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Podzamczer D, Imaz A, Lopez-Lirola A, Knobel H, Masiá M, Fanciulli C, Hernández C, Lagarde M, Gutierrez A, Curran A, Morano L, Montero-Alonso M, Troya J, Rigo R, Casadellà M, Navarro-Alcaraz A, Ardila F, Parera M, Bernal E, Echeverria P, Estrada V, Hidalgo-Tenorio C, Macias J, Prieto P, Portilla J, Valencia E, Vivancos MJ, Rivero A. Switching to bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) plus darunavir/cobicistat in heavily antiretroviral-experienced, virologically suppressed HIV-infected adults receiving complex regimens. J Antimicrob Chemother 2023; 78:2696-2701. [PMID: 37725999 DOI: 10.1093/jac/dkad285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/25/2023] [Indexed: 09/21/2023] Open
Abstract
OBJECTIVES To evaluate the efficacy and safety of the two-pill regimen bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) plus darunavir/cobicistat as a switching strategy in heavily treatment-experienced people living with HIV (PLWH). METHODS Multicentre, prospective, single-arm pilot clinical trial. Participants were virologically suppressed adults receiving a stable antiretroviral regimen of at least three pills from at least three drug families due to previous virological failures and/or toxicities with no documented resistance to integrase strand transfer inhibitors or darunavir (≥15 points, Stanford). Clinical and laboratory assessments were performed at 0, 4, 12, 24, 36 and 48 weeks. HIV-1 proviral DNA was amplified and sequenced by Illumina at baseline. Plasma bictegravir concentrations were determined in 22 patients using UHPLC-MS/MS. The primary study endpoint was viral load (VL)< 50 copies/mL at Week 48 (ITT). RESULTS We enrolled 63 participants (92% men) with median baseline CD4 count of 515 cells/mm3 (IQR: 334.5-734.5), 24 years on ART (IQR: 15.9-27.8). The median number of pills was 4 (range: 3-10). At baseline, proviral DNA was amplified in 39 participants: 33/39 had resistance mutations. Three participants discontinued owing to toxicity. At 48 weeks, 95% had VL < 50 copies/mL by ITT and 100% by PP analysis. A modest increase was observed in the bictegravir plasma concentration, and a significant decrease in estimated glomerular filtration rate was observed only at Week 4, probably related to interaction with renal transporters. CONCLUSIONS Our data suggest that BIC/FTC/TAF + darunavir/cobicistat is an effective, well-tolerated regimen that may improve convenience and, potentially, long-term success in stable heavily pre-treated PLWH.
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Affiliation(s)
| | - Arkaitz Imaz
- Infectious Diseases Department, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Hospitalet del Llobregat, Hospital Universitario de Bellvitge, Spain
| | - Ana Lopez-Lirola
- Infectious Diseases Department, Hospital universitario de Canarias, San Cristóbal de la Laguna, Spain
| | - Hernando Knobel
- Infectious Diseases Department, Hospital del Mar, Barcelona, Spain
| | - Mar Masiá
- Infectious Diseases Department, Hospital Universitario general de Elche, Elche, Spain
| | - Chiara Fanciulli
- Infectious Diseases Department, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Cristina Hernández
- Infectious Diseases Department, Hospital Príncipe de Asturias, Alcalá de Henares, Spain
| | - María Lagarde
- Infectious Diseases Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Angela Gutierrez
- Infectious Diseases Department, Hospital Universitario de la Princesa, Madrid, Spain
| | - Adrià Curran
- Infectious Diseases Department, Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | - Luis Morano
- Infectious Diseases Department, Hospital Universitario Álvaro Cunqueiro, Vigo, Spain
| | - Marta Montero-Alonso
- Infectious Diseases Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Jesús Troya
- Infectious Diseases Department, Hospital Universitario Infanta Leonor, Madrid, Spain
| | - Raúl Rigo
- Infectious Diseases Department, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Hospitalet del Llobregat, Hospital Universitario de Bellvitge, Spain
| | - María Casadellà
- Microbial Genomics Group, IrsiCaixa-Institut de Recerca de la SIDA, Badalona, Spain
| | | | - Fernando Ardila
- Infectious Diseases Department, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Hospitalet del Llobregat, Hospital Universitario de Bellvitge, Spain
| | - Mariona Parera
- Microbial Genomics Group, IrsiCaixa-Institut de Recerca de la SIDA, Badalona, Spain
| | - Enrique Bernal
- Infectious Diseases Department, Hospital Universitario Reina Sofía, Murcia, Spain
| | - Patricia Echeverria
- Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Vicente Estrada
- Infectious Diseases Department, Hospital Clínico San Carlos, Madrid, Spain
| | - Carmen Hidalgo-Tenorio
- Infectious Diseases Department, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Juan Macias
- Instituto de Biomedicina de Sevilla, Departamento de Medicina, CIBERINFEC, Unidad de Enfermedades Infecciosas y Microbiología, IBiS/Hospital Universitario Virgen de Valme/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Paula Prieto
- Infectious Diseases Department, Hospital Universitari de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Joaquín Portilla
- Infectious Diseases Department, Hospital General Universitario de Alicante, Alicante, Spain
| | - Eulalia Valencia
- Infectious Diseases Department, Hospital Universitario La Paz, Madrid, Spain
| | - María Jesús Vivancos
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Antonio Rivero
- Department of Infectious Diseases, Hospital Universitario Reina Sofia, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Córdoba, Spain
- CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas Instituto de Salud Carlos III, Madrid, Spain
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Novitsky V, Nyandiko W, Vreeman R, DeLong AK, Manne A, Scanlon M, Ngeresa A, Aluoch J, Sang F, Ashimosi C, Jepkemboi E, Orido M, Hogan JW, Kantor R. Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance. Microbiol Spectr 2022; 10:e0345422. [PMID: 36445146 PMCID: PMC9769539 DOI: 10.1128/spectrum.03454-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
HIV-1 drug resistance testing in children and adolescents in low-resource settings is both important and challenging. New (more sensitive) drug resistance testing technologies may improve clinical care, but evaluation of their added value is limited. We assessed the potential added value of using next-generation sequencing (NGS) over Sanger sequencing for detecting nucleoside reverse transcriptase inhibitor (NRTI) and nonnucleoside reverse transcriptase inhibitor (NNRTI) drug resistance mutations (DRMs). Participants included 132 treatment-experienced Kenyan children and adolescents with diverse HIV-1 subtypes and with already high levels of drug resistance detected by Sanger sequencing. We examined overall and DRM-specific resistance and its predicted impact on antiretroviral therapy and evaluated the discrepancy between Sanger sequencing and six NGS thresholds (1%, 2%, 5%, 10%, 15%, and 20%). Depending on the NGS threshold, agreement between the two technologies was 62% to 88% for any DRM, 83% to 92% for NRTI DRMs, and 73% to 94% for NNRTI DRMs, with more DRMs detected at low NGS thresholds. NGS identified 96% to 100% of DRMs detected by Sanger sequencing, while Sanger identified 83% to 99% of DRMs detected by NGS. Higher discrepancy between technologies was associated with higher DRM prevalence. Even in this resistance-saturated cohort, 12% of participants had higher, potentially clinically relevant predicted resistance detected only by NGS. These findings, in a young, vulnerable Kenyan population with diverse HIV-1 subtypes and already high resistance levels, suggest potential benefits of more sensitive NGS over existing technology. Good agreement between technologies at high NGS thresholds supports their interchangeable use; however, the significance of DRMs identified at lower thresholds to patient care should be explored further. IMPORTANCE HIV-1 drug resistance in children and adolescents remains a significant problem in countries facing the highest burden of the HIV epidemic. Surveillance of HIV-1 drug resistance in children and adolescents is an important public health strategy, particularly in resource-limited settings, and yet, it is limited due mostly to cost and infrastructure constraints. Whether newer and more sensitive next-generation sequencing (NGS) adds substantial value beyond traditional Sanger sequencing in detecting HIV-1 drug resistance in real life settings remains an open and debatable question. In this paper, we attempt to address this issue by performing a comprehensive comparison of drug resistance identified by Sanger sequencing and six NGS thresholds. We conducted this study in a well-characterized, vulnerable cohort of children and adolescents living with diverse HIV-1 subtypes in Kenya and, importantly, failing antiretroviral therapy (ART) with already extensive drug resistance. Our findings suggest a potential added value of NGS over Sanger even in this unique cohort.
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Affiliation(s)
- V. Novitsky
- Brown University, Providence, Rhode Island, USA
| | - W. Nyandiko
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University, Eldoret, Kenya
| | - R. Vreeman
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| | | | - A. Manne
- Brown University, Providence, Rhode Island, USA
| | - M. Scanlon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| | - A. Ngeresa
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - J. Aluoch
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - F. Sang
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - C. Ashimosi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - E. Jepkemboi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - M. Orido
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - J. W. Hogan
- Brown University, Providence, Rhode Island, USA
| | - R. Kantor
- Brown University, Providence, Rhode Island, USA
| | - for the RESistance in a PEdiatric CohorT (RESPECT) Study
- Brown University, Providence, Rhode Island, USA
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University, Eldoret, Kenya
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
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Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW. Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clin Microbiol Rev 2022; 35:e0005222. [PMID: 36102816 PMCID: PMC9769561 DOI: 10.1128/cmr.00052-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
HIV-1 DNA exists in nonintegrated linear and circular episomal forms and as integrated proviruses. In patients with plasma viremia, most peripheral blood mononuclear cell (PBMC) HIV-1 DNA consists of recently produced nonintegrated virus DNA while in patients with prolonged virological suppression (VS) on antiretroviral therapy (ART), most PBMC HIV-1 DNA consists of proviral DNA produced months to years earlier. Drug-resistance mutations (DRMs) in PBMCs are more likely to coexist with ancestral wild-type virus populations than they are in plasma, explaining why next-generation sequencing is particularly useful for the detection of PBMC-associated DRMs. In patients with ongoing high levels of active virus replication, the DRMs detected in PBMCs and in plasma are usually highly concordant. However, in patients with lower levels of virus replication, it may take several months for plasma virus DRMs to reach detectable levels in PBMCs. This time lag explains why, in patients with VS, PBMC genotypic resistance testing (GRT) is less sensitive than historical plasma virus GRT, if previous episodes of virological failure and emergent DRMs were either not prolonged or not associated with high levels of plasma viremia. Despite the increasing use of PBMC GRT in patients with VS, few studies have examined the predictive value of DRMs on the response to a simplified ART regimen. In this review, we summarize what is known about PBMC HIV-1 DNA dynamics, particularly in patients with suppressed plasma viremia, the methods used for PBMC HIV-1 GRT, and the scenarios in which PBMC GRT has been used clinically.
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Affiliation(s)
- Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, California, USA
| | - Daniele Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Charles Walworth
- LabCorp-Monogram Biosciences, South San Francisco, California, USA
| | - Maria M. Santoro
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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Armenia D, Santoro MM, Bellocchi MC, Carioti L, Galli L, Galli A, Scutari R, Salsi E, Mussini C, Sterrantino G, Calza L, Rossetti B, Zazzi M, Castagna A. Viral resistance burden and APOBEC editing correlate with virological response in heavily treatment-experienced people living with multi-drug resistant HIV. Int J Antimicrob Agents 2021; 59:106492. [PMID: 34871747 DOI: 10.1016/j.ijantimicag.2021.106492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/15/2021] [Accepted: 11/24/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND The impact of drug resistance mutational load and APOBEC editing in heavily treatment-experienced (HTE) people living with multidrug-resistant HIV has not been investigated. MATERIAL AND METHODS This study explored the HIV-DNA and HIV-RNA mutational load of drug resistance and APOBEC-related mutations through next-generation sequencing (NGS, Illumina MiSeq) in 20 failing HTE participants enrolled in the PRESTIGIO registry. RESULTS The patients showed high levels of both HIV-DNA (4.5 [4.0-5.2] log10 copies/106 T-CD4+ cell) and HIV-RNA (4.5 [4.1-5.0] log10 copies/mL) with complex resistance patterns in both compartments. Among the 255 drug-resistant mutations found, 66.3% were concordantly detected in both HIV-DNA and HIV-RNA; 71.3% of mutations were already present in historical Sanger genotypes. At an intra-patient frequency > 5%, a considerable proportion of mutations detected through DNA-NGS were found in historical genotypes but not through RNA-NGS, and few patients had APOBEC-related mutations. Of 14 patients who switched therapy, the five who failed treatment had DNA resistance with higher intra-patient frequency and higher DNA/RNA mutational load in a context of tendentially less pronounced APOBEC editing compared with those who responded. CONCLUSIONS Using NGS in HIV-DNA and HIV-RNA together with APOBEC editing evaluation might help to identify HTE individuals with MDR who are more prone to experience virological failure.
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Affiliation(s)
- Daniele Armenia
- Saint Camillus International University of Health Sciences, Rome, Italy; Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Luca Carioti
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Laura Galli
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy
| | - Andrea Galli
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy
| | - Rossana Scutari
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Gaetana Sterrantino
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | | | | | - Antonella Castagna
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy; Clinic of Infectious Diseases, Vita-Salute San Raffaele University, Milan, Italy
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5
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Tekin D, Gokengin D, Onay H, Erensoy S, Sertoz R. Investigation of drug resistance against protease, reverse transcriptase, and integrase inhibitors by next-generation sequencing in HIV-positive patients. J Med Virol 2021; 93:3627-3633. [PMID: 33026651 DOI: 10.1002/jmv.26582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
Our aim was to investigate the mutations in protease (PR), reverse transcriptase (RT), and integrase (IN) gene regions in human immunodeficiency virus (HIV) using a single amplicon via next-generation sequencing (NGS). The study included plasma samples from 49 HIV-1-positive patients, which were referred for HIV-1 drug resistance testing during 2017. A nested polymerase chain reaction (PCR) was performed after the RNA extraction and one-step reverse transcription stages. The sequencing of the HIV genome in the PR, RT, and IN gene regions was carried out using MiSeq NGS technology. Sanger sequencing (SS) was used to analyze resistance mutations in the PR and RT gene regions using a ViroSeq HIV-1 Genotyping System. PCR products were analyzed with an ABI3500 GeneticAnalyzer (Applied Biosystems). Resistance mutations detected with NGS at frequencies above 20% were identical to the SS results. Resistance to at least one antiretroviral (ARV) drug was 22.4% (11 of 49) with NGS and 10.2% (5 of 49) with SS. At least one low-frequency resistance mutation was detected in 18.3% (9 of 49) of the samples. Low-frequency resistance mutations resulted in virological failure in only one patient. The cost of the analyses was reduced by sample pooling and multiplex analysis using the MiSeq system. This is the first study in Turkey to use NGS technologies for the detection of resistance mutations in all three gene (PR, RT, IN) regions using a single amplicon. Our findings suggest that NGS is more sensitive and cost-effective than the SS method.
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Affiliation(s)
- Duygu Tekin
- Department of Medical Microbiology, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Deniz Gokengin
- Department of Clinical Microbiology and Infectious Diseases, Ege University Medical School, Izmir, Turkey
| | - Huseyin Onay
- Department of Medical Genetics, Ege University Medical School, Izmir, Turkey
| | - Selda Erensoy
- Department of Medical Microbiology, Ege University Medical School, Izmir, Turkey
| | - Ruchan Sertoz
- Department of Medical Microbiology, Ege University Medical School, Izmir, Turkey
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Maggiolo F, Bandera A, Bonora S, Borderi M, Calcagno A, Cattelan A, Cingolani A, Gianotti N, Lichtner M, Lo Caputo S, Madeddu G, Maggi P, Marchetti GC, Maserati R, Nozza S, Rusconi S, Zazzi M, Di Biagio A. Enhancing care for people living with HIV: current and future monitoring approaches. Expert Rev Anti Infect Ther 2020; 19:443-456. [PMID: 33054479 DOI: 10.1080/14787210.2021.1823217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Antiretroviral therapy (ART) is the most significant advance in the medical management of HIV-1 infection. Given the fact that HIV cannot be eradicated from the body, ART has to be indefinitely maintained. New approaches need to be defined for monitoring HIV-infected individuals (PLWHIV), including clinical, virologic, immunological parameters and also ways to collect individual points of view and quality of life. AREAS COVERED We discuss which tests may be used to improve the management of PLWHIV and respond to a comprehensive health demand. EXPERT OPINION Viral load and CD4 counts are well-validated outcome measures and we still need them, but they do not completely depict the health status of PLWHIV. We need to better understand and to apply to clinical practice what happens in sanctuaries, what is the role of HIV DNA, what is the meaning of low-level viremia. Most of these questions do not yet have a definitive response. Further, we need to understand how to modify these variables in order to improve outcomes.Similar points may be raised for immunological measures and for tests exploring the tolerability of drugs. The goal must be the evolution from a viro/immunologic-based to a comprehensive quality-of-health-based evaluation of PLWHIV.
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Affiliation(s)
- Franco Maggiolo
- Unit of Infectious Diseases, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Alessandra Bandera
- A Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico - B Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy
| | - Stefano Bonora
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Marco Borderi
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, S. Orsola Hospital, "Alma Mater Studiorum" University of Bologna, Italy
| | - Andrea Calcagno
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Annamaria Cattelan
- Unit of Infectious Diseases, Department of Internal Medicine, Azienda Ospedaliera and University of Padua, Italy
| | - Antonella Cingolani
- Department of Infectious Diseases, Università Cattolica, Fondazione Policlinico A. Gemelli, Roma, Italy
| | - Nicola Gianotti
- Department of Infectious Diseases, Ospedale San Raffaele, Milano, Italy
| | - Miriam Lichtner
- Dept of Public Health and Infectious Diseases - Sapienza, University of Rome, SM Goretti Hospital, Latina, Italy
| | - Sergio Lo Caputo
- Infection Disease Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia Italy
| | - Giordano Madeddu
- Unit of Infectious Diseases, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Paolo Maggi
- Department of Infectious Diseases, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Giulia Carla Marchetti
- Dept of Health Sciences, Clinic of Infectious Diseases, University of Milan, ASST Santi Paolo E Carlo, Milano, Italy
| | - Renato Maserati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Silvia Nozza
- Department of Infectious Diseases, Ospedale San Raffaele, Milano, Italy
| | - Stefano Rusconi
- Infectious Diseases Unit, DIBIC Luigi Sacco, University of Milan, Milano, Italy
| | - Maurizio Zazzi
- Dept of Medical Biotechnologies, University of Siena, A.O.U. Senese - Ospedale Santa Maria Alle Scotte, Siena, Italy
| | - Antonio Di Biagio
- Infectious Diseases Clinic, San Martino Hospital - IRCCS, Genoa, Italy - Department of Health Sciences, University of Genoa, Genova, Italy
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Pan-resistant HIV-1 emergence in the era of integrase strand-transfer inhibitors: a case report. THE LANCET MICROBE 2020; 1:e130-e135. [DOI: 10.1016/s2666-5247(20)30006-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/17/2020] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
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8
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Genome-Based Prediction of Bacterial Antibiotic Resistance. J Clin Microbiol 2019; 57:JCM.01405-18. [PMID: 30381421 PMCID: PMC6425178 DOI: 10.1128/jcm.01405-18] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023] Open
Abstract
Clinical microbiology has long relied on growing bacteria in culture to determine antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic susceptibility testing (WGS-AST) is now a powerful alternative. This review discusses the technologies that made this possible and presents results from recent studies to predict resistance based on genome sequences. Clinical microbiology has long relied on growing bacteria in culture to determine antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic susceptibility testing (WGS-AST) is now a powerful alternative. This review discusses the technologies that made this possible and presents results from recent studies to predict resistance based on genome sequences. We examine differences between calling antibiotic resistance profiles by the simple presence or absence of previously known genes and single-nucleotide polymorphisms (SNPs) against approaches that deploy machine learning and statistical models. Often, the limitations to genome-based prediction arise from limitations of accuracy of culture-based AST in addition to an incomplete knowledge of the genetic basis of resistance. However, we need to maintain phenotypic testing even as genome-based prediction becomes more widespread to ensure that the results do not diverge over time. We argue that standardization of WGS-AST by challenge with consistently phenotyped strain sets of defined genetic diversity is necessary to compare the efficacy of methods of prediction of antibiotic resistance based on genome sequences.
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Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing. J Clin Microbiol 2018; 56:JCM.00105-18. [PMID: 29618499 DOI: 10.1128/jcm.00105-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/20/2018] [Indexed: 11/20/2022] Open
Abstract
The ability of next-generation sequencing (NGS) technologies to detect low frequency HIV-1 drug resistance mutations (DRMs) not detected by dideoxynucleotide Sanger sequencing has potential advantages for improved patient outcomes. We compared the performance of an in vitro diagnostic (IVD) NGS assay, the Sentosa SQ HIV genotyping assay for HIV-1 genotypic resistance testing, with Sanger sequencing on 138 protease/reverse transcriptase (RT) and 39 integrase sequences. The NGS assay used a 5% threshold for reporting low-frequency variants. The level of complete plus partial nucleotide sequence concordance between Sanger sequencing and NGS was 99.9%. Among the 138 protease/RT sequences, a mean of 6.4 DRMs was identified by both Sanger and NGS, a mean of 0.5 DRM was detected by NGS alone, and a mean of 0.1 DRM was detected by Sanger sequencing alone. Among the 39 integrase sequences, a mean of 1.6 DRMs was detected by both Sanger sequencing and NGS and a mean of 0.15 DRM was detected by NGS alone. Compared with Sanger sequencing, NGS estimated higher levels of resistance to one or more antiretroviral drugs for 18.2% of protease/RT sequences and 5.1% of integrase sequences. There was little evidence for technical artifacts in the NGS sequences, but the G-to-A hypermutation was detected in three samples. In conclusion, the IVD NGS assay evaluated in this study was highly concordant with Sanger sequencing. At the 5% threshold for reporting minority variants, NGS appeared to attain a modestly increased sensitivity for detecting low-frequency DRMs without compromising sequence accuracy.
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Ntamatungiro AJ, Muri L, Glass TR, Erb S, Battegay M, Furrer H, Hatz C, Tanner M, Felger I, Klimkait T, Letang E. Strengthening HIV therapy and care in rural Tanzania affects rates of viral suppression. J Antimicrob Chemother 2018; 72:2069-2074. [PMID: 28387865 DOI: 10.1093/jac/dkx095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/28/2017] [Indexed: 12/19/2022] Open
Abstract
Objectives To assess viral suppression rates, to assess prevalence of acquired HIV drug resistance and to characterize the spectrum of HIV-1 drug resistance mutations (HIV-DRM) in HIV-1-infected patients in a rural Tanzanian HIV cohort. Methods This was a cross-sectional study nested within the Kilombero and Ulanga Antiretroviral Cohort. Virological failure was defined as HIV-1 RNA ≥50 copies/mL. Risk factors associated with virological failure and with the development of HIV-DRM were assessed using logistic regression. Results This study included 304 participants with a median time on ART of 3.5 years (IQR = 1.7-5.3 years); 91% were on an NNRTI-based regimen and 9% were on a boosted PI-based regimen. Viral suppression was observed in 277/304 patients (91%). Of the remaining 27 patients, 21 were successfully genotyped and 17/21 (81%) harboured ≥1 clinically relevant HIV-DRM. Of these, 13/17 (76.5%) had HIV-1 plasma viral loads of >1000 copies/mL. CD4 cell count <200 cells/mm(3) at the time of recruitment was independently associated with a close to 8-fold increased odds of virological failure [adjusted OR (aOR) = 7.71, 95% CI = 2.86-20.78, P < 0.001] and with a >8-fold increased odds of developing HIV-DRM (aOR = 8.46, 95% CI = 2.48-28.93, P = 0.001). Conclusions High levels of viral suppression can be achieved in rural sub-Saharan Africa when treatment and care programmes are well managed. In the absence of routine HIV sequencing, the WHO-recommended threshold of 1000 viral RNA copies/mL largely discriminates virological failure secondary to HIV-DRM.
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Affiliation(s)
| | - Lukas Muri
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Tracy R Glass
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Stefan Erb
- University of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, Department of Medicine and Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Manuel Battegay
- University of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, Department of Medicine and Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christoph Hatz
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Marcel Tanner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine Petersplatz, University of Basel, Basel, Switzerland
| | - Emilio Letang
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
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11
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Fernández-Caballero Rico JÁ, Chueca Porcuna N, Álvarez Estévez M, Mosquera Gutiérrez MDM, Marcos Maeso MÁ, García F. Validación de un método seguro y sencillo para la elaboración de secuencias consenso del virus de la inmunodeficiencia humana a partir de los datos de secuenciación masiva 454. Enferm Infecc Microbiol Clin 2018; 36:91-94. [DOI: 10.1016/j.eimc.2016.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 11/28/2022]
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12
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Abstract
In this chapter we will discuss the diagnosis and monitoring of individuals with HIV infection. The application and interpretation of these tests does not change dramatically when used in the immunocompromised host. The principal approach to the diagnosis of HIV infection involves serologic testing, although nucleic acid amplification tests play an important role in the diagnosis of acute HIV infection. The algorithm for diagnosis of HIV continues to evolve with newer assays that are able to detect infection within an earlier timeframe after HIV transmission. Viral load testing for HIV-1 is the cornerstone for monitoring patients on antiretroviral therapy. Genotypic and phenotypic resistance tests are employed when antiretroviral resistance is suspected and results help guide therapy. The tropism assay must be performed to determine the efficacy of CCR5 chemokine receptor antagonists. Next-generation sequencing methods are an innovative approach to assessing archived antiretroviral resistance in patients with virologic suppression. The success of antiretroviral therapy with improved long-term outcomes has made transplantation in HIV-infected patients a reality.
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13
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HIV-1 Drug Resistance by Ultra-Deep Sequencing Following Short Course Zidovudine, Single-Dose Nevirapine, and Single-Dose Tenofovir with Emtricitabine for Prevention of Mother-to-Child Transmission. J Acquir Immune Defic Syndr 2017; 73:384-389. [PMID: 27327263 PMCID: PMC5172515 DOI: 10.1097/qai.0000000000001116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Supplemental Digital Content is Available in the Text. Antiretroviral drug resistance following pMTCT strategies remains a significant problem. With rapid advancements in next generation sequencing technologies, there is more focus on HIV drug-resistant variants of low frequency, or the so-called minority variants. In South Africa, AZT monotherapy for pMTCT, similar to World Health Organization option A, has been used since 2008. In 2010, a single dose of co-formulated TDF/FTC was included in the strategy for prevention of resistance conferred by single-dose nevirapine (sd NVP). The study was conducted in KwaZulu-Natal, South Africa, among pMTCT participants who received AZT monotherapy from 14 weeks of gestation, intrapartum AZT and sd NVP, and postpartum sd TDF/FTC. Twenty-six specimens collected at 6 weeks post-delivery were successfully sequenced using 454 ultra-deep sequencing. Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance was detected in 17 of 26 (65%) patients, 2 (7%) had Thymidine analogue mutations, and 3 (11%) had K65R. Of the 17 patients with NNRTI resistance, 11 (65%) had high-level NNRTI resistance, whereas 6 (35%) had intermediate NNRTI resistance. The levels of NNRTI resistance are much higher than would be expected, given the inclusion of antepartum AZT and postpartum TDF/FTC. This high level of NNRTI resistance could impact future NNRTI-containing treatment for a large proportion of pMTCT-exposed women. The detection of Thymidine analogue mutations highlights the need to understand the clinical impact of these on AZT-containing antiretroviral treatment in women exposed to AZT monotherapy.
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14
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Hayashida T, Tsuchiya K, Kikuchi Y, Oka S, Gatanaga H. Emergence of CXCR4-tropic HIV-1 variants followed by rapid disease progression in hemophiliac slow progressors. PLoS One 2017; 12:e0177033. [PMID: 28472121 PMCID: PMC5417636 DOI: 10.1371/journal.pone.0177033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/20/2017] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE The association between emergence of CXCR4-tropic HIV-1 variants (X4 variants) and disease progression of HIV-1 infection has been reported. However, it is not known whether the emergence of X4 variants is the cause or result of HIV-1 disease progression. We tried to answer this question. DESIGN HIV-1 env sequences around the V3 region were analyzed in serially stocked samples in order to determine whether X4 variants emerged before or after the fall in CD4+ T-cell count. METHODS The study subjects were five HIV-1-infected hemophiliac slow progressors. Deep sequencing around the HIV-1 env V3 region was conducted in duplicate. Tropism was predicted by geno2pheno [coreceptor] 2.5 with cutoff value of false positive ratio at <5%. When X4 variant was identified in the latest stocked sample before the introduction of antiretroviral therapy, we checked viral genotype in previously stocked samples to determine the time of emergence of X4 variants. RESULTS Emergence of X4 variants was noted in two of the five patients when their CD4+ T-cell counts were still high. The rate of decrease of CD4+ T-cell count or of rise of HIV-1 load accelerated significantly after the emergence of X4 variants in these two cases. Phylogenetic analysis showed that these X4 variants emerged from CCR5-tropic HIV-1 viruses with several amino acid changes in the V3 region. CONCLUSIONS The emergence of X4 variants preceded HIV-1 disease progression in two hemophiliac slow progressors.
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Affiliation(s)
- Tsunefusa Hayashida
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kiyoto Tsuchiya
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshimi Kikuchi
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
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15
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Casadellà M, Cozzi-Lepri A, Phillips A, Noguera-Julian M, Bickel M, Sedlacek D, Zilmer K, Clotet B, Lundgren JD, Paredes R. Plasma HIV-1 Tropism and the Risk of Short-Term Clinical Progression to AIDS or Death. PLoS One 2017; 12:e0166613. [PMID: 28129343 PMCID: PMC5271314 DOI: 10.1371/journal.pone.0166613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/01/2016] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE To investigate if plasma HIV-1 tropism testing could identify subjects at higher risk for clinical progression and death in routine clinical management. DESIGN Nested case-control study within the EuroSIDA cohort. METHODS Cases were subjects with AIDS or who died from any cause, with a plasma sample with HIV-1 RNA >1000 copies/mL available for tropism testing 3 to 12 months prior to the event. At least 1 control matched for age, HIV-1 RNA and HCV status at the time of sampling were selected per each case. Conditional logistic regression was used to investigate exposures associated with clinical progression to AIDS or death. A linear mixed model with random intercept was used to compare CD4+T-cell slopes by HIV tropism over the 12 months following the date of sampling. RESULTS The study included 266 subjects, 100 cases and 166 controls; one quarter had X4 HIV; 26% were ART-naïve. Baseline factors independently associated with clinical progression or death were female gender (OR = 2.13 vs. male, 95CI = 1.04, 4.36), p = 0.038), CD4+T-cell count (OR = 0.90 (95CI = 0.80, 1.00) per 100 cells/mm3 higher, p = 0.058), being on ART (OR = 2.72 vs. being off-ART (95CI = 1.15, 6.41), p = 0.022) and calendar year of sample [OR = 0.84 (95CI = 0.77, 0.91) per more recent year, p<0.001). Baseline tropism was not associated with the risk of clinical progression or death. CD4+T-cell slopes did not differ within or between tropism groups. CONCLUSIONS The predictive role of plasma tropism determined using 454 sequencing in the context of people receiving cART with detectable VL is not helpful to identify subjects at higher risk for clinical progression to AIDS or death.
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Affiliation(s)
- Maria Casadellà
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, Catalonia, Spain
| | | | | | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
| | | | | | - Kai Zilmer
- West-Tallinn Central Hospital, Tallinn, Estonia
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
- HIV Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Jens D Lundgren
- CHIP, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
- HIV Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
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16
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Gonzalez-Serna A, Glas AC, Brumme CJ, Poon AFY, Nohpal De La Rosa A, Mudrikova T, Dias Lima V, Wensing AMJ, Harrigan R. Genotypic susceptibility score (GSS) and CD4+ T cell recovery in HIV-1 patients with suppressed viral load. J Antimicrob Chemother 2016; 72:496-503. [PMID: 27999069 DOI: 10.1093/jac/dkw455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES HIV drug resistance, measured by the genotypic susceptibility score (GSS), has a deleterious effect on the virological outcome of HIV-1-infected patients. However, it is not known if GSS retains any predictive value for CD4 recovery in patients with suppressed viral load. METHODS Four hundred and six patients on virological failure (>500 copies/mL) with GSS : <6 months prior to switch therapy who achieved undetectable plasma viral load (<50 copies/mL) within 1 year, remained undetectable >1 year on an unchanged regimen and had CD4 data available during entire follow-up were included. Adjusted and unadjusted analyses of all characteristics at switch related to CD4 recovery were made for three time frames: (i) 'switch-suppression'; (ii) 'suppression-1 year'; and (iii) 'switch-1 year'. RESULTS Higher GSS was associated with a greater CD4 recovery between 'switch' and '1 year' in the unadjusted analysis (P = 0.010); however, the effect of GSS was no longer statistically significant after adjusting for pre-switch clinical (CD4 count and plasma viral load) and demographic variables. Furthermore, only a lower pre-switch CD4 count was associated with increased CD4 recovery in the 'suppression-1 year' period in both unadjusted and adjusted models. The main CD4 recovery occurred in 'switch-suppression' and the variables associated, both unadjusted and adjusted, were CD4 and plasma viral load at switch, maintaining a trend for GSS (P = 0.06). CONCLUSIONS In individuals who re-suppressed HIV viraemia after switching therapy, regimens having a higher GSS were associated with improved CD4 recovery only during the period from switch to virological suppression, but, once viral load is re-suppressed, the GSS of the new regimen has no further effect on subsequent CD4 recovery.
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Affiliation(s)
- Alejandro Gonzalez-Serna
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada .,Laboratory of Molecular Immunobiology, Hospital General Universitario Gregorio Maranon, Madrid, Spain
| | - Arie C Glas
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Art F Y Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | - Tania Mudrikova
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Annemarie M J Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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17
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Casadellà M, Paredes R. Deep sequencing for HIV-1 clinical management. Virus Res 2016; 239:69-81. [PMID: 27818211 DOI: 10.1016/j.virusres.2016.10.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/10/2016] [Accepted: 10/18/2016] [Indexed: 02/05/2023]
Abstract
The emerging HIV-1 resistance epidemic is threatening the impressive global advances in HIV-1 infection treatment and prevention achieved in the last decade. Next-generation sequencing is improving our ability to understand, diagnose and prevent HIV-1 resistance, being increasingly cost-effective and more accessible. However, NGS still faces a number of limitations that need to be addressed to enable its widespread use. Here, we will review the main NGS platforms available for HIV-1 diagnosis, the factors affecting the clinical utility of NGS testing and the evidence supporting -or not- ultrasensitive genotyping over Sanger sequencing for routine HIV-1 diagnosis. Now that global HIV-1 eradication might be within our reach, making NGS accessible also to LMICs has become a priority. Reductions in sequencing costs, particularly in library preparation, and accessibility to low-cost, robust but simplified automated bioinformatic analyses of NGS data will remain essential to end the HIV-1 pandemic.
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Affiliation(s)
- Maria Casadellà
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Catalonia, Spain.
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Catalonia, Spain; Universitat de Vic - Central de Catalunya, Vic, Catalonia, Spain; HIV-1 Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
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18
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Gill VC, Lynch T, Ramazani S, Krentz HB. Reporting on the prevalence of antiretroviral drug resistance in a regional HIV population over 20 years: a word of caution. Antivir Ther 2016; 22:277-286. [PMID: 27805572 DOI: 10.3851/imp3105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Failure to achieve complete viral suppression with antiretroviral drugs (ARV) may lead to uncontrolled HIV replication, ARV resistance and negative outcomes. Monitoring and reporting of HIV resistance trends is important but problematic. We examined prevalent resistance rates in an HIV population over 20 years and document how rates may appear to vary greatly based solely on which parameters are utilized. METHODS We determined the annual use of genotypic antiretroviral resistance testing (GART) from 1995 to 2014 for all patients receiving HIV care in southern Alberta, Canada, and the presence of resistance mutations in those tested. The impact on prevalent resistance rates of using cumulative or latest GART was also determined. RESULTS Between 1995 and 2014, the number of patients with GART increased from <1% to 71%. Prevalent resistance in patients with GART decreased from a high of 52% in 2003 to 25.8% in 2014. However, if prevalence rates were reported using all active patients as denominator, including those without GART, prevalence increased from 0.7% to 18.5%. Prevalence rates were 7% to 9% higher in any given year if cumulative GART rather than latest GART results were used. CONCLUSIONS While prevalence resistance rates are decreasing, the precise rates being reported may vary due to increasing number of patients tested annually, using either the entire population as denominator or only patients with GART, and using either last or cumulative GART. Defining these parameters is critical if prevalence is to be compared over time or between HIV populations.
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Affiliation(s)
| | - Tarah Lynch
- Southern Alberta Clinic, Calgary, AB, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Hartmut B Krentz
- Southern Alberta Clinic, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
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19
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HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China. PLoS One 2016; 11:e0149215. [PMID: 26895182 PMCID: PMC4760947 DOI: 10.1371/journal.pone.0149215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
Objective Determine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF). Methods 29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels. Results DS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×104 c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1–4% and 24 (60%) at levels of 5–19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS. Conclusions DS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects.
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20
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Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing. Viruses 2016; 8:v8010012. [PMID: 26751471 PMCID: PMC4728572 DOI: 10.3390/v8010012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/08/2015] [Accepted: 12/15/2015] [Indexed: 12/24/2022] Open
Abstract
Genetic analyses play a central role in infectious disease research. Massively parallelized “mechanical cloning” and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure—from nucleic acid extraction to sequencing—should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping.
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21
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Molecular Detection and Characterization of Human Immunodeficiency Virus Type 1. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants. Clin Microbiol Infect 2015; 22:191-200. [PMID: 26482266 DOI: 10.1016/j.cmi.2015.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/07/2015] [Accepted: 10/03/2015] [Indexed: 11/20/2022]
Abstract
Plasma drug-resistant minority human immunodeficiency virus type 1 variants (DRMVs) increase the risk of virological failure to first-line non-nucleoside reverse transcriptase inhibitor antiretroviral therapy (ART). The origin of DRMVs in ART-naive patients, however, remains unclear. In a large pan-European case-control study investigating the clinical relevance of pre-existing DRMVs using 454 pyrosequencing, the six most prevalent plasma DRMVs detected corresponded to G-to-A nucleotide mutations (V90I, V106I, V108I, E138K, M184I and M230I). Here, we evaluated if such DRMVs could have emerged from apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3G/F (APOBEC3G/F) activity. Out of 236 ART-naive subjects evaluated, APOBEC3G/F hypermutation signatures were detected in plasma viruses of 14 (5.9%) individuals. Samples with minority E138K, M184I, and M230I mutations, but not those with V90I, V106I or V108I, were significantly associated with APOBEC3G/F activity (Fisher's P < 0.005), defined as the presence of > 0.5% of sample sequences with an APOBEC3G/F signature. Mutations E138K, M184I and M230I co-occurred in the same sequence as APOBEC3G/F signatures in 3/9 (33%), 5/11 (45%) and 4/8 (50%) of samples, respectively; such linkage was not found for V90I, V106I or V108I. In-frame STOP codons were observed in 1.5% of all clonal sequences; 14.8% of them co-occurred with APOBEC3G/F signatures. APOBEC3G/F-associated E138K, M184I and M230I appeared within clonal sequences containing in-frame STOP codons in 2/3 (66%), 5/5 (100%) and 4/4 (100%) of the samples. In a re-analysis of the parent case control study, the presence of APOBEC3G/F signatures was not associated with virological failure. In conclusion, the contribution of APOBEC3G/F editing to the development of DRMVs is very limited and does not affect the efficacy of non-nucleoside reverse transcriptase inhibitor ART.
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HIV-1 genotypic drug resistance testing: digging deep, reaching wide? Curr Opin Virol 2015; 14:16-23. [DOI: 10.1016/j.coviro.2015.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 06/10/2015] [Accepted: 06/10/2015] [Indexed: 12/26/2022]
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Abstract
PURPOSE OF REVIEW The review discusses new technologies for the sensitive detection of HIV drug resistance, with a focus on applications in antiretroviral treatment (ART)-naïve populations. RECENT FINDINGS Conventional sequencing is well established for detecting HIV drug resistance in routine care and guides optimal treatment selection in patients starting ART. Access to conventional sequencing is nearly universal in Western countries, but remains limited in Asia, Latin America, and Africa. Technological advances now allow detection of resistance with greatly improved sensitivity compared with conventional sequencing, variably increasing the yield of resistance testing in ART-naïve populations. There is strong cumulative evidence from retrospective studies that sensitive detection of resistant mutants in baseline plasma samples lacking resistance by conventional sequencing more than doubles the risk of virological failure after starting efavirenz-based or nevirapine-based ART. SUMMARY Sensitive resistance testing methods are mainly confined to research applications and in this context have provided great insight into the dynamics of drug resistance development, persistence, and transmission. Adoption in care settings is becoming increasingly possible, although important challenges remain. Platforms for diagnostic use must undergo technical improvements to ensure good performance and ease of use, and clinical validation is required to ensure utility.
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25
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Clinical value of ultradeep HIV-1 genotyping and tropism testing in late presenters with advanced disease. AIDS 2015; 29:1493-504. [PMID: 26244389 DOI: 10.1097/qad.0000000000000748] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE This article aims to investigate if the detection of preexisting drug-resistant minority variant (DRMV) and/or X4 HIV-1 variants could improve the efficacy of first-line combined antiretroviral therapy (ART) in late presenters. DESIGN Post-hoc, combined analysis of two open-label, prospective, randomized clinical trials comparing first-line ART with efavirenz (EFV) vs. ritonavir-boosted protease inhibitor (PI/r)-based regimens in ART-naive, HIV-1-infected patients, with CD4 T-cell counts less than 100 cells/μl and wild-type HIV-1 by bulk sequencing. METHODS Pre-ART samples were reanalyzed for the presence of DRMVs and X4 HIV-1 using 454 sequencing. Kaplan-Meier curves and Cox regression were used to evaluate the association between X4 HIV and DRMVs and risk of virological failure. RESULTS From 141 evaluable patients, 57 received EFV, and 84 received PI/r, including first-line ART. Median pre-ART CD4 T-cell counts and HIV-1 RNA levels were 39 cells/μl and 257 424 copies/ml, respectively; 35.5% of patients had X4 HIV variants. Detection of DRMVs leading to an ART-specific cumulative HIVdb score of at least 10 increased the risk of virological failure in patients initiating EFV [log-rank P = 0.048, hazard ratio = 4.3 (95% confidence interval: 0.8, 25.0), P = 0.074], but not in those starting PI/r. Presence of X4 HIV did not affect virological outcomes, but was associated with impaired CD4 T-cell count recovery over 2 years (214 vs. 315 cells/μl with X4 vs. R5 HIV-1 tropism, respectively, P = 0.017). CONCLUSION Accounting for preexisting DRMVs may improve the outcomes of first-line nonnucleoside reverse transcriptase inhibitor-based ART in late presenters with advanced immune suppression. Presence of X4 HIV-1 at diagnosis predicts impaired immune restoration under ART.
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Rupérez M, Pou C, Maculuve S, Cedeño S, Luis L, Rodríguez J, Letang E, Moltó J, Macete E, Clotet B, Alonso P, Menéndez C, Naniche D, Paredes R. Determinants of virological failure and antiretroviral drug resistance in Mozambique. J Antimicrob Chemother 2015; 70:2639-47. [PMID: 26084302 DOI: 10.1093/jac/dkv143] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/01/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The objective of this study was to inform public health actions to limit first-line ART failure and HIV drug resistance in Mozambique. METHODS This was a cross-sectional study. HIV-1-infected adults on first-line ART for at least 1 year attending routine visits in the Manhiça District Hospital, in a semi-rural area in southern Mozambique with no HIV-1 RNA monitoring available, were evaluated for clinical, socio-demographic, therapeutic, immunological and virological characteristics. Factors associated with HIV-1 RNA ≥1000 copies/mL and HIV drug resistance were determined using multivariate logistic regression. RESULTS The study included 334 adults on first-line ART for a median of 3 years, of which 65% (214/332) had suppressed viraemia, 11% (37/332) had low-level viraemia (HIV-1 RNA 150-999 copies/mL) and 24% (81/332) had overt virological failure (HIV-1 RNA ≥1000 copies/mL). HIV drug resistance was detected in 89% of subjects with virological failure, but in none with low-level viraemia. Younger age [OR = 0.97 per additional year (95% CI = 0.94-1.00), P = 0.039], ART initiation at WHO stage III/IV [OR = 2.10 (95% CI = 1.23-3.57), P = 0.003] and low ART adherence [OR = 2.69 (95% CI = 1.39-5.19), P = 0.003] were associated with virological failure. Longer time on ART [OR = 1.55 per additional year (95% CI = 1.00-2.43), P = 0.052] and illiteracy [OR = 0.24 (95% CI = 0.07-0.89), P = 0.033] were associated with HIV drug resistance. Compared with HIV-1 RNA, clinician's judgement of ART failure, based on clinical and immunological outcomes, only achieved 29% sensitivity and misdiagnosed 1 out of every 4.5 subjects. CONCLUSIONS Public health programmes in Mozambique should focus on early HIV diagnosis, early ART initiation and adherence support. Virological monitoring drastically improves the diagnosis of ART failure, enabling a better use of resources.
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Affiliation(s)
- María Rupérez
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | - Christian Pou
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
| | - Sonia Maculuve
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
| | - Samandhy Cedeño
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
| | - Leopoldina Luis
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
| | | | - Emilio Letang
- Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland
| | - José Moltó
- Lluita Contra la Sida Foundation, HIV Unit, Hosp Univ Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Eusébio Macete
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain Lluita Contra la Sida Foundation, HIV Unit, Hosp Univ Germans Trias i Pujol, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
| | - Pedro Alonso
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | - Clara Menéndez
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | - Denise Naniche
- Manhiça Health Research Center (CISM), Manhiça, Maputo, Mozambique Barcelona Centre for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain Lluita Contra la Sida Foundation, HIV Unit, Hosp Univ Germans Trias i Pujol, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
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[GESIDA/National AIDS Plan: Consensus document on antiretroviral therapy in adults infected by the human immunodeficiency virus (Updated January 2015)]. Enferm Infecc Microbiol Clin 2015; 33:543.e1-43. [PMID: 25959461 DOI: 10.1016/j.eimc.2015.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/08/2015] [Indexed: 11/20/2022]
Abstract
OBJECTIVE This consensus document is an update of combined antiretroviral therapy (cART) guidelines and recommendations for HIV-1 infected adult patients. METHODS To formulate these recommendations, a panel composed of members of the AIDS Study Group and the AIDS National Plan (GeSIDA/Plan Nacional sobre el Sida) reviewed the efficacy and safety advances in clinical trials, and cohort and pharmacokinetic studies published in medical journals (PubMed and Embase) or presented in medical scientific meetings. The strength of the recommendations, and the evidence that supports them, are based on modified criteria of the Infectious Diseases Society of America. RESULTS In this update, cART is recommended for all patients infected by type 1 human immunodeficiency virus (HIV-1). The strength and level of the recommendation depends on the CD4+T-lymphocyte count, the presence of opportunistic diseases or comorbid conditions, age, and prevention of transmission of HIV. The objective of cART is to achieve an undetectable plasma viral load. Initial cART should always comprise a combination of 3 drugs, including 2 nucleoside reverse transcriptase inhibitors, and a third drug from a different family. Three out of the ten recommended regimes are regarded as preferential (all of them with an integrase inhibitor as the third drug), and the other seven (based on a non-nucleoside reverse transcriptase inhibitor, a ritonavir-boosted protease inhibitor, or an integrase inhibitor) as alternatives. This update presents the causes and criteria for switching cART in patients with undetectable plasma viral load, and in cases of virological failure where rescue cART should comprise 3 (or at least 2) drugs that are fully active against the virus. An update is also provided for the specific criteria for cART in special situations (acute infection, HIV-2 infection, and pregnancy) and with comorbid conditions (tuberculosis or other opportunistic infections, kidney disease, liver disease, and cancer). CONCLUSIONS These new guidelines update previous recommendations related to cART (when to begin and what drugs should be used), how to monitor and what to do in case of viral failure or drug adverse reactions. cART specific criteria in comorbid patients and special situations are equally updated.
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Charpentier C, Lee GQ, Rodriguez C, Visseaux B, Storto A, Fagard C, Molina JM, Katlama C, Yazdanpanah Y, Harrigan PR, Descamps D. Highly frequent HIV-1 minority resistant variants at baseline of the ANRS 139 TRIO trial had a limited impact on virological response. J Antimicrob Chemother 2015; 70:2090-6. [PMID: 25755001 DOI: 10.1093/jac/dkv048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/06/2015] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To assess the prevalence of minority resistant variants (MRVs) at baseline and their impact on the virological response. The ANRS 139 TRIO trial evaluated the combination of raltegravir, etravirine and darunavir, plus an optimized background therapy, in 87% of cases. Patients were highly experienced and harboured multiresistant viruses, but were naive to the three drugs, and showed a high level of virological suppression. METHODS Ultra-deep sequencing of reverse transcriptase, protease and integrase regions was performed at the trial baseline, and sequences were interpreted according to the ANRS algorithm. MRVs were assessed using MiSeq and 454 technologies (limit of detection 1%). RESULTS At baseline, minority variants with at least one NRTI, one NNRTI, one PI, one major PI or an integrase inhibitor resistance-associated mutation were present in 46%, 45%, 68%, 24% and 13% of patients, respectively. When minority variants are taken into account, the prevalence of resistance to etravirine, darunavir and raltegravir at baseline was 29%, 40% and 9%, respectively. No difference was observed in the prevalence of MRVs between patients with virological failure and those with virological success, except a trend for patients exhibiting baseline etravirine MRVs (50% versus 26%, P = 0.09). CONCLUSIONS We have shown a high level of MRVs at baseline in highly pre-treated patients harbouring multiresistant viruses. However, these MRVs were not associated with an increased risk of virological failure, except for a trend for etravirine MRVs.
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Affiliation(s)
- Charlotte Charpentier
- INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - Guinevere Q Lee
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada University of British Columbia, Vancouver, BC, Canada
| | - Christophe Rodriguez
- Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France INSERM U955 Team 18, Créteil, France
| | - Benoit Visseaux
- INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - Alexandre Storto
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - Catherine Fagard
- INSERM, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, F-33000 Bordeaux, France Université Bordeaux, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, F-33000 Bordeaux, France
| | - Jean-Michel Molina
- AP-HP, Hôpital Saint-Louis, Service de Maladies Infectieuses et Tropicales, INSERM U941, Université Paris Diderot, Paris, France
| | - Christine Katlama
- AP-HP, Hôpital de la Pitié-Salpétrière, Service de Maladies Infectieuses et Tropicales, F-75013 Paris, France
| | - Yazdan Yazdanpanah
- INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France AP-HP, Hôpital Bichat, Service de Maladies Infectieuses et Tropicales, F-75018 Paris, France
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada University of British Columbia, Vancouver, BC, Canada
| | - Diane Descamps
- INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
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Todesco E, Rodriguez C, Morand-Joubert L, Mercier-Darty M, Desire N, Wirden M, Girard PM, Katlama C, Calvez V, Marcelin AG. Improved detection of resistance at failure to a tenofovir, emtricitabine and efavirenz regimen by ultradeep sequencing. J Antimicrob Chemother 2015; 70:1503-6. [PMID: 25614045 DOI: 10.1093/jac/dku557] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/12/2014] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Resistant minority variants present before ART can be a source of virological failure. This has been shown for NRTIs, NNRTIs and CCR5 inhibitors. However, very few data are available for the detection of such minority resistant variants that could be selected at virological failure and not detected using classical Sanger sequencing. METHODS We studied 26 patients treated with tenofovir, emtricitabine and efavirenz with their first virological failure (defined as two consecutive viral loads >50 copies/mL). We performed standard Sanger sequencing and ultradeep sequencing (UDS; Roche 454(®) Life Sciences) in plasma at failure. For UDS, mutations >1% were considered. We compared the presence of reverse transcriptase mutations between the two techniques, using the latest ANRS algorithm. RESULTS UDS detected more resistance mutations in 38.5% of cases (10/26 patients) and the genotypic sensitivity score (GSS) was reduced for 6 of them (23.1%). The GSS was impacted more often for NRTIs than for NNRTIs, for which most mutations were already detected by Sanger sequencing. Resistant minority variants were detected even in patients with low viral load at failure. CONCLUSIONS These results strongly argue for the use of next-generation sequencing in patients failing on an NRTI+NNRTI regimen, as UDS has the potential to modify the choice of the subsequent regimen.
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Affiliation(s)
- Eve Todesco
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Christophe Rodriguez
- Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France INSERM U955, Créteil, France
| | - Laurence Morand-Joubert
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Saint Antoine, AP-HP Paris, France
| | | | - Nathalie Desire
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Marc Wirden
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Pierre-Marie Girard
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Infectious Diseases, Hôpital Saint Antoine, AP-HP Paris, France
| | - Christine Katlama
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Infectious Diseases, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Vincent Calvez
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
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Dudley DM, Bailey AL, Mehta SH, Hughes AL, Kirk GD, Westergaard RP, O'Connor DH. Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq. Retrovirology 2014; 11:122. [PMID: 25533166 PMCID: PMC4302432 DOI: 10.1186/s12977-014-0122-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 12/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background Viral resistance to antiretroviral therapy threatens our best methods to control and prevent HIV infection. Current drug resistance genotyping methods are costly, optimized for subtype B virus, and primarily detect resistance mutations to protease and reverse transcriptase inhibitors. With the increasing use of integrase inhibitors in first-line therapies, monitoring for integrase inhibitor drug resistance mutations is a priority. We designed a universal primer pair to PCR amplify all major group M HIV-1 viruses for genotyping using Illumina MiSeq to simultaneously detect drug resistance mutations associated with protease, nucleoside reverse transcriptase, non-nucleoside reverse transcriptase, and integrase inhibitors. Results A universal primer pair targeting the HIV pol gene was used to successfully PCR amplify HIV isolates representing subtypes A, B, C, D, CRF01_AE and CRF02_AG. The universal primers were then tested on 62 samples from a US cohort of injection drug users failing treatment after release from prison. 94% of the samples were successfully genotyped for known drug resistance mutations in the protease, reverse transcriptase and integrase gene products. Control experiments demonstrate that mutations present at ≥ 2% frequency are reliably detected and above the threshold of error for this method. New drug resistance mutations not found in the baseline sample were identified in 54% of the patient samples after treatment failure. 86% of patients with major drug resistance mutations had 1 or more mutations associated with drug resistance to the treatment regimen at the time point of treatment failure. 59% of the emerging mutations were found at frequencies between 2% and 20% of the total sequences generated, below the estimated limit of detection of current FDA-approved genotyping techniques. Primary plasma samples with viral loads as low as 799 copies/ml were successfully genotyped using this method. Conclusions Here we present an Illumina MiSeq-based HIV drug resistance genotyping assay. Our data suggests that this universal assay works across all major group M HIV-1 subtypes and identifies all drug resistance mutations in the pol gene known to confer resistance to protease, reverse transcriptase and integrase inhibitors. This high-throughput and sensitive assay could significantly improve access to drug resistance genotyping worldwide. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0122-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Shruti H Mehta
- Department of Epidemiology, Epidemiology and Oncology, Johns Hopkins University, Baltimore, MD, USA.
| | - Austin L Hughes
- Department of Biology, University of South Carolina, Columbia, South Carolina, USA.
| | - Gregory D Kirk
- Departments of Medicine, Epidemiology and Oncology, Johns Hopkins University, Baltimore, MD, USA.
| | - Ryan P Westergaard
- Department of Medicine, Division of Infectious Disease, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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Ram D, Leshkowitz D, Gonzalez D, Forer R, Levy I, Chowers M, Lorber M, Hindiyeh M, Mendelson E, Mor O. Evaluation of GS Junior and MiSeq next-generation sequencing technologies as an alternative to Trugene population sequencing in the clinical HIV laboratory. J Virol Methods 2014; 212:12-6. [PMID: 25445792 DOI: 10.1016/j.jviromet.2014.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/02/2014] [Accepted: 11/04/2014] [Indexed: 01/20/2023]
Abstract
Population HIV-1 sequencing is currently the method of choice for the identification and follow-up of HIV-1 antiretroviral drug resistance. It has limited sensitivity and results in a consensus sequence showing the most prevalent nucleotide per position. Moreover concomitant sequencing and interpretation of the results for several samples together is laborious and time consuming. In this study, the practical use of GS Junior and MiSeq bench-top next generation sequencing (NGS) platforms as an alternative to Trugene Sanger-based population sequencing in the clinical HIV laboratory was assessed. DeepChek(®)-HIV TherapyEdge software was used for processing all the protease and reverse transcriptase sequences and for resistance interpretation. Plasma samples from nine HIV-1 carriers, representing the major HIV-1 subtypes in Israel, were compared. The total number of amino acid substitutions identified in the nine samples by GS Junior (232 substitutions) and MiSeq (243 substitutions) was similar and higher than Trugene (181 substitutions), emphasizing the advantage of deep sequencing on population sequencing. More than 80% of the identified substitutions were identical between the GS Junior and MiSeq platforms, most of which (184 of 199) at similar frequency. Low abundance substitutions accounted for 20.9% of the MiSeq and 21.9% of the GS Junior output, the majority of which were not detected by Trugene. More drug resistance mutations were identified by both the NGS platforms, primarily, but not only, at low abundance. In conclusion, in combination with DeepChek, both GS Junior and MiSeq were found to be more sensitive than Trugene and adequate for HIV-1 resistance analysis in the clinical HIV laboratory.
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Affiliation(s)
- Daniela Ram
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel.
| | - Dena Leshkowitz
- Bioinformatics Unit, The Nancy and Stephen Grand National Center for Personalized Medicine, Weizmann Institute, Rehovot, Israel.
| | | | | | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Israel.
| | - Michal Chowers
- Infectious Disease Unit, Meir Medical Center, Kfar Saba, Israel.
| | - Margalit Lorber
- Autoimmune Disease Unit, Rambam Medical Center, Haifa, Israel.
| | - Musa Hindiyeh
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel; Tel-Aviv University, Tel-Aviv, Israel.
| | - Ella Mendelson
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel; Tel-Aviv University, Tel-Aviv, Israel.
| | - Orna Mor
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel.
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