH who started a RPV-based regimen (11% ART-naïve), as well as 333 initiating an EFV-containing regimen were included. Participants who started RPV differed from those starting EFV for demographics (age, geographical region) and immune-virological profiles (CD4 count, HIV RNA). The cumulative risk of VF for the RPV-based group was 4.5% (95% CI 3.3-5.7%) by 2 years from starting treatment (71 total VF events). Five out of 15 (33%) with resistance data available in the RPV group showed resistance-associated mutations vs. 3/13 (23%) among those in the EFV group. Discontinuations due to intolerance/toxicity were reported for 73 (15%) of RPV- vs. 45 (30%) of EFV-treated participants (p = 0.0001). The main difference was for toxicity of central nervous system (CNS, 3% vs. 22%, p < 0.001). CONCLUSION Our estimates of VF > 50 copies/mL and resistance in participants treated with RPV were similar to those reported by other studies. RPV safety profile was favourable with less frequent discontinuation due to toxicity than EFV (especially for CNS).
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Affiliation(s)
- Alessandro Cozzi-Lepri
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME), Institute for Global Health, University College London, Rowland Hill St, London, NW3 2PF, UK.
| | - Lars Peters
- CHIP, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Annegret Pelchen-Matthews
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME), Institute for Global Health, University College London, Rowland Hill St, London, NW3 2PF, UK
| | | | - Stephane De Wit
- Department of Infectious Diseases, CHU Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Simon Edwards
- Mortimer Market Centre, Department of HIV, London, UK
| | - Christoph Stephan
- Infectious Diseases Unit, Goethe-University Hospital, Frankfurt, Germany
| | - Georgios Adamis
- 1St Department of Internal Medicine and Infectious Diseases Unit, General Hospital of Athens G. Gennimatas, Athens, Greece
| | - Therese Staub
- Centre Hospitalier de Luxembourg, Service des Maladies Infectieuses, Luxembourg City, Luxembourg
| | - Alexandra Zagalo
- Department of Infectious Diseases, Santa Maria University Hospital, Lisbon, Portugal
| | - Pere Domingo
- Hospital de La Santa Creu I Sant Pau, Barcelona, Spain
| | - Daniel Elbirt
- Allergy, Immunology and HIV Unit
- Kaplan, Medical Center, Rehovot, Israel
| | - Katharina Kusejko
- Division of Infectious Diseases, University Hospital Zürich, Zurich, Switzerland
| | - Johanna Brännström
- Department of Infectious Diseases, Venhälsan Södersjukhuset, Stockholm, Sweden
| | | | - Tatyana Trofimova
- Novgorod Centre for AIDS Prevention and Control, Novgorod the Great, Russia
| | - Janos Szlavik
- South-Pest Hospital Centre-National Institute for Infectiology and Haematology, Budapest, Hungary
| | - Kai Zilmer
- West-Tallinn Central Hospital, Infectious Diseases Clinic, Talinn, Estonia
| | | | | | - Helen Pai
- Janssen Research & Development, Raritan, NJ, USA
| | - Jens Lundgren
- CHIP, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Amanda Mocroft
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME), Institute for Global Health, University College London, Rowland Hill St, London, NW3 2PF, UK.,CHIP, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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6
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Beckwith CG, Min S, Manne A, Novitsky V, Howison M, Liu T, Kuo I, Kurth A, Bazerman L, Agopian A, Kantor R. HIV Drug Resistance and Transmission Networks Among a Justice-Involved Population at the Time of Community Reentry in Washington, D.C. AIDS Res Hum Retroviruses 2021; 37:903-912. [PMID: 33896212 PMCID: PMC8716515 DOI: 10.1089/aid.2020.0267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Justice-involved (JI) populations bear a disproportionate burden of HIV infection and are at risk of poor treatment outcomes. Drug resistance prevalence and emergence, and phylogenetic inference of transmission networks, understudied in vulnerable JI populations, can inform care and prevention interventions, particularly around the critical community reentry period. We analyzed banked blood specimens from CARE+ Corrections study participants in Washington, D.C. (DC) across three time points and conducted HIV drug resistance testing using next-generation sequencing (NGS) at 20% and 5% thresholds to identify prevalent and evolving resistance during community reentry. Phylogenetic analysis was used to identify molecular clusters within participants, and in an extended analysis between participants and publicly available DC sequences. HIV sequence data from 54 participants (99 specimens) were analyzed. The prevalence of transmitted drug resistance was 14% at both thresholds, and acquired drug resistance was 47% at 20%, and 57% at 5% NGS thresholds, respectively. The overall prevalence of drug resistance was 43% at 20%, and 52% at 5% NGS thresholds, respectively. Among 34 participants sampled longitudinally, 21%–35% accumulated 10–17 new resistance mutations during a mean 4.3 months. In phylogenetic analysis within the JI population, 11% were found in three molecular clusters. The extended phylogenetic analysis identified 46% of participants in 22 clusters, of which 21 also included publicly-available DC sequences, and one JI-only unique dyad. This is the first study to identify a high prevalence of HIV drug resistance and its accumulation in a JI population during community reentry and suggests phylogenetic integration of this population into the non-JI DC HIV community. These data support the need for new, effective, and timely interventions to improve HIV treatment during this vulnerable period, and for JI populations to be included in broader surveillance and prevention efforts.
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Affiliation(s)
- Curt G. Beckwith
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island, USA
- The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Sugi Min
- The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Akarsh Manne
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island, USA
- The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Vladimir Novitsky
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island, USA
- The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Mark Howison
- Research Improving People's Lives, Providence, Rhode Island, USA
| | - Tao Liu
- Department of Biostatistics, Brown University School of Public Health, Providence, Rhode Island, USA
| | - Irene Kuo
- George Washington University Milken Institute School of Public Health, Washington, District of Columbia, USA
| | - Ann Kurth
- Yale University School of Nursing, Orange, Connecticut, USA
| | - Lauri Bazerman
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island, USA
| | - Anya Agopian
- George Washington University Milken Institute School of Public Health, Washington, District of Columbia, USA
| | - Rami Kantor
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island, USA
- The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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7
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Mbunkah HA, Bertagnolio S, Hamers RL, Hunt G, Inzaule S, Rinke De Wit TF, Paredes R, Parkin NT, Jordan MR, Metzner KJ. Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact. J Infect Dis 2021; 221:1584-1597. [PMID: 31809534 DOI: 10.1093/infdis/jiz650] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/04/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The presence of high-abundance drug-resistant HIV-1 jeopardizes success of antiretroviral therapy (ART). Despite numerous investigations, the clinical impact of low-abundance drug-resistant HIV-1 variants (LA-DRVs) at levels <15%-25% of the virus population in antiretroviral (ARV) drug-naive individuals remains controversial. METHODS We systematically reviewed 103 studies assessing prevalence, detection methods, technical and clinical detection cutoffs, and clinical significance of LA-DRVs in antiretroviral drug-naive adults. RESULTS In total, 14 919 ARV drug-naive individuals were included. Prevalence of LA-DRVs (ie, proportion of individuals harboring LA-DRVs) was 0%-100%. Technical detection cutoffs showed a 4 log range (0.001%-10%); 42/103 (40.8%) studies investigating the impact of LA-DRVs on ART; 25 studies included only individuals on first-line nonnucleoside reverse transcriptase inhibitor-based ART regimens. Eleven of those 25 studies (44.0%) reported a significantly association between preexisting LA-DRVs and risk of virological failure whereas 14/25 (56.0%) did not. CONCLUSIONS Comparability of the 103 studies is hampered by high heterogeneity of the studies' designs and use of different methods to detect LA-DRVs. Thus, evaluating clinical impact of LA-DRVs on first-line ART remains challenging. We, the WHO HIVResNet working group, defined central areas of future investigations to guide further efforts to implement ultrasensitive resistance testing in routine settings.
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Affiliation(s)
- Herbert A Mbunkah
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland.,Paul-Ehrlich-Institut, Langen, Germany
| | | | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Eijkman-Oxford Clinical Research Unit, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gillian Hunt
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Seth Inzaule
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tobias F Rinke De Wit
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute for AIDS Research, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | | | - Michael R Jordan
- Division of Geographic Medicine and Infectious Disease, Tufts University School of Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland
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8
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Kroidl A, Burger T, Urio A, Mugeniwalwo R, Mgaya J, Mlagalila F, Hoelscher M, Däumer M, Salehe O, Sangare A, Lennemann T, Maganga L. High turnaround times and low viral resuppression rates after reinforced adherence counselling following a confirmed virological failure diagnostic algorithm in HIV-infected patients on first-line antiretroviral therapy from Tanzania. Trop Med Int Health 2020; 25:579-589. [PMID: 31984634 DOI: 10.1111/tmi.13373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Early identification of confirmed virological failure is paramount to avoid accumulation of drug resistance in patients on antiretroviral therapy (ART). Scale-up of HIV-RNA monitoring in Africa and timely switch to second-line regimens are challenged. METHODS A WHO adapted confirmed virological treatment screening algorithm (HIV-RNA screening, enhanced adherence counselling, confirmatory HIV-RNA testing) was evaluated in HIV-infected patients on first-line ART from Tanzania. The main endpoints included viral resuppression and virological failure rates, retention and turnaround time of the screening algorithm until second-line ART initiation. Secondary endpoints included risk factors for virological treatment failure and patterns of genotypic drug resistance. RESULTS HIV-RNA >1000 copies/ml at first screening was detected in 58/356 (16.3%) patients (median time-on-treatment 6.3 years, 25% immunological treatment failure). Adjusted risk factors for virological failure were age <30 years (RR 5.2 [95% CI: 2.5-10.8]), years on ART ≥3 years (RR 3.0 [1.0-8.9]), CD4-counts <200 cells/µl (RR 9.3 [4.0-21.8]) and poor self-reported treatment adherence (RR 2.0 [1.2-3.4]). Resuppression of HIV-RNA <1000 copies/ml was observed in 5/50 (10%) cases after enhanced adherence counselling. Confirmatory testing within 3 months was performed in only 46.6% and switch to second-line ART within 6 months in 60.4% of patients. Major NNRTI-mutation were detected in all of 30 patients, NRTI mutations in 96.7% and ≥3 thymidine-analogue mutations in 40%. No remaining NRTI options were predicted in 57% and limited susceptibility in 23% of patients. CONCLUSION We observed low levels of viral resuppression following adherence counselling, associated with high levels of accumulated drug resistance. High visit burden and turnaround times for confirmed virological failure diagnosis further delayed switching to second-line treatment which could be improved using novel point-of-care viral load monitoring systems.
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Affiliation(s)
- Arne Kroidl
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany.,German Center for Infection Research, Partner site Munich, Munich, Germany
| | - Tassilo Burger
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany
| | - Agatha Urio
- NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | | | - Jimson Mgaya
- NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | | | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany.,German Center for Infection Research, Partner site Munich, Munich, Germany
| | - Martin Däumer
- Institute of Immunology and Genetics, Kaiserslautern, Germany
| | - Omar Salehe
- Mbeya Zonal Referral Hospital, Mbeya, Tanzania
| | | | - Tessa Lennemann
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany.,NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
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9
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Boltz VF, Shao W, Bale MJ, Halvas EK, Luke B, McIntyre JA, Schooley RT, Lockman S, Currier JS, Sawe F, Hogg E, Hughes MD, Kearney MF, Coffin JM, Mellors JW. Linked dual-class HIV resistance mutations are associated with treatment failure. JCI Insight 2019; 4:130118. [PMID: 31487271 DOI: 10.1172/jci.insight.130118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/27/2019] [Indexed: 01/23/2023] Open
Abstract
We hypothesized that HIV-1 with dual-class but not single-class drug resistance mutations linked on the same viral genome, present in the virus population before initiation of antiretroviral therapy (ART), would be associated with failure of ART to suppress viremia. To test this hypothesis, we utilized an ultrasensitive single-genome sequencing assay that detects rare HIV-1 variants with linked drug resistance mutations (DRMs). A case (ART failure) control (nonfailure) study was designed to assess whether linkage of DRMs in pre-ART plasma samples was associated with treatment outcome in the nevirapine/tenofovir/emtricitabine arm of the AIDS Clinical Trials Group A5208/Optimal Combined Therapy After Nevirapine Exposure (OCTANE) Trial 1 among women who had received prior single-dose nevirapine. Ultrasensitive single-genome sequencing revealed a significant association between pre-ART HIV variants with DRMs to 2 drug classes linked on the same genome (dual class) and failure of combination ART with 3 drugs to suppress viremia. In contrast, linked, single-class DRMs were not associated with ART failure. We conclude that linked dual-class DRMs present before the initiation of ART are associated with ART failure, whereas linked single-class DRMs are not.
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Affiliation(s)
- Valerie F Boltz
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | | | - Brian Luke
- Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | | | | | - Shahin Lockman
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Fred Sawe
- Kenya Medical Research Institute, Kericho, Kenya
| | - Evelyn Hogg
- Social & Scientific Systems, Silver Spring, Maryland, USA
| | - Michael D Hughes
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
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10
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A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance. Sci Rep 2019; 9:8970. [PMID: 31222149 PMCID: PMC6586679 DOI: 10.1038/s41598-019-45328-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/31/2019] [Indexed: 12/02/2022] Open
Abstract
Conventional HIV drug resistance (HIVDR) genotyping utilizes Sanger sequencing (SS) methods, which are limited by low data throughput and the inability of detecting low abundant drug resistant variants (LADRVs). Here we present a next generation sequencing (NGS)-based HIVDR typing platform that leverages the advantages of Illumina MiSeq and HyDRA Web. The platform consists of a fully validated sample processing protocol and HyDRA web, an open web portal that allows automated customizable NGS-based HIVDR data processing. This platform was characterized and validated using a panel of HIV-spiked plasma representing all major HIV-1 subtypes, pedigreed plasmids, HIVDR proficiency specimens and clinical specimens. All examined major HIV-1 subtypes were consistently amplified at viral loads of ≥1,000 copies/ml. The gross error rate of this platform was determined at 0.21%, and minor variations were reliably detected down to 0.50% in plasmid mixtures. All HIVDR mutations identifiable by SS were detected by the MiSeq-HyDRA protocol, while LADRVs at frequencies of 1~15% were detected by MiSeq-HyDRA only. As compared to SS approaches, the MiSeq-HyDRA platform has several notable advantages including reduced cost and labour, and increased sensitivity for LADRVs, making it suitable for routine HIVDR monitoring for both patient care and surveillance purposes.
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11
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Stecher M, Hoenigl M, Eis-Hübinger AM, Lehmann C, Fätkenheuer G, Wasmuth JC, Knops E, Vehreschild JJ, Mehta S, Chaillon A. Hotspots of Transmission Driving the Local Human Immunodeficiency Virus Epidemic in the Cologne-Bonn Region, Germany. Clin Infect Dis 2019; 68:1539-1546. [PMID: 30169606 PMCID: PMC6481988 DOI: 10.1093/cid/ciy744] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/24/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Geographical allocation of interventions focusing on hotspots of human immunodeficiency virus (HIV) transmission has the potential to improve efficiency. We used phylogeographic analyses to identify hotspots of the HIV transmission in Cologne-Bonn, Germany. METHODS We included 714 HIV-1 infected individuals, followed up at the University Hospitals Cologne and Bonn. Distance-based molecular network analyses were performed to infer putative relationships. Characteristics of genetically linked individuals and assortativity (shared characteristics) were analyzed. Geospatial diffusion (ie, viral gene flow) was evaluated using a Slatkin-Maddison approach. Geospatial dispersal was determined by calculating the average distance between the residences of linked individuals (centroids of 3-digit zip code). RESULTS In sum, 217/714 (30.4%) sequences had a putative genetic linkage, forming 77 clusters (size range: 2-8). Linked individuals were more likely to live in areas surrounding the city center (P = .043), <30 years of age (P = .009). and infected with HIV-1 subtype B (P = .002). Clustering individuals were nonassortative by area of residency (-.0026, P = .046). Geospatial analyses revealed a median distance between genetically linked individuals of 23.4 kilometers (km), lower than expected (P < .001). Slatkin-Maddison analyses revealed increased gene flow from central Cologne toward the surrounding areas (P < .001). CONCLUSION Phylogeographic analysis suggests that central Cologne may be a significant driver of the regional epidemic. Although clustering individuals lived closer than unlinked individuals, they were less likely to be linked to others from their same zip code. These results could help public health entities better understand transmission dynamics, facilitating allocation of resources to areas of greatest need.
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Affiliation(s)
- Melanie Stecher
- Department I of Internal Medicine, University Hospital of Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
| | - Martin Hoenigl
- Division of Infectious Diseases, University of California San Diego
- Division of Pulmonology and Section of Infectious Diseases, Medical University of Graz, Austria
| | - Anna Maria Eis-Hübinger
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
- Institute of Virology, University of Bonn Medical Center, Germany
| | - Clara Lehmann
- Department I of Internal Medicine, University Hospital of Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
| | - Gerd Fätkenheuer
- Department I of Internal Medicine, University Hospital of Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
| | - Jan-Christian Wasmuth
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
- Department for Internal Medicine I, University Hospital of Bonn, Germany
| | - Elena Knops
- Institute of Virology, University Hospital of Cologne, Germany
| | - Jörg Janne Vehreschild
- Department I of Internal Medicine, University Hospital of Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
| | - Sanjay Mehta
- Division of Infectious Diseases, University of California San Diego
- Department of Medicine, San Diego VA Medical Center, California
| | - Antoine Chaillon
- Division of Infectious Diseases, University of California San Diego
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12
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Gopalan BP, D'Souza RR, Rajnala N, Arumugam K, Dias M, Ranga U, Shet A. Viral evolution in the cell-associated HIV-1 DNA during early ART can lead to drug resistance and virological failure in children. J Med Virol 2019; 91:1036-1047. [PMID: 30695102 DOI: 10.1002/jmv.25413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/08/2019] [Accepted: 01/24/2019] [Indexed: 11/07/2022]
Abstract
Using cell-associated DNA and cell-free RNA of human immunodeficiency virus type-1 (HIV-1), we investigated the role of drug-resistant viral variants that emerged during early antiretroviral therapy (ART) in determining virological outcome. This case-control study compared virologic nonresponder children (two viral loads [VLs] ≥ 200 copies/mL within 2 years of ART) and responder children (two VLs < 200 copies/mL after six months of ART) infected with HIV-1 initiated on nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based ART. The partial reverse-transcriptase gene of HIV-1 in cell-associated DNA was genotyped using next-generation sequencing (NGS; Illumina; threshold 0.5%; at baseline and month six of ART) and in cell-free RNA (concurrently and at virological failure; VL > 1000 copies/mL at ≥ 12 months of ART) using the Sanger method. Among 30 nonresponders and 37 responders, baseline differences were insignificant while adherence, VL, and drug resistance mutations (DRMs) observed at month six differed significantly ( P ≥ 0.05). At month six, NGS estimated a higher number of DRMs compared with Sanger (50% vs 33%; P = 0.001). Among the nonresponders carrying a resistant virus (86.6%) at virological failure, 26% harbored clinically relevant low-frequency DRMs in the cell-associated DNA at month six (0.5%-20%; K103N, G190A, Y181C, and M184I). Plasma VL of > 3 log 10 copies/mL (AOR, 30.4; 95% CI, 3.3-281; P = 0.003) and treatment-relevant DRMs detected in the cell-associated DNA at month six (AOR, 24.2; 95% CI, 2.6-221; P = 0.005) were independently associated with increased risk for early virological failure. Our findings suggest that treatment-relevant DRMs acquired in cell-associated DNA during the first six months of ART can predict virological failure in children initiated on NNRTI-based ART.
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Affiliation(s)
- Bindu Parachalil Gopalan
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,School of Integrative Health Sciences, University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Reena R D'Souza
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Niharika Rajnala
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Karthika Arumugam
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Udaykumar Ranga
- Molecular Biology and Genetics Unit, HIV/AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Anita Shet
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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13
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Silver N, Paynter M, McAllister G, Atchley M, Sayir C, Short J, Winner D, Alouani DJ, Sharkey FH, Bergefall K, Templeton K, Carrington D, Quiñones-Mateu ME. Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Res Ther 2018; 15:18. [PMID: 30409215 PMCID: PMC6223033 DOI: 10.1186/s12981-018-0206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals. METHODS We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals. RESULTS Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4+ T cell counts in the NHS Lothian patients. CONCLUSIONS This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
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14
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HIV-1 Proviral Sequence and Treatment Outcome of Virologically Suppressed Patients Switching to Coformulated Elvitegravir/Cobicistat/Emtricitabine/Tenofovir Disoproxil Fumarate. J Acquir Immune Defic Syndr 2018; 79:e45-e51. [DOI: 10.1097/qai.0000000000001757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Nicot F, Jeanne N, Raymond S, Delfour O, Carcenac R, Lefebvre C, Sauné K, Delobel P, Izopet J. Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene. J Med Virol 2018; 90:1486-1492. [PMID: 29750364 DOI: 10.1002/jmv.25224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/01/2018] [Indexed: 01/08/2023]
Abstract
The present study compares the performances of an in-house sequencing protocol developed on MiSeq, the Sanger method, and the 454 GS-FLX for detecting and quantifying drug-resistant mutations (DRMs) in the human immunodeficiency virus polymerase gene (reverse transcriptase [RT] and protease [PR]). MiSeq sequencing identified all the resistance mutations detected by bulk sequencing (n = 84). Both the MiSeq and 454 GS-FLX platforms identified 67 DRMs in the RT and PR regions, but a further 25 DRMs were identified by only one or other of them. Pearson's analysis showed good concordance between the percentage of drug-resistant variants determined by MiSeq and 454 GS-FLX sequencing (ρ = .77, P < .0001). The MiSeq platform is as accurate as the 454 GS-FLX Roche system for determining RT and PR DRMs and could be used for monitoring human immunodeficiency virus type 1 drug resistance.
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Affiliation(s)
- Florence Nicot
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Nicolas Jeanne
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Stéphanie Raymond
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Olivier Delfour
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Romain Carcenac
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Caroline Lefebvre
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Karine Sauné
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Pierre Delobel
- INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Jacques Izopet
- Laboratoire de Virologie, CHU de Toulouse, Hôpital Purpan, Toulouse, France.,INSERM, U1043, Toulouse, France.,Faculté de Médecine Toulouse-Purpan, Université Toulouse III Paul-Sabatier, Toulouse, France
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16
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Kulkarni R, Hodder SL, Cao H, Chang S, Miller MD, White KL. Week 48 resistance analysis of Elvitegravir/Cobicistat/Emtricitabine/Tenofovir DF versus Atazanavir + Ritonavir + Emtricitabine/Tenofovir DF in HIV-1 infected women (WAVES study GS-US-236-0128). HIV CLINICAL TRIALS 2017; 18:164-173. [PMID: 28891788 PMCID: PMC5942200 DOI: 10.1080/15284336.2017.1370059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Background Women and those with non-B subtype HIV-1 are typically underrepresented in clinical trials. WAVES (GS-US-236-0128) was a double-blind phase 3b study among treatment-naïve HIV-1-infected women that demonstrated that elvitegravir/cobicistat/emtricitabine/tenofovir DF (EVG/COBI/FTC/TDF; N = 289) was superior to atazanavir + ritonavir + FTC/TDF (ATV + RTV + FTC/TDF; N = 286) for HIV-1 RNA < 50 copies/mL by FDA snapshot analysis at week 48. Here, we describe resistance development through week 48 in women with virologic failure and determine the impact of pre-existing mutations and HIV-1 subtype on viral suppression. Methods Genotypic analyses (population and deep sequencing) and phenotypic analyses of HIV-1 protease, reverse transcriptase (RT), and integrase (IN) were performed. The resistance analysis population (participants with HIV-1 RNA ≥ 400 copies/mL at confirmed virologic failure, at discontinuation ≥ week 8, or at week 48) had genotypic and phenotypic analyses at failure and baseline. Results The proportion of women qualifying for resistance analyses was similar between treatment groups (6.2% EVG/COBI/FTC/TDF; 7.3% ATV + RTV + FTC/TDF). Emergent resistance was rare (0% EVG/COBI/FTC/TDF; 1% ATV + RTV + FTC/TDF - 3 with M184V/I in RT). Deep sequencing of HIV-1 did not detect additional resistance development. Pre-existing mutations did not lead to virologic failure; most with the polymorphic primary IN substitution T97A (92%), or with substitutions in RT (i.e. A62V, V90I, K103N, or E138A/G/K/Q; 68-82%) demonstrated virologic suppression at week 48, with no resistance development except for one patient with M184V and pre-existing K103N in the ATV + RTV + FTC/TDF group. Most participants (74%) had non-B HIV-1, and subtype did not affect outcome. Conclusions Emergent resistance to study drugs was rare in this study of women, with no resistance observed among EVG/COBI/FTC/TDF-treated participants, despite a high proportion of participants with natural or transmitted viral mutations and non-B HIV-1 subtypes.
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Affiliation(s)
- Rima Kulkarni
- Clinical Virology, Gilead Sciences, Inc., Foster City, CA, USA
| | - Sally L. Hodder
- Health Sciences Center, West Virginia Clinical and Translational Science Institute, Morgantown, WV, USA
| | - Huyen Cao
- Clinical Research, Gilead Sciences, Inc., Foster City, CA, USA
| | - Silvia Chang
- Clinical Virology, Gilead Sciences, Inc., Foster City, CA, USA
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17
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Leung P, Eltahla AA, Lloyd AR, Bull RA, Luciani F. Understanding the complex evolution of rapidly mutating viruses with deep sequencing: Beyond the analysis of viral diversity. Virus Res 2016; 239:43-54. [PMID: 27888126 DOI: 10.1016/j.virusres.2016.10.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 12/24/2022]
Abstract
With the advent of affordable deep sequencing technologies, detection of low frequency variants within genetically diverse viral populations can now be achieved with unprecedented depth and efficiency. The high-resolution data provided by next generation sequencing technologies is currently recognised as the gold standard in estimation of viral diversity. In the analysis of rapidly mutating viruses, longitudinal deep sequencing datasets from viral genomes during individual infection episodes, as well as at the epidemiological level during outbreaks, now allow for more sophisticated analyses such as statistical estimates of the impact of complex mutation patterns on the evolution of the viral populations both within and between hosts. These analyses are revealing more accurate descriptions of the evolutionary dynamics that underpin the rapid adaptation of these viruses to the host response, and to drug therapies. This review assesses recent developments in methods and provide informative research examples using deep sequencing data generated from rapidly mutating viruses infecting humans, particularly hepatitis C virus (HCV), human immunodeficiency virus (HIV), Ebola virus and influenza virus, to understand the evolution of viral genomes and to explore the relationship between viral mutations and the host adaptive immune response. Finally, we discuss limitations in current technologies, and future directions that take advantage of publically available large deep sequencing datasets.
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Affiliation(s)
- Preston Leung
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Auda A Eltahla
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Andrew R Lloyd
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia.
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Ávila-Ríos S, García-Morales C, Matías-Florentino M, Romero-Mora KA, Tapia-Trejo D, Quiroz-Morales VS, Reyes-Gopar H, Ji H, Sandstrom P, Casillas-Rodríguez J, Sierra-Madero J, León-Juárez EA, Valenzuela-Lara M, Magis-Rodríguez C, Uribe-Zuñiga P, Reyes-Terán G. Pretreatment HIV-drug resistance in Mexico and its impact on the effectiveness of first-line antiretroviral therapy: a nationally representative 2015 WHO survey. Lancet HIV 2016; 3:e579-e591. [PMID: 27658867 DOI: 10.1016/s2352-3018(16)30119-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/10/2016] [Accepted: 08/04/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND WHO has developed a global HIV-drug resistance surveillance strategy, including assessment of pretreatment HIV-drug resistance. We aimed to do a nationally representative survey of pretreatment HIV-drug resistance in Mexico using WHO-recommended methods. METHODS Among 161 Ministry of Health antiretroviral therapy (ART) clinics in Mexico, the largest, including 90% of ART initiators within the Ministry of Health (66 in total), were eligible for the survey. We used a probability-proportional-to-size design method to sample 25 clinics throughout the country. Consecutive ART-naive patients with HIV about to initiate treatment were invited to participate in the survey; individuals with previous exposure to ART were excluded. We assessed pretreatment HIV-drug resistance by Sanger sequencing and next-generation sequencing of viruses from plasma specimens from eligible participants with Stanford University HIV Drug Resistance Database methods. We obtained follow-up data for a median of 9·4 months (range 6-12) after enrolment. We investigated possible relations between demographic variables and pretreatment drug resistance with univariate and multivariate logistic regression. FINDINGS Between Feb 3 and July 30, 2015, we screened 288 patients in 25 clinics, from whom 264 provided successfully sequenced viruses with no evidence of current exposure to antiretroviral drugs. With the Sanger method, of these 264 participants, 41 (15·5%, 95% CI 11·4-20·5) had pretreatment resistance to any antiretroviral drug and 28 (10·6%, 7·2-15·0) had pretreatment resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs). At least low-level pretreatment resistance (Stanford penalty score ≥15) was noted in 13 (4 · 9%) of participants to efavirenz and in 23 (8·7%) to the combination tenofovir plus emtricitabine plus efavirenz. With next-generation sequencing, of 264 participants, 38 (14·4%, 95% CI 10·4-19·2) had pretreatment resistance to any antiretroviral drug and 26 (9·8%, 6·5-14·1) had pretreatment resistance to NNRTIs. After median follow-up of 8 months (IQR 6·5-9·4, range 5-11) after ART initiation, 97 (72%) of 135 NNRTI initiators achieved viral suppression (<50 copies per mL) compared with ten (40%) of 25 individuals who started with protease inhibitor-based regimens (p=0·0045). After multivariate regression considering pretreatment resistance and initial ART regimen as composite variables, people starting NNRTIs with pretreatment drug resistance achieved significantly lower viral suppression (odds ratio 0·24, 95% CI 0·07-0·74; p=0·014) than patients without NNRTI resistance. INTERPRETATION High levels of pretreatment drug resistance were noted in Mexico, and NNRTI pretreatment drug resistance significantly reduced the effectiveness of first-line ART regimens based on these drugs. Baseline HIV-drug resistance testing for initial ART follow-up and decision making should be considered. FUNDING The Mexican Government and Consejo Nacional de Ciencia y Tecnología.
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Affiliation(s)
- Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Karla A Romero-Mora
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Verónica S Quiroz-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Helena Reyes-Gopar
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Juan Sierra-Madero
- National Institute of Medical Sciences and Nutrition Salvador Zubirán, Colonia Sección XVI, Mexico City, Mexico
| | - Eddie A León-Juárez
- National Centre for HIV/AIDS Prevention and Control, Colonia Anzures, Mexico City, Mexico
| | | | - Carlos Magis-Rodríguez
- National Centre for HIV/AIDS Prevention and Control, Colonia Anzures, Mexico City, Mexico
| | - Patricia Uribe-Zuñiga
- National Centre for HIV/AIDS Prevention and Control, Colonia Anzures, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico.
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