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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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Ouyang F, Yuan D, Zhai W, Liu S, Zhou Y, Yang H. HIV-1 Drug Resistance Detected by Next-Generation Sequencing among ART-Naïve Individuals: A Systematic Review and Meta-Analysis. Viruses 2024; 16:239. [PMID: 38400015 PMCID: PMC10893194 DOI: 10.3390/v16020239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/31/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND There are an increasing number of articles focused on the prevalence and clinical impact of pretreatment HIV drug resistance (PDR) detected by Sanger sequencing (SGS). PDR may contribute to the increased likelihood of virologic failure and the emergence of new resistance mutations. As SGS is gradually replaced by next-generation sequencing (NGS), it is necessary to assess the levels of PDR using NGS in ART-naïve patients systematically. NGS can detect the viral variants (low-abundance drug-resistant HIV-1 variants (LA-DRVs)) of virus quasi-species at levels below 20% that SGS may fail to detect. NGS has the potential to optimize current HIV drug resistance surveillance methods and inform future research directions. As the NGS technique has high sensitivity, it is highly likely that the level of pretreatment resistance would be underestimated using conventional techniques. METHODS For the systematic review and meta-analysis, we searched for original studies published in PubMed, Web of Science, Scopus, and Embase before 30 March 2023 that focused exclusively on the application of NGS in the detection of HIV drug resistance. Pooled prevalence estimates were calculated using a random effects model using the 'meta' package in R (version 4.2.3). We described drug resistance detected at five thresholds (>1%, 2%, 5%, 10%, and 20% of virus quasi-species). Chi-squared tests were used to analyze differences between the overall prevalence of PDR reported by SGS and NGS. RESULTS A total of 39 eligible studies were selected. The studies included a total of 15,242 ART-naïve individuals living with HIV. The prevalence of PDR was inversely correlated with the mutation detection threshold. The overall prevalence of PDR was 29.74% at the 1% threshold, 22.43% at the 2% threshold, 15.47% at the 5% threshold, 12.95% at the 10% threshold, and 11.08% at the 20% threshold. The prevalence of PDR to INSTIs was 1.22% (95%CI: 0.58-2.57), which is the lowest among the values for all antiretroviral drugs. The prevalence of LA-DRVs was 9.45%. At the 2% and 20% detection threshold, the prevalence of PDR was 22.43% and 11.08%, respectively. Resistance to PIs and INSTIs increased 5.52-fold and 7.08-fold, respectively, in those with a PDR threshold of 2% compared with those with PDR at 20%. However, resistance to NRTIs and NNRTIs increased 2.50-fold and 2.37-fold, respectively. There was a significant difference between the 2% and 5% threshold for detecting HIV drug resistance. There was no statistically significant difference between the results reported by SGS and NGS when using the 20% threshold for reporting resistance mutations. CONCLUSION In this study, we found that next-generation sequencing facilitates a more sensitive detection of HIV-1 drug resistance than SGS. The high prevalence of PDR emphasizes the importance of baseline resistance and assessing the threshold for optimal clinical detection using NGS.
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Affiliation(s)
- Fei Ouyang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Defu Yuan
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Wenjing Zhai
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Shanshan Liu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Ying Zhou
- Department of HIV/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Haitao Yang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
- Jiangsu Health Development Research Center, Nanjing 210029, China
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3
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Montejano R, Dominguez-Dominguez L, de Miguel R, Rial-Crestelo D, Esteban-Cantos A, Aranguren-Rivas P, García-Álvarez M, Alejos B, Bisbal O, Santacreu-Guerrero M, Hernando A, Bermejo-Plaza L, Cadiñanos J, Mayoral M, Castro JM, Moreno V, Martin-Carbonero L, Rodés B, Delgado R, Rubio R, Pulido F, Arribas JR. Detection of archived lamivudine-associated resistance mutations in virologically suppressed, lamivudine-experienced HIV-infected adults by different genotyping techniques (GEN-PRO study). J Antimicrob Chemother 2021; 76:3263-3271. [PMID: 34459889 DOI: 10.1093/jac/dkab323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/04/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Previously selected lamivudine resistance-associated mutations (RAMs) may remain archived within the proviral HIV-DNA. OBJECTIVES To evaluate the ability of proviral DNA genotyping to detect lamivudine RAMs in HIV-1 virologically suppressed participants; the correlation between Sanger and next generation sequencing (NGS); and predictive factors for detection of lamivudine RAMs in proviral DNA. METHODS Cross-sectional study of participants on stable antiretroviral therapy and suppressed for ≥1 year. Analysis of proviral DNA was performed by Sanger sequencing in whole blood and by NGS in PBMCs. RESULTS We analysed samples from 102 subjects (52 with and 50 without lamivudine RAMs in historical plasma RNA-genotypes). Among participants with previous lamivudine resistance, Sanger sequencing detected RAMs in 26.9%. Detection rates significantly increased using NGS: 47.9%, 64.6%, 75% and 87.5% with the 20%, 10%, 5% and 1% thresholds, respectively. As for participants without historical lamivudine resistance, Sanger detected the RAMs in 1/49 (2%), and NGS (5% threshold) in 8/45 (17.8%). Multivariate models fitted to the whole population revealed that having a history of lamivudine resistance was a risk factor for detection of lamivudine RAMs by NGS. Among participants with historical lamivudine resistance, multivariate analysis showed that a longer time since HIV diagnosis was associated with persistence of archived mutations by NGS at thresholds of >10% [OR 1.10 (95% CI: 1.00-1.24)] and >5% [OR 1.16 (95% CI: 1.02-1.32)]. CONCLUSIONS Proviral DNA Sanger sequencing does not detect the majority of historical lamivudine RAMs. NGS increases the sensitivity of detection at lower thresholds, although the relevance of these minority populations with lamivudine RAMs needs further evaluation.
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Affiliation(s)
- Rocio Montejano
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Lourdes Dominguez-Dominguez
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Rosa de Miguel
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - David Rial-Crestelo
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Andrés Esteban-Cantos
- Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Paula Aranguren-Rivas
- Microbiology Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Mónica García-Álvarez
- Microbiology Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Belén Alejos
- Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - Otilia Bisbal
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Mireia Santacreu-Guerrero
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Asunción Hernando
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Laura Bermejo-Plaza
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Julen Cadiñanos
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Mario Mayoral
- HIV Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261 28046, Madrid, Spain
| | - Juan Miguel Castro
- HIV Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261 28046, Madrid, Spain
| | - Victoria Moreno
- HIV Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261 28046, Madrid, Spain
| | - Luz Martin-Carbonero
- HIV Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261 28046, Madrid, Spain
| | - Berta Rodés
- Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Rafael Delgado
- Microbiology Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Rafael Rubio
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Federico Pulido
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - José Ramón Arribas
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
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4
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Mbisa JL, Ledesma J, Kirwan P, Bibby DF, Manso C, Skingsley A, Murphy G, Brown A, Dunn DT, Delpech V, Geretti AM. Surveillance of HIV-1 transmitted integrase strand transfer inhibitor resistance in the UK. J Antimicrob Chemother 2021; 75:3311-3318. [PMID: 32728703 PMCID: PMC7566560 DOI: 10.1093/jac/dkaa309] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Background HIV treatment guidelines have traditionally recommended that all HIV-positive individuals are tested for evidence of drug resistance prior to starting ART. Testing for resistance to reverse transcriptase inhibitors and PIs is well established in routine care. However, testing for integrase strand transfer inhibitor (InSTI) resistance is less consistent. Objectives To inform treatment guidelines by determining the prevalence of InSTI resistance in a national cohort of recently infected individuals. Patients and methods Recent (within 4 months) HIV-1 infections were identified using a Recent Infection Testing Algorithm of new HIV-1 diagnoses in the UK. Resistance-associated mutations (RAMs) in integrase, protease and reverse transcriptase were detected by ultradeep sequencing, which allows for the sensitive estimation of the frequency of each resistant variant in a sample. Results The analysis included 655 randomly selected individuals (median age = 33 years, 95% male, 83% MSM, 78% white) sampled in the period 2014 to 2016 and determined to have a recent infection. These comprised 320, 138 and 197 samples from 2014, 2015 and 2016, respectively. None of the samples had major InSTI RAMs occurring at high variant frequency (≥20%). A subset (25/640, 3.9%) had major InSTI RAMs occurring only as low-frequency variants (2%–20%). In contrast, 47/588 (8.0%) had major reverse transcriptase inhibitor and PI RAMs at high frequency. Conclusions Between 2014 and 2016, major InSTI RAMs were uncommon in adults with recent HIV-1 infection, only occurring as low-frequency variants of doubtful clinical significance. Continued surveillance of newly diagnosed patients for evidence of transmitted InSTI resistance is recommended to inform clinical practice.
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Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Juan Ledesma
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Peter Kirwan
- National Infection Service, Public Health England, London, UK
| | - David F Bibby
- National Infection Service, Public Health England, London, UK
| | - Carmen Manso
- National Infection Service, Public Health England, London, UK
| | | | - Gary Murphy
- National Infection Service, Public Health England, London, UK
| | - Alison Brown
- National Infection Service, Public Health England, London, UK
| | - David T Dunn
- Institute for Global Health, University College London, London, UK
| | - Valerie Delpech
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Anna Maria Geretti
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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5
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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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6
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Mbisa JL, Kirwan P, Tostevin A, Ledesma J, Bibby DF, Brown A, Myers R, Hassan AS, Murphy G, Asboe D, Pozniak A, Kirk S, Gill ON, Sabin C, Delpech V, Dunn DT. Determining the Origins of Human Immunodeficiency Virus Type 1 Drug-resistant Minority Variants in People Who Are Recently Infected Using Phylogenetic Reconstruction. Clin Infect Dis 2020; 69:1136-1143. [PMID: 30534981 PMCID: PMC6743824 DOI: 10.1093/cid/ciy1048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Drug-resistant minority variants (DRMinVs) detected in patients who recently acquired human immunodeficiency virus type 1 (HIV-1) can be transmitted, generated de novo through virus replication, or technical errors. The first form is likely to persist and result in treatment failure, while the latter two could be stochastic and transient. METHODS Ultradeep sequencing of plasma samples from 835 individuals with recent HIV-1 infection in the United Kingdom was performed to detect DRMinVs at a mutation frequency between 2% and 20%. Sequence alignments including >110 000 HIV-1 partial pol consensus sequences from the UK HIV Drug Resistance Database (UK-HDRD), linked to epidemiological and clinical data from the HIV and AIDS Reporting System, were used for transmission cluster analysis. Transmission clusters were identified using Cluster Picker with a clade support of >90% and maximum genetic distances of 4.5% or 1.5%, the latter to limit detection to likely direct transmission events. RESULTS Drug-resistant majority variants (DRMajVs) were detected in 66 (7.9%) and DRMinVs in 84 (10.1%) of the recently infected individuals. High levels of clustering to sequences in UK-HDRD were observed for both DRMajV (n = 48; 72.7%) and DRMinV (n = 63; 75.0%) sequences. Of these, 43 (65.2%) with DRMajVs were in a transmission cluster with sequences that harbored the same DR mutation compared to only 3 (3.6%) sequences with DRMinVs (P < .00001, Fisher exact test). Evidence of likely direct transmission of DRMajVs was observed for 25/66 (37.9%), whereas none were observed for the DRMinVs (P < .00001). CONCLUSIONS Using a densely sampled HIV-infected population, we show no evidence of DRMinV transmission among recently infected individuals.
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Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Peter Kirwan
- National Infection Service, Public Health England, London, United Kingdom
| | - Anna Tostevin
- Institute for Global Health, University College London, London, United Kingdom
| | - Juan Ledesma
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David F Bibby
- National Infection Service, Public Health England, London, United Kingdom
| | - Alison Brown
- National Infection Service, Public Health England, London, United Kingdom
| | - Richard Myers
- National Infection Service, Public Health England, London, United Kingdom
| | - Amin S Hassan
- HIV/STI Group, Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Gary Murphy
- National Infection Service, Public Health England, London, United Kingdom
| | - David Asboe
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Anton Pozniak
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Stuart Kirk
- University College London Hospital, London, United Kingdom
| | - O Noel Gill
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Caroline Sabin
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom.,Institute for Global Health, University College London, London, United Kingdom
| | - Valerie Delpech
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David T Dunn
- Institute for Global Health, University College London, London, United Kingdom
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7
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Zhou S, Sizemore S, Moeser M, Zimmerman S, Samoff E, Mobley V, Frost S, Cressman A, Clark M, Skelly T, Kelkar H, Veluvolu U, Jones C, Eron J, Cohen M, Nelson JAE, Swanstrom R, Dennis AM. Near Real-Time Identification of Recent Human Immunodeficiency Virus Transmissions, Transmitted Drug Resistance Mutations, and Transmission Networks by Multiplexed Primer ID-Next-Generation Sequencing in North Carolina. J Infect Dis 2020; 223:876-884. [PMID: 32663847 DOI: 10.1093/infdis/jiaa417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/13/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The identification of recent human immunodeficiency virus (HIV) 1 infections among people with new HIV diagnoses is important to both tailoring and assessing the impact of HIV-1 prevention strategies. METHODS We developed a multiplexed Primer ID-next-generation sequencing approach to identify recent infections by measuring the intrahost viral diversity over multiple regions of the HIV-1 genome, in addition to detecting drug resistance mutations (DRMs) and phylogenetically linked clusters. We summarize the field implementation of this all-in-one platform among persons with newly diagnosed HIV-1 by the North Carolina State Laboratory of Public Health in 2018. RESULTS Overall, recent infection was identified in 94 (35%) of 268 patients with new HIV diagnoses. People <30 years old, and people who inject drugs were more likely to have diagnoses of recent infection. The reverse-transcriptase region K103N was the most commonly detected DRM (prevalence, approximately 15%). We found a total of 28 clusters, and persons with recent infection were more likely to be cluster members than were those with chronic infections (P = .03). CONCLUSIONS We demonstrate the rapid identification of recent infection and pretreatment DRMs coupled with cluster analysis that will allow prioritization of linkage to care, treatment, and prevention interventions to those at highest risk of onward transmission.
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Affiliation(s)
- Shuntai Zhou
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sabrina Sizemore
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matt Moeser
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Scott Zimmerman
- North Carolina Department of Health and Human Services, Raleigh, North Carolina, USA
| | - Erika Samoff
- North Carolina Department of Health and Human Services, Raleigh, North Carolina, USA
| | - Victoria Mobley
- North Carolina Department of Health and Human Services, Raleigh, North Carolina, USA
| | - Simon Frost
- University of Cambridge, Cambridge, United Kingdom
| | - Andy Cressman
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael Clark
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tara Skelly
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hemant Kelkar
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Umadevi Veluvolu
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corbin Jones
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joseph Eron
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Myron Cohen
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julie A E Nelson
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ronald Swanstrom
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ann M Dennis
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Dolutegravir plus lamivudine for maintenance of HIV viral suppression in adults with and without historical resistance to lamivudine: 48-week results of a non-randomized, pilot clinical trial (ART-PRO). EBioMedicine 2020; 55:102779. [PMID: 32408111 PMCID: PMC7225620 DOI: 10.1016/j.ebiom.2020.102779] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/11/2020] [Accepted: 04/20/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND We investigated the efficacy of a switch to dolutegravir plus lamivudine in aviremic individuals without evidence of persistent lamivudine resistance-associated mutations in baseline proviral DNA population sequencing. METHODS Open-label, single-arm, 48-week pilot trial. HIV-1 infected adults, naïve to integrase inhibitors, with CD4+ above 350 cell/μL and fewer than 50 HIV-1 RNA copies per mL the year prior to study entry switched to dolutegravir plus lamivudine. Participants were excluded if baseline proviral DNA population genotyping detected lamivudine resistance-associated mutations. To detect resistance minority variants, proviral DNA next-generation sequencing was retrospectively performed from baseline samples. Primary efficacy endpoint was proportion of participants with fewer than 50 HIV-1 RNA copies per mL at week 48. Safety and tolerability outcomes were incidence of adverse events and treatment discontinuations. ART-PRO is registered with ClinicalTrials.gov, NCT03539224. FINDINGS 41 participants switched to dolutegravir plus lamivudine, 21 with lamivudine resistance mutations in historical plasma genotypes. Baseline next-generation sequencing detected lamivudine resistance mutations (M184V/I and/or K65R/E/N) over a 5% threshold in 15/21 (71·4%) and 3/20 (15%) of participants with and without history of lamivudine resistance, respectively. At week 48, 92·7% of participants (38/41) had fewer than 50 HIV-1 RNA copies per mL. There were no cases of virologic failure. Three participants with historical lamivudine resistance were prematurely discontinued from the study (2 protocol violations, one adverse event). Ten participants (4 in the group with historical lamivudine resistance) had a transient viral rebound, all resuppressed on dolutegravir plus lamivudine. There were 28 drug-related adverse events, only one leading to discontinuation. INTERPRETATION In this pilot trial, dolutegravir plus lamivudine was effective in maintaining virologic control despite past historical lamivudine resistance and presence of archived lamivudine resistance-associated mutations detected by next generation sequencing. Further studies are needed to confirm our results. FUNDING Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III PI16/00837-PI16/00678.
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Ferretti F, Mackie NE, Singh GKJ, Fox J, Kaye S, McClure MO, Taylor G, Boffito M. Characterization of low level viraemia in HIV-infected patients receiving boosted protease inhibitor-based antiretroviral regimens. HIV Res Clin Pract 2020; 20:107-110. [DOI: 10.1080/25787489.2020.1716159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Francesca Ferretti
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Nicola E. Mackie
- Department of HIV, Sexual Health and Infections, Imperial College Healthcare NHS Trust, London, UK
| | - Gurmit Kaur Jagjit Singh
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Julie Fox
- Guy’s and St Thomas Hospital NHS Foundation Trust, London, UK
| | - Steve Kaye
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Myra O. McClure
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Graham Taylor
- Division of Infectious Diseases, Imperial College London, London, UK
| | - Marta Boffito
- Department of HIV, Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
- Division of Infectious Diseases, Imperial College London, London, UK
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Nguyen T, Fofana DB, Lê MP, Charpentier C, Peytavin G, Wirden M, Lambert-Niclot S, Desire N, Grude M, Morand-Joubert L, Flandre P, Katlama C, Descamps D, Calvez V, Todesco E, Marcelin AG. Prevalence and clinical impact of minority resistant variants in patients failing an integrase inhibitor-based regimen by ultra-deep sequencing. J Antimicrob Chemother 2019; 73:2485-2492. [PMID: 29873733 DOI: 10.1093/jac/dky198] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
Background Integrase strand transfer inhibitors (INSTIs) are recommended by international guidelines as first-line therapy in antiretroviral-naive and -experienced HIV-1-infected patients. Objectives This study aimed at evaluating the prevalence at failure of INSTI-resistant variants and the impact of baseline minority resistant variants (MiRVs) on the virological response to an INSTI-based regimen. Methods Samples at failure of 134 patients failing a raltegravir-containing (n = 65), an elvitegravir-containing (n = 20) or a dolutegravir-containing (n = 49) regimen were sequenced by Sanger sequencing and ultra-deep sequencing (UDS). Baseline samples of patients with virological failure (VF) (n = 34) and of those with virological success (VS) (n = 31) under INSTI treatment were sequenced by UDS. Data were analysed using the SmartGene platform, and resistance was interpreted according to the ANRS algorithm version 27. Results At failure, the prevalence of at least one INSTI-resistant variant was 39.6% by Sanger sequencing and 57.5% by UDS, changing the interpretation of resistance in 17/134 (13%) patients. Among 53 patients harbouring at least one resistance mutation detected by both techniques, the most dominant INSTI resistance mutations were N155H (45%), Q148H/K/R (23%), T97A (19%) and Y143C (11%). There was no difference in prevalence of baseline MiRVs between patients with VF and those with VS. MiRVs found at baseline in patients with VF were not detected at failure either in majority or minority mutations. Conclusions UDS is more sensitive than Sanger sequencing at detecting INSTI MiRVs at treatment failure. The presence of MiRVs at failure could be important to the decision to switch to other INSTIs. However, there was no association between the presence of baseline MiRVs and the response to INSTI-based therapies in our study.
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Affiliation(s)
- T Nguyen
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - D B Fofana
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - M P Lê
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Département de Pharmaco-Toxicologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - C Charpentier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - G Peytavin
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Département de Pharmaco-Toxicologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - M Wirden
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - S Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - N Desire
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - M Grude
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), F-75013 Paris, France
| | - L Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, F-75012 Paris, France
| | - P Flandre
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), F-75013 Paris, France
| | - C Katlama
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de maladies infectieuses, F-75013 Paris, France
| | - D Descamps
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - V Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - E Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - A G Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
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Storto A, Visseaux B, Bertine M, Le Hingrat Q, Collin G, Damond F, Khuong MA, Blum L, Tubiana R, Karmochkine M, Cazanave C, Matheron S, Descamps D, Charpentier C. Minority resistant variants are also present in HIV-2-infected antiretroviral-naive patients. J Antimicrob Chemother 2019; 73:1173-1176. [PMID: 29415189 DOI: 10.1093/jac/dkx530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 12/14/2017] [Indexed: 12/26/2022] Open
Abstract
Objectives To assess the prevalence of minority resistant variants (MRV) and X4-tropic minority variants in ART-naive HIV-2-infected patients. Patients and methods ART-naive HIV-2-infected patients with detectable plasma viral load (>100 copies/mL) included in the ANRS HIV-2 CO5 Cohort were assessed. We performed ultra-deep sequencing (UDS) of protease, RT, integrase and gp105 regions. Only mutations in the HIV-2 ANRS list >1% were considered. HIV-2 tropism was assessed by V3 loop region UDS, and each read was interpreted with determinants of CXCR4-coreceptor use. Results Among the 47 patients assessed, three displayed plasma viruses with a resistance-associated mutation (RAM) above the 20% detection threshold, all in RT, resulting in a prevalence of transmitted drug resistance for NRTI of 7.9% (95% CI 0.0%-16.5%). No RAM above the 20% detection threshold was found in protease or integrase. At the 1% detection threshold the transmitted drug resistance prevalence was 9.8% (95% CI 0.6%-19.0%), 13.2% (95% CI 3.5%-22.9%) and 4.5% (95% CI 0%-17.5%) for PI, NRTI and integrase inhibitors. The most prevalent MRV was the PI RAM I50V detected in three samples. Tropism analysis showed that 21% of patients (4 of 19) exhibited X4-tropic viruses: two in majority proportion and two in minority proportions (1.5% and 1.9%). Conclusions In this first study assessing the prevalence of MRV in HIV-2 infection among ART-naive patients, we observed a 2-3-fold higher prevalence of RAM when a 1% detection threshold of mutations was used compared with a 20% threshold. Similarly, the proportion of patients with X4-tropic viruses was twice as high when UDS was used.
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Affiliation(s)
- Alexandre Storto
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Benoit Visseaux
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Mélanie Bertine
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Quentin Le Hingrat
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Gilles Collin
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Florence Damond
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Marie-Aude Khuong
- Service de Maladies Infectieuses et Tropicales, Centre Hospitalier de Saint Denis, Saint-Denis, France
| | - Laurent Blum
- Service de pathologies infectieuses, VIH, Centre Hospitalier René Dubos, Pontoise, France
| | - Roland Tubiana
- Department of Infectious Diseases, AP-HP Hôpital Pitié-Salpêtrière, Paris, Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France
| | - Marina Karmochkine
- Service d'Immunologie Clinique, Hôpital Européen Georges Pompidou, Paris, France
| | - Charles Cazanave
- CHU Bordeaux, Services des Maladies Infectieuses et Tropicales, Bordeaux, France
| | - Sophie Matheron
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - Diane Descamps
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Charlotte Charpentier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
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Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors. J Clin Microbiol 2018; 56:JCM.01443-18. [PMID: 30305383 PMCID: PMC6258839 DOI: 10.1128/jcm.01443-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/02/2018] [Indexed: 02/02/2023] Open
Abstract
HIV drug resistance genotyping is a critical tool in the clinical management of HIV infections. Although resistance genotyping has traditionally been conducted using Sanger sequencing, next-generation sequencing (NGS) is emerging as a powerful tool due to its ability to detect low-frequency alleles. HIV drug resistance genotyping is a critical tool in the clinical management of HIV infections. Although resistance genotyping has traditionally been conducted using Sanger sequencing, next-generation sequencing (NGS) is emerging as a powerful tool due to its ability to detect low-frequency alleles. However, the clinical value added from NGS approaches to antiviral resistance testing remains to be demonstrated. We compared the variant detection capacity of NGS versus Sanger sequencing methods for resistance genotyping in 144 drug resistance tests (105 protease-reverse transcriptase tests and 39 integrase tests) submitted to our clinical virology laboratory over a four-month period in 2016 for Sanger-based HIV drug resistance testing. NGS detected all true high-frequency drug resistance mutations (>20% frequency) found by Sanger sequencing, with greater accuracy in one instance of a Sanger-detected false positive. Freely available online NGS variant callers HyDRA and PASeq were superior to Sanger methods for interpretations of allele linkage and automated variant calling. NGS additionally detected low-frequency mutations (1 to 20% frequency) associated with higher levels of drug resistance in 30/105 (29%) protease-reverse transcriptase tests and 4/39 (10%) integrase tests. In clinical follow-up of 69 individuals for a median of 674 days, we did not find a difference in rates of virological failure between individuals with and without low-frequency mutations, although rates of virological failure were higher for individuals with drug-relevant low-frequency mutations. However, all 27 individuals who experienced virological failure reported poor adherence to their drug regimen during the preceding follow-up time, and all 19 who subsequently improved their adherence achieved viral suppression at later time points, consistent with a lack of clinical resistance. In conclusion, in a population with low antiviral resistance emergence, NGS methods detected numerous instances of minor alleles that did not result in subsequent bona fide virological failure due to antiviral resistance.
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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: 52] [Impact Index Per Article: 8.7] [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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