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Point-of-Care Tests for HIV Drug Resistance Monitoring: Advances and Potentials. Pathogens 2022; 11:pathogens11070724. [PMID: 35889970 PMCID: PMC9321160 DOI: 10.3390/pathogens11070724] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 01/25/2023] Open
Abstract
HIV/AIDS is a global public health crisis that is yet to be contained. Effective management of HIV drug resistance (HIVDR) supported by close resistance monitoring is essential in achieving the WHO 95-95-95 targets, aiming to end the AIDS epidemic by 2030. Point-of-care tests (POCT) enable decentralized HIVDR testing with a short turnaround time and minimal instrumental requirement, allowing timely initiation of effective antiretroviral therapy (ART) and regimen adjustment as needed. HIVDR POCT is of particular significance in an era when ART access is scaling up at a global level and enhanced HIVDR monitoring is urgently needed, especially for low-to-middle-income countries. This article provides an overview of the currently available technologies that have been applied or potentially used in HIVDR POCT. It may also benefit the continued research and development efforts toward more innovative HIVDR diagnostics.
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2
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Gomez-Martinez J, Foulongne V, Laureillard D, Nagot N, Montès B, Cantaloube JF, Van de Perre P, Fournier-Wirth C, Molès JP, Brès JC. Near-point-of-care assay with a visual readout for detection of HIV-1 drug resistance mutations: A proof-of-concept study. Talanta 2021; 231:122378. [PMID: 33965042 DOI: 10.1016/j.talanta.2021.122378] [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: 01/08/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 11/25/2022]
Abstract
Human immunodeficiency virus (HIV) infection is a chronic disease that can be treated with antiretroviral (ARV) therapy. However, the success of this treatment has been jeopardized by the emergence of HIV infections resistant to ARV drugs. In low-to middle-income countries (LMICs), where transmission of resistant viruses has increased over the past decade, there is an urgent need to improve access to HIV drug resistance testing. Here, we present a proof-of-concept study of a rapid and simple molecular method to detect two major mutations (K103 N, Y181C) conferring resistance to first-line nonnucleoside reverse transcriptase inhibitor regimens. Our near-point-of-care (near-POC) diagnostic test, combining a sequence-specific primer extension and a lateral flow DNA microarray strip, allows visual detection of HIV drug resistance mutations (DRM) in a short turnaround time (4 h 30). The assay has a limit of detection of 100 copies of plasmid DNA and has a higher sensitivity than standard Sanger sequencing. The analytical performance was assessed by use of 16 plasma samples from individuals living with HIV-1 and results demonstrated the specificity and the sensitivity of this approach for multiplex detection of the two DRMs in a single test. Furthermore, this near-POC assay could be easily taylored to detect either new DRMs or DRM of from various HIV clades and might be useful for pre-therapy screening in LMICs with high levels of transmitted drug resistance.
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Affiliation(s)
- Julien Gomez-Martinez
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France
| | - Vincent Foulongne
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France; Laboratoire de Virologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Didier Laureillard
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France; Department of Infectious and Tropical Diseases, Centre Hospitalier Universitaire Carémeau, Nîmes, France
| | - Nicolas Nagot
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France
| | - Brigitte Montès
- Laboratoire de Virologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Jean-François Cantaloube
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France
| | - Chantal Fournier-Wirth
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France
| | - Jean-Charles Brès
- Pathogenesis and Control of Chronic and Emerging Infections, EFS, Inserm, University of Montpellier, F-34394, Montpellier, France.
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3
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Zuo L, Peng K, Hu Y, Xu Q. Genotypic Methods for HIV Drug Resistance Monitoring: The Opportunities and Challenges Faced by China. Curr HIV Res 2020; 17:225-239. [PMID: 31560290 DOI: 10.2174/1570162x17666190927154110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/05/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022]
Abstract
AIDS is a globalized infectious disease. In 2014, UNAIDS launched a global project of "90-90-90" to end the HIV epidemic by 2030. The second and third 90 require 90% of HIV-1 infected individuals receiving antiretroviral therapy (ART) and durable virological suppression. However, wide use of ART will greatly increase the emergence and spreading of HIV drug resistance and current HIV drug resistance test (DRT) assays in China are seriously lagging behind, hindering to achieve virological suppression. Therefore, recommending an appropriate HIV DRT method is critical for HIV routine surveillance and prevention in China. In this review, we summarized the current existing HIV drug resistance genotypic testing methods around the world and discussed the advantages and disadvantages of these methods.
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Affiliation(s)
- Lulu Zuo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212002, China.,Pathogen Discovery & Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences; Shanghai 200031, China
| | - Ke Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yihong Hu
- Pathogen Discovery & Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences; Shanghai 200031, China
| | - Qinggang Xu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212002, China
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4
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Panpradist N, Beck IA, Vrana J, Higa N, McIntyre D, Ruth PS, So I, Kline EC, Kanthula R, Wong-On-Wing A, Lim J, Ko D, Milne R, Rossouw T, Feucht UD, Chung M, Jourdain G, Ngo-Giang-Huong N, Laomanit L, Soria J, Lai J, Klavins ED, Frenkel LM, Lutz BR. OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories. EBioMedicine 2019; 50:34-44. [PMID: 31767540 PMCID: PMC6921160 DOI: 10.1016/j.ebiom.2019.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/21/2023] Open
Abstract
Background HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels. Methods The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated on 672 codons (168 specimens) from subtypes A, B, C, D, and AE. The kit uses dry reagents to facilitate assay setup, lateral flow devices for visual HIVDR detections, and in-house software with an interface for guiding users and analyzing results. Findings HIVDR analysis of specimens by OLA-Simple compared to Sanger sequencing revealed 99.6 ± 0.3% specificity and 98.2 ± 0.9% sensitivity, and compared to high-sensitivity assays, 99.6 ± 0.6% specificity and 86.2 ± 2.5% sensitivity, with 2.6 ± 0.9% indeterminate results. OLA-Simple was performed more rapidly compared to Sanger sequencing (<4 h vs. 35–72 h). Forty-one untrained volunteers blindly tested two specimens each with 96.8 ± 0.8% accuracy. Interpretation OLA-Simple compares favorably with HIVDR genotyping by Sanger and sensitive comparators. Instructional software enabled inexperienced, first-time users to perform the assay with high accuracy. The reduced complexity, cost, and training requirements of OLA-Simple could improve access to HIVDR testing in low-resource settings and potentially allow same-day selection of appropriate antiretroviral therapy. Fund USA National Institutes of Health R01; the Clinical and Retrovirology Research Core and the Molecular Profiling and Computational Biology Core of the UW CFAR; Seattle Children's Research Institute; UW Holloman Innovation Challenge Award; Pilcher Faculty Fellowship.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Global WACh Program, Department of Global Health, University of Washington, Seattle, WA 98104, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Justin Vrana
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Nikki Higa
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - David McIntyre
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Parker S Ruth
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Isaac So
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Enos C Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ruth Kanthula
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Medstar Georgetown University Hospital, DC, 20007, USA
| | - Annie Wong-On-Wing
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Jonathan Lim
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Daisy Ko
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ross Milne
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Theresa Rossouw
- Department of Immunology, University of Pretoria, Pretoria 0002, South Africa
| | - Ute D Feucht
- Research Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, Department of Paediatrics, University of Pretoria, Pretoria 0002, South Africa; Research Unit for Maternal and Infant Health Care Strategies, South African Medical Research Council, Kalafong Hospital, Atteridgeville 0008, South Africa
| | - Michael Chung
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Gonzague Jourdain
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Laddawan Laomanit
- Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Jaime Soria
- Department of Infectious Diseases, Hospital Nacional Dos de Mayo, Av. Miguel Grau 13, Cercado de Lima 15003, Peru
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Eric D Klavins
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Virology, Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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5
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Clutter DS, Mazarei G, Sinha R, Manasa J, Nouhin J, LaPrade E, Bolouki S, Tzou PL, Hannita-Hui J, Sahoo MK, Kuimelis P, Kuimelis RG, Pinsky BA, Schoolnik GK, Hassibi A, Shafer RW. Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance. J Mol Diagn 2019; 21:580-592. [PMID: 31026601 DOI: 10.1016/j.jmoldx.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/05/2019] [Accepted: 02/19/2019] [Indexed: 11/16/2022] Open
Abstract
A point-of-care HIV-1 genotypic resistance assay that could be performed during a clinic visit would enable care providers to make informed treatment decisions for patients starting therapy or experiencing virologic failure on therapy. The main challenge for such an assay is the genetic variability at and surrounding each drug-resistance mutation (DRM). We analyzed a database of diverse global HIV sequences and used thermodynamic simulations to design an array of surface-bound oligonucleotide probe sets with each set sharing distinct 5' and 3' flanking sequences but having different centrally located nucleotides complementary to six codons at HIV-1 DRM reverse transcriptase position 103: AAA, AAC, AAG, AAT, AGA, and AGC. We then performed in vitro experiments using 80-mer oligonucleotides and PCR-amplified DNA from clinical plasma HIV-1 samples and culture supernatants that contained subtype A, B, C, D, CRF01_AE, and CRF02_AG viruses. Multiplexed solid-phase melt curve analysis discriminated perfectly among each of the six reported reverse transcriptase position 103 codons in both 80-mers and clinical samples. The sensitivity and specificity for detecting targets that contained AAC mixed with targets that contained AAA were >98% when AAC was present at a proportion of ≥10%. Multiplexed solid-phase melt curve analysis is a promising approach for developing point-of-care assays to distinguish between different codons in genetically variable regions such as those surrounding HIV-1 DRMs.
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Affiliation(s)
- Dana S Clutter
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | | | | | - Justen Manasa
- African Institute of Biomedical Science and Technology, Harare, Zimbabwe
| | - Janin Nouhin
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | - Ellen LaPrade
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Philip L Tzou
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | - Jessica Hannita-Hui
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | - Malaya K Sahoo
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | | | | | - Benjamin A Pinsky
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | | | | | - Robert W Shafer
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California.
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6
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Reslova N, Huvarova V, Hrdy J, Kasny M, Kralik P. A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay. Sci Rep 2019; 9:2719. [PMID: 30804418 PMCID: PMC6389906 DOI: 10.1038/s41598-019-40035-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/06/2019] [Indexed: 12/28/2022] Open
Abstract
Multiplex oligonucleotide ligation-PCR (MOL-PCR) is a rapid method for simultaneous detection of multiple molecular markers within a single reaction. MOL-PCR is increasingly employed in microbial detection assays, where its ability to facilitate identification and further characterization via simple analysis is of great benefit and significantly simplifies routine diagnostics. When adapted to microsphere suspension arrays on a MAGPIX reader, MOL-PCR has the potential to outperform standard nucleic acid-based diagnostic assays. This study represents the guideline towards in-house MOL-PCR assay optimization using the example of foodborne pathogens (bacteria and parasites) with an emphasis on the appropriate choice of crucial parameters. The optimized protocol focused on specific sequence detection utilizes the fluorescent reporter BODIPY-TMRX and self-coupled magnetic microspheres and allows for a smooth and brisk workflow which should serve as a guide for the development of MOL-PCR assays intended for pathogen detection.
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Affiliation(s)
- Nikol Reslova
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic. .,Faculty of Science, Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Veronika Huvarova
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic.,Faculty of Science, Department of Experimental Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jakub Hrdy
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic.,Faculty of Science, Department of Experimental Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Martin Kasny
- Faculty of Science, Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Petr Kralik
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic
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Abstract
HIV diagnostics have played a central role in the remarkable progress in identifying, staging, initiating, and monitoring infected individuals on life-saving antiretroviral therapy. They are also useful in surveillance and outbreak responses, allowing for assessment of disease burden and identification of vulnerable populations and transmission "hot spots," thus enabling planning, appropriate interventions, and allocation of appropriate funding. HIV diagnostics are critical in achieving epidemic control and require a hybrid of conventional laboratory-based diagnostic tests and new technologies, including point-of-care (POC) testing, to expand coverage, increase access, and positively impact patient management. In this review, we provide (i) a historical perspective on the evolution of HIV diagnostics (serologic and molecular) and their interplay with WHO normative guidelines, (ii) a description of the role of conventional and POC testing within the tiered laboratory diagnostic network, (iii) information on the evaluations and selection of appropriate diagnostics, (iv) a description of the quality management systems needed to ensure reliability of testing, and (v) strategies to increase access while reducing the time to return results to patients. Maintaining the central role of HIV diagnostics in programs requires periodic monitoring and optimization with quality assurance in order to inform adjustments or alignment to achieve epidemic control.
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8
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Duarte HA, Panpradist N, Beck IA, Lutz B, Lai J, Kanthula RM, Kantor R, Tripathi A, Saravanan S, MacLeod IJ, Chung MH, Zhang G, Yang C, Frenkel LM. Current Status of Point-of-Care Testing for Human Immunodeficiency Virus Drug Resistance. J Infect Dis 2017; 216:S824-S828. [PMID: 29040621 DOI: 10.1093/infdis/jix413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Healthcare delivery has advanced due to the implementation of point-of-care testing, which is often performed within minutes to hours in minimally equipped laboratories or at home. Technologic advances are leading to point-of-care kits that incorporate nucleic acid-based assays, including polymerase chain reaction, isothermal amplification, ligation, and hybridization reactions. As a limited number of single-nucleotide polymorphisms are associated with clinically significant human immunodeficiency virus (HIV) drug resistance, assays to detect these mutations have been developed. Early versions of these assays have been used in research. This review summarizes the principles underlying each assay and discusses strategic needs for their incorporation into the management of HIV infection.
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Affiliation(s)
| | | | | | - Barry Lutz
- Department of Bioengineering, University of Washington
| | - James Lai
- Department of Bioengineering, University of Washington
| | - Ruth M Kanthula
- Department of Pediatrics, Division of Infectious Diseases
- Seattle Children's Research Instituten
| | - Rami Kantor
- Department of Medicine, Division of Infectious Diseases
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering
- Alpert Medical School, Divisions of Biology and Medicine, Brown University, Providence
| | | | - Iain J MacLeod
- Aldatu Biosciences, Harvard Life Lab
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health
| | - Michael H Chung
- Department of Global Health
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington
| | - Guoqing Zhang
- Center for Global Health, Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention
| | - Chunfu Yang
- Center for Global Health, Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention
| | - Lisa M Frenkel
- Department of Pediatrics, Division of Infectious Diseases
- Seattle Children's Research Instituten
- Department of Global Health
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington
- Department of Laboratory Medicine, Division of Virology, University of Washington
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9
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Martín V, Perales C, Fernández-Algar M, Dos Santos HG, Garrido P, Pernas M, Parro V, Moreno M, García-Pérez J, Alcamí J, Torán JL, Abia D, Domingo E, Briones C. An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies. PLoS One 2016; 11:e0166902. [PMID: 27959928 PMCID: PMC5154500 DOI: 10.1371/journal.pone.0166902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023] Open
Abstract
The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice. Here we describe the development and testing of a HIV-1 genotyping DNA microarray that detects and quantifies, in majority and minority viral subpopulations, relevant mutations and amino acid insertions in 42 codons of the pol gene associated with drug- and multidrug-resistance to protease (PR) and reverse transcriptase (RT) inhibitors. A customized bioinformatics protocol has been implemented to analyze the microarray hybridization data by including a new normalization procedure and a stepwise filtering algorithm, which resulted in the highly accurate (96.33%) detection of positive/negative signals. This microarray has been tested with 57 subtype B HIV-1 clinical samples extracted from multi-treated patients, showing an overall identification of 95.53% and 89.24% of the queried PR and RT codons, respectively, and enough sensitivity to detect minority subpopulations representing as low as 5–10% of the total quasispecies. The developed genotyping platform represents an efficient diagnostic and prognostic tool useful to personalize antiviral treatments in clinical practice.
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Affiliation(s)
- Verónica Martín
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d’Hebron Institut de Recerca-Hospital Universitari Vall d´Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona. Barcelona, Spain
| | - María Fernández-Algar
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Helena G. Dos Santos
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Patricia Garrido
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - María Pernas
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Miguel Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
| | - Javier García-Pérez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - José Alcamí
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - José Luis Torán
- Biotherapix, SLU. Parque Tecnológico de Madrid, Tres Cantos, Madrid. Spain
| | - David Abia
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO, CSIC-UAM). Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
- Department of Molecular Evolution, Centro de Astrobiología (CAB, CSIC-INTA). Torrejón de Ardoz, Madrid, Spain
- * E-mail:
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10
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HIV-1 drug resistance and resistance testing. INFECTION GENETICS AND EVOLUTION 2016; 46:292-307. [PMID: 27587334 DOI: 10.1016/j.meegid.2016.08.031] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
The global scale-up of antiretroviral (ARV) therapy (ART) has led to dramatic reductions in HIV-1 mortality and incidence. However, HIV drug resistance (HIVDR) poses a potential threat to the long-term success of ART and is emerging as a threat to the elimination of AIDS as a public health problem by 2030. In this review we describe the genetic mechanisms, epidemiology, and management of HIVDR at both individual and population levels across diverse economic and geographic settings. To describe the genetic mechanisms of HIVDR, we review the genetic barriers to resistance for the most commonly used ARVs and describe the extent of cross-resistance between them. To describe the epidemiology of HIVDR, we summarize the prevalence and patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in both high-income and low- and middle-income countries (LMICs). We also review to two categories of HIVDR with important public health relevance: (i) pre-treatment drug resistance (PDR), a World Health Organization-recommended HIVDR surveillance metric and (ii) and pre-exposure prophylaxis (PrEP)-related drug resistance, a type of ADR that can impact clinical outcomes if present at the time of treatment initiation. To summarize the implications of HIVDR for patient management, we review the role of genotypic resistance testing and treatment practices in both high-income and LMIC settings. In high-income countries where drug resistance testing is part of routine care, such an understanding can help clinicians prevent virological failure and accumulation of further HIVDR on an individual level by selecting the most efficacious regimens for their patients. Although there is reduced access to diagnostic testing and to many ARVs in LMIC, understanding the scientific basis and clinical implications of HIVDR is useful in all regions in order to shape appropriate surveillance, inform treatment algorithms, and manage difficult cases.
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Inzaule SC, Ondoa P, Peter T, Mugyenyi PN, Stevens WS, de Wit TFR, Hamers RL. Affordable HIV drug-resistance testing for monitoring of antiretroviral therapy in sub-Saharan Africa. THE LANCET. INFECTIOUS DISEASES 2016; 16:e267-e275. [PMID: 27569762 DOI: 10.1016/s1473-3099(16)30118-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/28/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022]
Abstract
Increased provision of antiretroviral therapy in sub-Saharan Africa has led to a growing number of patients with therapy failure and acquired drug-resistant HIV, driving the demand for more costly further lines of antiretroviral therapy. In conjunction with accelerated access to viral load monitoring, feasible and affordable technologies to detect drug-resistant HIV could help maximise the durability and rational use of available drug regimens. Potential low-cost technologies include in-house Sanger and next-generation sequencing in centralised laboratories, and point mutation assays and genotype-free systems that predict response to antiretroviral therapy at point-of-care. Strengthening of centralised high-throughput laboratories, including efficient systems for sample referral and results delivery, will increase economies-of-scale while reducing costs. Access barriers can be mitigated by standardisation of in-house assays into commercial kits, use of polyvalent instruments, and adopting price-reducing strategies. A stepwise rollout approach should improve feasibility, prioritising WHO-recommended population-based surveillance and management of complex patient categories, such as patients failing protease inhibitor-based antiretroviral therapy. Implementation research, adaptations of existing WHO guidance, and political commitment, will be key to support the appropriate investments and policy changes. In this Personal View, we discuss the potential role of HIV drug resistance testing for population-based surveillance and individual patient management in sub-Saharan Africa. We review the strengths and challenges of promising low-cost technologies and how they can be implemented.
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Affiliation(s)
- Seth C Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Pascale Ondoa
- Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Trevor Peter
- African Society for Laboratory Medicine, Addis Abeba, Ethiopia; Clinton Health Access Initiative, Gaborone, Botswana
| | | | - Wendy S Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Tobias F Rinke de Wit
- Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Raph L Hamers
- Department of Global Health and Department of Internal Medicine, Division of Infectious Diseases, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands.
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Rapid and Simultaneous Detection of Major Drug Resistance Mutations in Reverse Transcriptase Gene for HIV-1 CRF01_AE, CRF07_BC and Subtype B in China Using Sequenom MassARRAY® System. PLoS One 2016; 11:e0153641. [PMID: 27092551 PMCID: PMC4836728 DOI: 10.1371/journal.pone.0153641] [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: 11/29/2015] [Accepted: 04/01/2016] [Indexed: 01/10/2023] Open
Abstract
The development of a rapid, high-throughput and cost-effective HIV-1 drug resistance (HIV-DR) testing system is a challenge for areas consisting different HIV-1 strains. In this study, we established a broadly reactive multiplex assay that could simultaneously detect major drug resistance mutations at 8 loci, which are associated with resistance to commonly used nucleoside reverse transcriptase inhibitors (NRTIs) and Non-nucleoside reverse transcriptase inhibitors (NNRTIs), in specimens of HIV-1 CRF01_AE, CRF07_BC and subtype B, the three major circulating strains in China, using the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) provided by Sequenom MassARRAY® system. To establish the assay, pol gene fragments were prepared from the plasma viral RNA of 159 patients by nested PCR and the presence of wild type and mutant alleles at the 8 loci were analyzed by MALDI-TOF MS. In terms of loci, the detection rate of the alleles was greater than 97% for M41L, K65R, M184V and G190A, 91.2% for K101E/Q/P, 91.2% for T215F/Y, 89.9% for K103N/S and 80.5% for L210W. In terms of individuals, 80% of the alleles were detected in 95.4% CRF01_AE patients, 100% CRF07_BC patients and 83.3% subtype B patients. Importantly, the MALDI-TOF MS results were concordant to the drug resistance profiles of patients obtained from conventional sequencing analysis after excluded the failed detections. Using plasmid templates, the assay was estimated to be sensitive to detect drug resistant variants at level about 20% of the circulating viral population. The capability of this assay to detect mixed viral populations was further verified by two different patient specimens. In conclusion, this study evaluated the use of Sequenom MassARRAY® system for high-throughput detection of HIV-DR mutations towards the commonly used reverse transcriptase inhibitors in China.
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13
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Clutter DS, Rojas Sánchez P, Rhee SY, Shafer RW. Genetic Variability of HIV-1 for Drug Resistance Assay Development. Viruses 2016; 8:v8020048. [PMID: 26875985 PMCID: PMC4776203 DOI: 10.3390/v8020048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 12/17/2022] Open
Abstract
A hybridization-based point-of-care (POC) assay for HIV-1 drug resistance would be useful in low- and middle-income countries (LMICs) where resistance testing is not routinely available. The major obstacle in developing such an assay is the extreme genetic variability of HIV-1. We analyzed 27,203 reverse transcriptase (RT) sequences from the Stanford HIV Drug Resistance Database originating from six LMIC regions. We characterized the variability in a 27-nucleotide window surrounding six clinically important drug resistance mutations (DRMs) at positions 65, 103, 106, 181, 184, and 190. The number of distinct codons at each DRM position ranged from four at position 184 to 11 at position 190. Depending on the mutation, between 11 and 15 of the 24 flanking nucleotide positions were variable. Nonetheless, most flanking sequences differed from a core set of 10 flanking sequences by just one or two nucleotides. Flanking sequence variability was also lower in each LMIC region compared with overall variability in all regions. We also describe an online program that we developed to perform similar analyses for mutations at any position in RT, protease, or integrase.
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Affiliation(s)
- Dana S Clutter
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, L-134, Stanford, CA 94035, USA.
| | - Patricia Rojas Sánchez
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBER-ESP, Madrid 28034, Spain.
| | - Soo-Yon Rhee
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, L-134, Stanford, CA 94035, USA.
| | - Robert W Shafer
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, L-134, Stanford, CA 94035, USA.
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14
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Rhee SY, Jordan MR, Raizes E, Chua A, Parkin N, Kantor R, Van Zyl GU, Mukui I, Hosseinipour MC, Frenkel LM, Ndembi N, Hamers RL, Rinke de Wit TF, Wallis CL, Gupta RK, Fokam J, Zeh C, Schapiro JM, Carmona S, Katzenstein D, Tang M, Aghokeng AF, De Oliveira T, Wensing AMJ, Gallant JE, Wainberg MA, Richman DD, Fitzgibbon JE, Schito M, Bertagnolio S, Yang C, Shafer RW. HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing. PLoS One 2015; 10:e0145772. [PMID: 26717411 PMCID: PMC4696791 DOI: 10.1371/journal.pone.0145772] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 12/08/2015] [Indexed: 01/10/2023] Open
Abstract
The increasing prevalence of acquired and transmitted HIV-1 drug resistance is an obstacle to successful antiretroviral therapy (ART) in the low- and middle-income countries (LMICs) hardest hit by the HIV-1 pandemic. Genotypic drug resistance testing could facilitate the choice of initial ART in areas with rising transmitted drug resistance (TDR) and enable care-providers to determine which individuals with virological failure (VF) on a first- or second-line ART regimen require a change in treatment. An inexpensive near point-of-care (POC) genotypic resistance test would be useful in settings where the resources, capacity, and infrastructure to perform standard genotypic drug resistance testing are limited. Such a test would be particularly useful in conjunction with the POC HIV-1 viral load tests that are currently being introduced in LMICs. A POC genotypic resistance test is likely to involve the use of allele-specific point mutation assays for detecting drug-resistance mutations (DRMs). This study proposes that two major nucleoside reverse transcriptase inhibitor (NRTI)-associated DRMs (M184V and K65R) and four major NNRTI-associated DRMs (K103N, Y181C, G190A, and V106M) would be the most useful for POC genotypic resistance testing in LMIC settings. One or more of these six DRMs was present in 61.2% of analyzed virus sequences from ART-naïve individuals with intermediate or high-level TDR and 98.8% of analyzed virus sequences from individuals on a first-line NRTI/NNRTI-containing regimen with intermediate or high-level acquired drug resistance. The detection of one or more of these DRMs in an ART-naïve individual or in a individual with VF on a first-line NRTI/NNRTI-containing regimen may be considered an indication for a protease inhibitor (PI)-containing regimen or closer virological monitoring based on cost-effectiveness or country policy.
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Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - Michael R. Jordan
- Tufts University School of Medicine, Boston, MA, United States of America
| | - Elliot Raizes
- Division of Global HIV/AIDS, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Arlene Chua
- Medecins Sans Frontieres, Access Campaign, Geneva, Switzerland
- Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Neil Parkin
- Data First Consulting, Belmont, CA, United States of America
| | - Rami Kantor
- Alpert Medical School, Brown University, Providence, RI, United States of America
| | - Gert U. Van Zyl
- National Health Laboratory Service, Tygerberg, Coastal Branch, South Africa
- Division of Medical Virology, Stellenbosch University, Parow, South Africa
| | - Irene Mukui
- National AIDS and Sexually Transmitted Infection (STI) Control Programme, Ministry of Health, Nairobi, Kenya
| | | | - Lisa M. Frenkel
- University of Washington and Seattle Children’s Research Institute, Seattle, WA, United States of America
| | | | - Raph L. Hamers
- Amsterdam Institute for Global Health and Development (AIGHD), Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands
| | - Tobias F. Rinke de Wit
- Amsterdam Institute for Global Health and Development (AIGHD), Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands
| | | | - Ravindra K. Gupta
- Department of Infection, University College London, London, United Kingdom
| | - Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences (FMBS) of the University of Yaounde 1, Yaounde, Cameroon
| | - Clement Zeh
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Sergio Carmona
- Department of Haematology and Molecular Medicine, University of Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - David Katzenstein
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - Michele Tang
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | | | - Tulio De Oliveira
- Africa Centre for Health and Population Studies, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Annemarie M. J. Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joel E. Gallant
- Southwest CARE Center, Santa Fe, NM, United States of America
| | - Mark A. Wainberg
- McGill University AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Douglas D. Richman
- Department of Pathology, University of California San Diego, La Jolla, CA, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, CA, United States of America
| | - Joseph E. Fitzgibbon
- Drug Development and Clinical Sciences Branch, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Marco Schito
- HJF-DAIDS, A Division of The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | | | - Chunfu Yang
- Division of Global HIV/AIDS, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, CA, United States of America
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Simultaneous Detection of Major Drug Resistance Mutations of HIV-1 Subtype B Viruses from Dried Blood Spot Specimens by Multiplex Allele-Specific Assay. J Clin Microbiol 2015; 54:220-2. [PMID: 26560533 DOI: 10.1128/jcm.02833-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/02/2015] [Indexed: 02/02/2023] Open
Abstract
A multiplex allele-specific (MAS) assay has been developed for the detection of HIV-1 subtype C drug resistance mutations (DRMs). We have optimized the MAS assay to determine subtype B DRMs in dried blood spots (DBS) collected from patients on antiretroviral therapy. The new assay accurately detected DRMs, including low-abundance mutations that were often missed by Sanger sequencing.
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16
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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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Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering. J Clin Microbiol 2015; 53:2581-92. [PMID: 26041893 DOI: 10.1128/jcm.00756-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022] Open
Abstract
The goal of the study was to improve the methodology of HIV genotyping for analysis of HIV drug resistance and HIV clustering. Using the protocol of Gall et al. (A. Gall, B. Ferns, C. Morris, S. Watson, M. Cotten, M. Robinson, N. Berry, D. Pillay, and P. Kellam, J Clin Microbiol 50:3838-3844, 2012, doi:10.1128/JCM.01516-12), we developed a robust methodology for amplification of two large fragments of viral genome covering about 80% of the unique HIV-1 genome sequence. Importantly, this method can be applied to both viral RNA and proviral DNA amplification templates, allowing genotyping in HIV-infected subjects with suppressed viral loads (e.g., subjects on antiretroviral therapy [ART]). The two amplicons cover critical regions across the HIV-1 genome (including pol and env), allowing analysis of mutations associated with resistance to protease inhibitors, reverse transcriptase inhibitors (nucleoside reverse transcriptase inhibitors [NRTIs] and nonnucleoside reverse transcriptase inhibitors [NNRTIs]), integrase strand transfer inhibitors, and virus entry inhibitors. The two amplicons generated span 7,124 bp, providing substantial sequence length and numbers of informative sites for comprehensive phylogenic analysis and greater refinement of viral linkage analyses in HIV prevention studies. The long-range HIV genotyping from proviral DNA was successful in about 90% of 212 targeted blood specimens collected in a cohort where the majority of patients had suppressed viral loads, including 65% of patients with undetectable levels of HIV-1 RNA loads. The generated amplicons could be sequenced by different methods, such as population Sanger sequencing, single-genome sequencing, or next-generation ultradeep sequencing. The developed method is cost-effective-the cost of the long-range HIV genotyping is under $140 per subject (by Sanger sequencing)-and has the potential to enable the scale up of public health HIV prevention interventions.
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Miller S, Karaoz U, Brodie E, Dunbar S. Solid and Suspension Microarrays for Microbial Diagnostics. METHODS IN MICROBIOLOGY 2015; 42:395-431. [PMID: 38620236 PMCID: PMC7172482 DOI: 10.1016/bs.mim.2015.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.
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Affiliation(s)
- Steve Miller
- Clinical Microbiology Laboratory, University of California, San Francisco, California, USA
| | - Ulas Karaoz
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Eoin Brodie
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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19
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Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, Rinke de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CAB, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HHM, van de Vijver DAMC, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JPA, Vandamme AM, Shafer RW. Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. PLoS Med 2015; 12:e1001810. [PMID: 25849352 PMCID: PMC4388826 DOI: 10.1371/journal.pmed.1001810] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 02/27/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes. METHODS AND FINDINGS We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05-1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06-1.25), North America (OR = 1.19; 95% CI: 1.12-1.26), Europe (OR = 1.07; 95% CI: 1.01-1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12-1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92-1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs—K101E, K103N, Y181C, and G190A—accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling. CONCLUSIONS Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen.
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Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, California, United States of America. Leuven—University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Jose Luis Blanco
- Hospital Clinic Universitari-Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Michael R Jordan
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Jonathan Taylor
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Philippe Lemey
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Vici Varghese
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Raph L Hamers
- Department of Global Health and Internal Medicine, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | | | - Tobias F Rinke de Wit
- Department of Global Health and Internal Medicine, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | | | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Radko Avi
- Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Santiago Avila-Rios
- National Institute of Respiratory Diseases, Centre for Research in Infectious Diseases, Mexico City, Mexico
| | - Pascal O Bessong
- HIV/AIDS & Global Health Research Programme, Department of Microbiology, University of Venda, Thohoyandou, South Africa
| | - James I Brooks
- National HIV and Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Charles A B Boucher
- Department of Viroscience, Erasmus Medical Centre, Erasmus University, Rotterdam, Netherlands
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael P Busch
- Blood Systems Research Institute, San Francisco, California, United States of America
| | | | - Marie-Laure Chaix
- Laboratoire de Virologie, Hôpital Saint Louis, Université Paris Diderot, INSERM U941, Paris, France
| | - Bum Sik Chin
- Center for Infectious Diseases, National Medical Center, Seoul, Republic of Korea
| | | | - Cillian F De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Anne Derache
- Department of Virology, Pitie-Salpetriere Hospital, Paris, France
| | - Diane Descamps
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris Hôpital Bichat-Claude Bernard, INSERM UMR 1137, Université Paris Diderot, Paris, France
| | - Alaka K Deshpande
- Department of Medicine, Grant Medical College and Sir Jamshedjee Jeejeebhoy Group of Hospitals, Mumbai, India
| | - Cyrille F Djoko
- Global Viral Cameroon, Intendance Round About, EMAT/CRESAR, Yaoundé, Cameroon
| | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Herve Fleury
- Laboratoire de Virologie, Centre Hospitalier Universitaire de Bordeaux, CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Pierre Frange
- Microbiology Department, Hôpital Necker-Enfants Malades, Paris, France
| | - Seiichiro Fujisaki
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Junko Hattori
- National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Africa Holguin
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Gillian M Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Hiroshi Ichimura
- Department of Viral Infection and International Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - David Katzenstein
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | | | - Jerome H Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sung Soon Kim
- Division of AIDS, Korea National Institute of Health, Osong, Chungcheongbuk-do, Republic of Korea
| | - Yanpeng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Irja Lutsar
- Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Kee Peng Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ramesh S Paranjape
- National AIDS Research Institute, Indian Council of Medical Research, Pune, India
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, 34394 Montpellier, France; Computational Biology Institute, Montpellier, France
| | - Mario Poljak
- Institute of Microbiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Matt A Price
- Department of Medical Affairs, International AIDS Vaccine Initiative, New York, New York, United States of America; Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, California, United States of America
| | | | - Gustavo Reyes-Terán
- National Institute of Respiratory Diseases, Centre for Research in Infectious Diseases, Mexico City, Mexico
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | | | - Davey M Smith
- University of California San Diego, La Jolla, California, United States of America
| | | | - Vincent V Soriano
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain
| | | | - Maja Stanojevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Wataru Sugiura
- National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | | | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hong-Ha M Truong
- Department of Medicine, University of California, San Francisco, California, United States of America
| | | | - Nicole Vidal
- Institut de Recherche pour le Développement, University of Montpellier 1, Montpellier, France
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rongge Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Gonzalo Yebra
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - John P A Ioannidis
- Stanford Prevention Research Center, Department of Medicine, Stanford University, Stanford, California, United States of America; Meta-Research Innovation Center at Stanford, Stanford University, Stanford, California, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium; Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, California, United States of America
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Emerging antiretroviral drug resistance in sub-Saharan Africa: novel affordable technologies are needed to provide resistance testing for individual and public health benefits. AIDS 2014; 28:2643-8. [PMID: 25493592 DOI: 10.1097/qad.0000000000000502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Emerging rapid resistance testing methods for clinical microbiology laboratories and their potential impact on patient management. BIOMED RESEARCH INTERNATIONAL 2014; 2014:375681. [PMID: 25343142 PMCID: PMC4197867 DOI: 10.1155/2014/375681] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/22/2014] [Accepted: 08/28/2014] [Indexed: 12/25/2022]
Abstract
Atypical and multidrug resistance, especially ESBL and carbapenemase expressing Enterobacteriaceae, is globally spreading. Therefore, it becomes increasingly difficult to achieve therapeutic success by calculated antibiotic therapy. Consequently, rapid antibiotic resistance testing is essential. Various molecular and mass spectrometry-based approaches have been introduced in diagnostic microbiology to speed up the providing of reliable resistance data. PCR- and sequencing-based approaches are the most expensive but the most frequently applied modes of testing, suitable for the detection of resistance genes even from primary material. Next generation sequencing, based either on assessment of allelic single nucleotide polymorphisms or on the detection of nonubiquitous resistance mechanisms might allow for sequence-based bacterial resistance testing comparable to viral resistance testing on the long term. Fluorescence in situ hybridization (FISH), based on specific binding of fluorescence-labeled oligonucleotide probes, provides a less expensive molecular bridging technique. It is particularly useful for detection of resistance mechanisms based on mutations in ribosomal RNA. Approaches based on MALDI-TOF-MS, alone or in combination with molecular techniques, like PCR/electrospray ionization MS or minisequencing provide the fastest resistance results from pure colonies or even primary samples with a growing number of protocols. This review details the various approaches of rapid resistance testing, their pros and cons, and their potential use for the diagnostic laboratory.
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