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Vashisht A, Mondal AK, Vashisht V, Ananth S, Alptekin A, Jones K, Farmaha JK, Kolhe R. Enhancing Precision in HIV Treatment: Validation of a Robust Next-Generation Sequencing System for Drug Resistance Mutation Analysis. Diagnostics (Basel) 2024; 14:1766. [PMID: 39202254 PMCID: PMC11353995 DOI: 10.3390/diagnostics14161766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 09/03/2024] Open
Abstract
BACKGROUND Multidrug-resistant HIV strains challenge treatment efficacy and increase mortality rates. Next-generation sequencing (NGS) technology swiftly detects variants, facilitating personalized antiretroviral therapy. AIM This study aimed to validate the Vela Diagnostics NGS platform for HIV drug resistance mutation analysis, rigorously assessed with clinical samples and CAP proficiency testing controls previously analyzed by Sanger sequencing. METHOD The experimental approach involved the following: RNA extraction from clinical specimens, reverse transcription polymerase chain reaction (RT-PCR) utilizing the Sentosa SX 101 platform, library preparation with the Sentosa SQ HIV Genotyping Assay, template preparation, sequencing using the Sentosa SQ301 instrument, and subsequent data analysis employing the Sentosa SQ Suite and SQ Reporter software. Drug resistance profiles were interpreted using the Stanford HIV Drug Resistance Database (HIVdb) with the HXB2 reference sequence. RESULTS The Vela NGS system successfully identified a comprehensive array of drug resistance mutations across the tested samples: 28 nucleoside reverse transcriptase inhibitors (NRTI), 25 non-nucleoside reverse transcriptase inhibitors (NNRTI), 25 protease inhibitors (PI), and 10 integrase gene-specific variants. Dilution experiments further validated the system's sensitivity, detecting drug resistance mutations even at viral loads lower than the recommended threshold (1000 copies/mL) set by Vela Diagnostics. SCOPE This study underscores the validation and clinical applicability of the Vela NGS system, and its implementation may offer clinicians enhanced precision in therapeutic decision-making for individuals living with HIV.
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Affiliation(s)
- Ashutosh Vashisht
- Georgia Esoteric and Molecular Biology Laboratory, Department of Pathology, Augusta University, Augusta, GA 30912, USA; (A.V.); (A.K.M.); (V.V.); (S.A.); (A.A.); (K.J.); (J.K.F.)
| | - Ashis K. Mondal
- Georgia Esoteric and Molecular Biology Laboratory, Department of Pathology, Augusta University, Augusta, GA 30912, USA; (A.V.); (A.K.M.); (V.V.); (S.A.); (A.A.); (K.J.); (J.K.F.)
| | - Vishakha Vashisht
- Georgia Esoteric and Molecular Biology Laboratory, Department of Pathology, Augusta University, Augusta, GA 30912, USA; (A.V.); (A.K.M.); (V.V.); (S.A.); (A.A.); (K.J.); (J.K.F.)
| | - Sudha Ananth
- Georgia Esoteric and Molecular Biology Laboratory, Department of Pathology, Augusta University, Augusta, GA 30912, USA; (A.V.); (A.K.M.); (V.V.); (S.A.); (A.A.); (K.J.); (J.K.F.)
- Reagent Sciences Department, Research and Development, Illumina, San Diego, CA 92122, USA
| | - Ahmet Alptekin
- Georgia Esoteric and Molecular Biology Laboratory, Department of Pathology, Augusta University, Augusta, GA 30912, USA; (A.V.); (A.K.M.); (V.V.); (S.A.); (A.A.); (K.J.); (J.K.F.)
| | - Kimya Jones
- Georgia Esoteric and Molecular Biology Laboratory, Department of Pathology, Augusta University, Augusta, GA 30912, USA; (A.V.); (A.K.M.); (V.V.); (S.A.); (A.A.); (K.J.); (J.K.F.)
| | - Jaspreet K. Farmaha
- Georgia Esoteric and Molecular Biology Laboratory, Department of Pathology, Augusta University, Augusta, GA 30912, USA; (A.V.); (A.K.M.); (V.V.); (S.A.); (A.A.); (K.J.); (J.K.F.)
| | - Ravindra Kolhe
- Georgia Esoteric and Molecular Biology Laboratory, Department of Pathology, Augusta University, Augusta, GA 30912, USA; (A.V.); (A.K.M.); (V.V.); (S.A.); (A.A.); (K.J.); (J.K.F.)
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Parkin N, Harrigan PR, Inzaule S, Bertagnolio S. Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001948. [PMID: 37851634 PMCID: PMC10584185 DOI: 10.1371/journal.pgph.0001948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Resistance to antiretroviral drugs used to treat HIV is an important and evolving concern, particularly in low- and middle-income countries (LMICs) which have been impacted to the greatest extent by the HIV pandemic. Efforts to monitor the emergence and transmission of resistance over the past decade have shown that drug resistance-especially to the nucleoside analogue and non-nucleoside reverse transcriptase inhibitors-can (and have) increased to levels that can jeopardize the efficacy of available treatment options at the population level. The global shift to integrase-based regimens as the preferred first-line therapy as well as technological advancements in the methods for detecting resistance have had an impact in broadening and diversifying the landscape of and use case for HIV drug resistance testing. This review estimates the potential demand for HIV drug resistance tests, and surveys current testing methodologies, with a focus on their application in LMICs.
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Affiliation(s)
- Neil Parkin
- Data First Consulting, Sebastopol, CA, United States of America
| | - P. Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Seth Inzaule
- Amsterdam Institute for Global Health and Development, and Department of Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Hume J, Lowry K, Whiley DM, Irwin AD, Bletchly C, Sweeney EL. Application of the ViroKey® SQ FLEX assay for detection of cytomegalovirus antiviral resistance. J Clin Virol 2023; 167:105556. [PMID: 37566984 DOI: 10.1016/j.jcv.2023.105556] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND Cytomegalovirus (CMV) is a viral infection which establishes lifelong latency, often reactivating and causing disease in immunosuppressed individuals, including haematopoietic stem cell transplant (HSCT) recipients. Treatment can be problematic due to antiviral resistance which substantially increases the risk of patient mortality. Diagnostic testing capabilities for CMV antiviral resistance in Australia and elsewhere have traditionally relied on gene-specific Sanger sequencing approaches, however, are now being superseded by next generation sequencing protocols. OBJECTIVE Provide a snapshot of local mutations and explore the feasibility of the ViroKeyࣨ® SQ FLEX Genotyping Assay (Vela Diagnostics Pty Ltd) by examining sequencing success. METHOD Performed sequencing on adult (n = 38) and paediatric (n = 81) plasma samples, over a large range of viral loads (above and below the assay recommended threshold of ≥1,000 International Units (IU)/mL; noting most of our paediatric samples have loads <1,000 IU/mL). RESULTS Eleven test runs (including three repeat runs; 14 to 15 samples per run) were conducted, and four runs were deemed valid. The overall individual sample success rate for the four evaluable test runs was 71.2% (42/59 samples); 80.4% (37/46) samples ≥1,000 IU/mL were valid. Ten clinically important antiviral resistance mutations were detected, the most common being A594V in the UL97 gene, found in 6 (5%) samples. CONCLUSIONS A range of technical issues were experienced, however with improvement this platform could be a useful addition to routine pathology workflows, providing timely antiviral resistance results for patients undergoing HSCT.
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Affiliation(s)
- Jocelyn Hume
- Faculty of Medicine, The University of Queensland Centre for Clinical Research (UQCCR), The University of Queensland, Brisbane, Queensland, Australia; Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia
| | - Kym Lowry
- Faculty of Medicine, The University of Queensland Centre for Clinical Research (UQCCR), The University of Queensland, Brisbane, Queensland, Australia; Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Centre for Children's Health Research, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - David M Whiley
- Faculty of Medicine, The University of Queensland Centre for Clinical Research (UQCCR), The University of Queensland, Brisbane, Queensland, Australia; Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia
| | - Adam D Irwin
- Faculty of Medicine, The University of Queensland Centre for Clinical Research (UQCCR), The University of Queensland, Brisbane, Queensland, Australia; Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Cheryl Bletchly
- Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia
| | - Emma L Sweeney
- Faculty of Medicine, The University of Queensland Centre for Clinical Research (UQCCR), The University of Queensland, Brisbane, Queensland, Australia.
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Novitsky V, Nyandiko W, Vreeman R, DeLong AK, Manne A, Scanlon M, Ngeresa A, Aluoch J, Sang F, Ashimosi C, Jepkemboi E, Orido M, Hogan JW, Kantor R. Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance. Microbiol Spectr 2022; 10:e0345422. [PMID: 36445146 PMCID: PMC9769539 DOI: 10.1128/spectrum.03454-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
HIV-1 drug resistance testing in children and adolescents in low-resource settings is both important and challenging. New (more sensitive) drug resistance testing technologies may improve clinical care, but evaluation of their added value is limited. We assessed the potential added value of using next-generation sequencing (NGS) over Sanger sequencing for detecting nucleoside reverse transcriptase inhibitor (NRTI) and nonnucleoside reverse transcriptase inhibitor (NNRTI) drug resistance mutations (DRMs). Participants included 132 treatment-experienced Kenyan children and adolescents with diverse HIV-1 subtypes and with already high levels of drug resistance detected by Sanger sequencing. We examined overall and DRM-specific resistance and its predicted impact on antiretroviral therapy and evaluated the discrepancy between Sanger sequencing and six NGS thresholds (1%, 2%, 5%, 10%, 15%, and 20%). Depending on the NGS threshold, agreement between the two technologies was 62% to 88% for any DRM, 83% to 92% for NRTI DRMs, and 73% to 94% for NNRTI DRMs, with more DRMs detected at low NGS thresholds. NGS identified 96% to 100% of DRMs detected by Sanger sequencing, while Sanger identified 83% to 99% of DRMs detected by NGS. Higher discrepancy between technologies was associated with higher DRM prevalence. Even in this resistance-saturated cohort, 12% of participants had higher, potentially clinically relevant predicted resistance detected only by NGS. These findings, in a young, vulnerable Kenyan population with diverse HIV-1 subtypes and already high resistance levels, suggest potential benefits of more sensitive NGS over existing technology. Good agreement between technologies at high NGS thresholds supports their interchangeable use; however, the significance of DRMs identified at lower thresholds to patient care should be explored further. IMPORTANCE HIV-1 drug resistance in children and adolescents remains a significant problem in countries facing the highest burden of the HIV epidemic. Surveillance of HIV-1 drug resistance in children and adolescents is an important public health strategy, particularly in resource-limited settings, and yet, it is limited due mostly to cost and infrastructure constraints. Whether newer and more sensitive next-generation sequencing (NGS) adds substantial value beyond traditional Sanger sequencing in detecting HIV-1 drug resistance in real life settings remains an open and debatable question. In this paper, we attempt to address this issue by performing a comprehensive comparison of drug resistance identified by Sanger sequencing and six NGS thresholds. We conducted this study in a well-characterized, vulnerable cohort of children and adolescents living with diverse HIV-1 subtypes in Kenya and, importantly, failing antiretroviral therapy (ART) with already extensive drug resistance. Our findings suggest a potential added value of NGS over Sanger even in this unique cohort.
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Affiliation(s)
- V. Novitsky
- Brown University, Providence, Rhode Island, USA
| | - W. Nyandiko
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University, Eldoret, Kenya
| | - R. Vreeman
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| | | | - A. Manne
- Brown University, Providence, Rhode Island, USA
| | - M. Scanlon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| | - A. Ngeresa
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - J. Aluoch
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - F. Sang
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - C. Ashimosi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - E. Jepkemboi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - M. Orido
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - J. W. Hogan
- Brown University, Providence, Rhode Island, USA
| | - R. Kantor
- Brown University, Providence, Rhode Island, USA
| | - for the RESistance in a PEdiatric CohorT (RESPECT) Study
- Brown University, Providence, Rhode Island, USA
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University, Eldoret, Kenya
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
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Analytical Assessment of the Vela Diagnostics NGS Assay for HIV Genotyping and Resistance Testing: The Apulian Experience. Int J Mol Sci 2022; 23:ijms23052727. [PMID: 35269868 PMCID: PMC8911269 DOI: 10.3390/ijms23052727] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/22/2023] Open
Abstract
Drug-resistance monitoring is one of the hardest challenges in HIV management. Next-generation sequencing (NGS) technologies speed up the detection of drug resistance, allowing the adjustment of antiretroviral therapy and enhancing the quality of life of people living with HIV. Recently, the NGS Sentosa® SQ HIV Genotyping Assay (Vela Diagnostics) received approval for in vitro diagnostics use. This work is the first Italian evaluation of the performance of the Vela Diagnostics NGS platform, assessed with 420 HIV-1 clinical samples. A comparison with Sanger sequencing performance is also reported, highlighting the advantages and disadvantages of the Sentosa® NGS assay. The precision of the technology was studied with reference specimens, while intra- and inter-assay reproducibility were evaluated for selected clinical samples. Vela Diagnostics’ NGS assay reached an 87% success rate through 30 runs of analysis in a real-world clinical context. The concordance with Sanger sequencing outcomes was equal to 97.2%. Several detected mismatches were due to NGS’s superior sensitivity to low-frequency variants. A high accuracy was observed in testing reference samples. Repeatability and reproducibility assays highlighted the good performance of the NGS platform. Beyond a few technical issues that call for further optimization, the key improvement will be a better balance between costs and processing speed. Once these issues have been solved, the Sentosa® SQ HIV Genotyping Assay will be the way forward for HIV resistance testing.
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Vrana JD, Panpradist N, Higa N, Ko D, Ruth P, Kanthula R, Lai JJ, Yang Y, Sakr SR, Chohan B, Chung MH, Frenkel LM, Lutz BR, Klavins E, Beck IA. Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000185. [PMID: 36962187 PMCID: PMC10021139 DOI: 10.1371/journal.pgph.0000185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/09/2022] [Indexed: 04/24/2023]
Abstract
Usability is an overlooked aspect of implementing lab-based assays, particularly novel assays in low-resource-settings. Esoteric instructions can lead to irreproducible test results and patient harm. To address these issues, we developed a software application based on "Aquarium", a laboratory-operating system run on a computer tablet that provides step-by-step digital interactive instructions, protocol management, and sample tracking. Aquarium was paired with a near point-of-care HIV drug resistance test, "OLA-Simple", that detects mutations associated with virologic failure. In this observational study we evaluated the performance of Aquarium in guiding untrained users through the multi-step laboratory protocol with little supervision. To evaluate the training by Aquarium software we conducted a feasibility study in a laboratory at Coptic Hope Center in Nairobi, Kenya. Twelve volunteers who were unfamiliar with the kit performed the test on blinded samples (2 blood specimens; 5 codons/sample). Steps guided by Aquarium included: CD4+ T-Cell separation, PCR, ligation, detection, and interpretation of test results. Participants filled out a short survey regarding their demographics and experience with the software and kit. None of the laboratory technicians had prior experience performing CD4+ separation and 7/12 had no experience performing laboratory-based molecular assays. 12/12 isolated CD4+ T cells from whole blood with yields comparable to isolations performed by trained personnel. The OLA-Simple workflow was completed by all, with genotyping results interpreted correctly by unaided-eye in 108/120 (90%) and by software in 116/120 (97%) of codons analyzed. In the surveys, participants favorably assessed the use of software guidance. The Aquarium digital instructions enabled first-time users in Kenya to complete the OLA-simple kit workflow with minimal training. Aquarium could increase the accessibility of laboratory assays in low-resource-settings and potentially standardize implementation of clinical laboratory tests.
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Affiliation(s)
- Justin D. Vrana
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Nikki Higa
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Parker Ruth
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ruth Kanthula
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Yaoyu Yang
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Samar R. Sakr
- Coptic Hope Center for Infectious Diseases, Nairobi, Kenya
| | - Bhavna Chohan
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Departments of Global Health, Medicine, Pediatrics, and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
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Vrana JD, Panpradist N, Higa N, Ko D, Ruth P, Kanthula R, Lai JJ, Yang Y, Sakr SR, Chohan B, Chung MH, Frenkel LM, Lutz BR, Klavins E, Beck IA. Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya. PLOS GLOBAL PUBLIC HEALTH 2022. [PMID: 36962187 DOI: 10.1101/2021.05.06.21256654v1.full.pdf+html] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Usability is an overlooked aspect of implementing lab-based assays, particularly novel assays in low-resource-settings. Esoteric instructions can lead to irreproducible test results and patient harm. To address these issues, we developed a software application based on "Aquarium", a laboratory-operating system run on a computer tablet that provides step-by-step digital interactive instructions, protocol management, and sample tracking. Aquarium was paired with a near point-of-care HIV drug resistance test, "OLA-Simple", that detects mutations associated with virologic failure. In this observational study we evaluated the performance of Aquarium in guiding untrained users through the multi-step laboratory protocol with little supervision. To evaluate the training by Aquarium software we conducted a feasibility study in a laboratory at Coptic Hope Center in Nairobi, Kenya. Twelve volunteers who were unfamiliar with the kit performed the test on blinded samples (2 blood specimens; 5 codons/sample). Steps guided by Aquarium included: CD4+ T-Cell separation, PCR, ligation, detection, and interpretation of test results. Participants filled out a short survey regarding their demographics and experience with the software and kit. None of the laboratory technicians had prior experience performing CD4+ separation and 7/12 had no experience performing laboratory-based molecular assays. 12/12 isolated CD4+ T cells from whole blood with yields comparable to isolations performed by trained personnel. The OLA-Simple workflow was completed by all, with genotyping results interpreted correctly by unaided-eye in 108/120 (90%) and by software in 116/120 (97%) of codons analyzed. In the surveys, participants favorably assessed the use of software guidance. The Aquarium digital instructions enabled first-time users in Kenya to complete the OLA-simple kit workflow with minimal training. Aquarium could increase the accessibility of laboratory assays in low-resource-settings and potentially standardize implementation of clinical laboratory tests.
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Affiliation(s)
- Justin D Vrana
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Nikki Higa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Parker Ruth
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ruth Kanthula
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - James J Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Yaoyu Yang
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Samar R Sakr
- Coptic Hope Center for Infectious Diseases, Nairobi, Kenya
| | - Bhavna Chohan
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael H Chung
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- Departments of Global Health, Medicine, Pediatrics, and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
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8
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Zhang Y, Ma L. Application of high-throughput sequencing technology in HIV drug resistance detection. BIOSAFETY AND HEALTH 2021. [DOI: 10.1016/j.bsheal.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Manyana S, Gounder L, Pillay M, Manasa J, Naidoo K, Chimukangara B. HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies. Viruses 2021; 13:1125. [PMID: 34208165 PMCID: PMC8230827 DOI: 10.3390/v13061125] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
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Affiliation(s)
- Sontaga Manyana
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Lilishia Gounder
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Melendhran Pillay
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Justen Manasa
- Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa
| | - Benjamin Chimukangara
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
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Li M, Liang S, Zhou C, Chen M, Liang S, Liu C, Zuo Z, Liu L, Feng Y, Song C, Xing H, Ruan Y, Shao Y, Liao L. HIV Drug Resistance Mutations Detection by Next-Generation Sequencing during Antiretroviral Therapy Interruption in China. Pathogens 2021; 10:pathogens10030264. [PMID: 33668946 PMCID: PMC7996606 DOI: 10.3390/pathogens10030264] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 11/24/2022] Open
Abstract
Patients with antiretroviral therapy interruption have a high risk of virological failure when re-initiating antiretroviral therapy (ART), especially those with HIV drug resistance. Next-generation sequencing may provide close scrutiny on their minority drug resistance variant. A cross-sectional study was conducted in patients with ART interruption in five regions in China in 2016. Through Sanger and next-generation sequencing in parallel, HIV drug resistance was genotyped on their plasma samples. Rates of HIV drug resistance were compared by the McNemar tests. In total, 174 patients were included in this study, with a median 12 (interquartile range (IQR), 6–24) months of ART interruption. Most (86.2%) of them had received efavirenz (EFV)/nevirapine (NVP)-based first-line therapy for a median 16 (IQR, 7–26) months before ART interruption. Sixty-one (35.1%) patients had CRF07_BC HIV-1 strains, 58 (33.3%) CRF08_BC and 35 (20.1%) CRF01_AE. Thirty-four (19.5%) of the 174 patients were detected to harbor HIV drug-resistant variants on Sanger sequencing. Thirty-six (20.7%), 37 (21.3%), 42 (24.1%), 79 (45.4%) and 139 (79.9) patients were identified to have HIV drug resistance by next-generation sequencing at 20% (v.s. Sanger, p = 0.317), 10% (v.s. Sanger, p = 0.180), 5% (v.s. Sanger, p = 0.011), 2% (v.s. Sanger, p < 0.001) and 1% (v.s. Sanger, p < 0.001) of detection thresholds, respectively. K65R was the most common minority mutation, of 95.1% (58/61) and 93.1% (54/58) in CRF07_BC and CRF08_BC, respectively, when compared with 5.7% (2/35) in CRF01_AE (p < 0.001). In 49 patients that followed-up a median 10 months later, HIV drug resistance mutations at >20% frequency such as K103N, M184VI and P225H still existed, but with decreased frequencies. The prevalence of HIV drug resistance in ART interruption was higher than 15% in the survey. Next-generation sequencing was able to detect more minority drug resistance variants than Sanger. There was a sharp increase in minority drug resistance variants when the detection threshold was below 5%.
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Affiliation(s)
- Miaomiao Li
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Shujia Liang
- Guangxi Center for Disease Control and Prevention, Nanning 530028, China;
| | - Chao Zhou
- Chongqing Center for Disease Control and Prevention, Chongqing 400042, China;
| | - Min Chen
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China;
| | - Shu Liang
- Sichuan Center for Disease Control and Prevention, Chengdu 610041, China;
| | - Chunhua Liu
- Henan Center for Disease Control and Prevention, Zhengzhou 450016, China;
| | - Zhongbao Zuo
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Lei Liu
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yi Feng
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Chang Song
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Hui Xing
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yuhua Ruan
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Lingjie Liao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
- Correspondence:
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11
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Yeo JY, Koh DWS, Yap P, Goh GR, Gan SKE. Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types. Int J Mol Sci 2020; 22:E370. [PMID: 33396460 PMCID: PMC7796399 DOI: 10.3390/ijms22010370] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
While drug resistant mutations in HIV-1 are largely credited to its error prone HIV-1 RT, the time point in the infection cycle that these mutations can arise and if they appear spontaneously without selection pressures both remained enigmatic. Many HIV-1 RT mutational in vitro studies utilized reporter genes (LacZ) as a template to investigate these questions, thereby not accounting for the possible contribution of viral codon usage. To address this gap, we investigated HIV-1 RT mutation rates and biases on its own Gag, protease, and RT p66 genes in an in vitro selection pressure free system. We found rare clinical mutations with a general avoidance of crucial functional sites in the background mutations rates for Gag, protease, and RT p66 at 4.71 × 10-5, 6.03 × 10-5, and 7.09 × 10-5 mutations/bp, respectively. Gag and p66 genes showed a large number of 'A to G' mutations. Comparisons with silently mutated p66 sequences showed an increase in mutation rates (1.88 × 10-4 mutations/bp) and that 'A to G' mutations occurred in regions reminiscent of ADAR neighbor sequence preferences. Mutational free energies of the 'A to G' mutations revealed an avoidance of destabilizing effects, with the natural p66 gene codon usage providing barriers to disruptive amino acid changes. Our study demonstrates the importance of studying mutation emergence in HIV genes in a RT-PCR in vitro selection pressure free system to understand how fast drug resistance can emerge, providing transferable applications to how new viral diseases and drug resistances can emerge.
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Affiliation(s)
- Joshua Yi Yeo
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Darius Wen-Shuo Koh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Ping Yap
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
| | - Ghin-Ray Goh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
| | - Samuel Ken-En Gan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
- p53 Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore
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12
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King DJ, Freimanis G, Lasecka-Dykes L, Asfor A, Ribeca P, Waters R, King DP, Laing E. A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations. Viruses 2020; 12:E1187. [PMID: 33092085 PMCID: PMC7594041 DOI: 10.3390/v12101187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022] Open
Abstract
High-throughput sequencing such as those provided by Illumina are an efficient way to understand sequence variation within viral populations. However, challenges exist in distinguishing process-introduced error from biological variance, which significantly impacts our ability to identify sub-consensus single-nucleotide variants (SNVs). Here we have taken a systematic approach to evaluate laboratory and bioinformatic pipelines to accurately identify low-frequency SNVs in viral populations. Artificial DNA and RNA "populations" were created by introducing known SNVs at predetermined frequencies into template nucleic acid before being sequenced on an Illumina MiSeq platform. These were used to assess the effects of abundance and starting input material type, technical replicates, read length and quality, short-read aligner, and percentage frequency thresholds on the ability to accurately call variants. Analyses revealed that the abundance and type of input nucleic acid had the greatest impact on the accuracy of SNV calling as measured by a micro-averaged Matthews correlation coefficient score, with DNA and high RNA inputs (107 copies) allowing for variants to be called at a 0.2% frequency. Reduced input RNA (105 copies) required more technical replicates to maintain accuracy, while low RNA inputs (103 copies) suffered from consensus-level errors. Base errors identified at specific motifs identified in all technical replicates were also identified which can be excluded to further increase SNV calling accuracy. These findings indicate that samples with low RNA inputs should be excluded for SNV calling and reinforce the importance of optimising the technical and bioinformatics steps in pipelines that are used to accurately identify sequence variants.
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Affiliation(s)
- David J. King
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Graham Freimanis
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Lidia Lasecka-Dykes
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Amin Asfor
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical sciences, School of Veterinary Medicine, University of Surrey, Guilford GU2 7XH, UK
| | - Paolo Ribeca
- Biomathematics and Statistics Scotland, Edinburgh, Midlothian EH9 3FD, UK;
| | - Ryan Waters
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Donald P. King
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Emma Laing
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
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13
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Reta DH, Tessema TS, Ashenef AS, Desta AF, Labisso WL, Gizaw ST, Abay SM, Melka DS, Reta FA. Molecular and Immunological Diagnostic Techniques of Medical Viruses. Int J Microbiol 2020; 2020:8832728. [PMID: 32908530 PMCID: PMC7474384 DOI: 10.1155/2020/8832728] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/24/2020] [Accepted: 08/15/2020] [Indexed: 01/12/2023] Open
Abstract
Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.
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Affiliation(s)
- Daniel Hussien Reta
- School of Veterinary Medicine, Wollo University, Dessie, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Adey Feleke Desta
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wajana Lako Labisso
- Department of Pathology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Mequanente Abay
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Seifu Melka
- Department of Medical Biochemistry, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fisseha Alemu Reta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, College of Natural and Computational Sciences, Jigjiga University, Jigjiga, Ethiopia
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14
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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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15
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Becker MG, Liang D, Cooper B, Le Y, Taylor T, Lee ER, Wu S, Sandstrom P, Ji H. Development and Application of Performance Assessment Criteria for Next-Generation Sequencing-Based HIV Drug Resistance Assays. Viruses 2020; 12:E627. [PMID: 32532083 PMCID: PMC7354553 DOI: 10.3390/v12060627] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/29/2020] [Accepted: 06/07/2020] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays outperform conventional Sanger sequencing in scalability, sensitivity, and quantitative detection of minority resistance variants. Thus far, HIVDR assays have been applied primarily in research but rarely in clinical settings. One main obstacle is the lack of standardized validation and performance evaluation systems that allow regulatory agencies to benchmark and accredit new assays for clinical use. By revisiting the existing principles for molecular assay validation, here we propose a new validation and performance evaluation system that helps to both qualitatively and quantitatively assess the performance of an NGS-based HIVDR assay. To accomplish this, we constructed a 70-specimen proficiency test panel that includes plasmid mixtures at known ratios, viral RNA from infectious clones, and anonymized clinical specimens. We developed assessment criteria and benchmarks for NGS-based HIVDR assays and used these to assess data from five separate MiSeq runs performed in two experienced HIVDR laboratories. This proposed platform may help to pave the way for the standardization of NGS HIVDR assay validation and performance evaluation strategies for accreditation and quality assurance purposes in both research and clinical settings.
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Affiliation(s)
- Michael G. Becker
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Dun Liang
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Breanna Cooper
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Yan Le
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Tracy Taylor
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Sutan Wu
- SutanStats, St. Louis, MO 63017, USA;
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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16
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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17
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Raymond S, Nicot F, Abravanel F, Minier L, Carcenac R, Lefebvre C, Harter A, Martin-Blondel G, Delobel P, Izopet J. Performance evaluation of the Vela Dx Sentosa next-generation sequencing system for HIV-1 DNA genotypic resistance. J Clin Virol 2019; 122:104229. [PMID: 31809945 DOI: 10.1016/j.jcv.2019.104229] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Patients on antiretroviral therapy could benefit from HIV-1 DNA resistance genotyping for exploring virological failure with low viral load or to guide treatment simplification. Few new generation sequencing data are available. OBJECTIVE To check that the automated deep sequencing Sentosa platform (Vela DX) detected minority resistant variants well enough for HIV DNA genotyping. STUDY DESIGN We evaluated the Sentosa SQ HIV genotyping assay with automated extraction on 40 DNA longitudinal samples from treatment-experienced patients by comparison with Sanger sequencing. HIV drug resistance was interpreted using the ANRS algorithm (v29) at the threshold of 20 % and 3 %. RESULTS The Sentosa SQ HIV genotyping assay was 100 % successful to amplify and sequence PR and RT and 86 % to amplify and sequence IN when the HIV DNA load was >2.5 log copies/million cells. The Sentosa and Sanger sequencing were concordant for predicting PR-RT resistance at the threshold of 20 % in 14/18 samples successfully sequenced. A higher level of resistance was predicted by Sentosa in three samples and by Sanger in one sample. The prevalence of resistance was 7 % to PI, 59 % to NRTI, 31 % to NNRTI and 20 % to integrase inhibitors using the Sentosa SQ genotyping assay at the threshold of 3 %. Seven additional mutations <20 % were detected using the Sentosa assay. CONCLUSION Automated DNA extraction and sequencing using the Sentosa SQ HIV genotyping assay accurately predicted HIV DNA drug resistance by comparison with Sanger. Prospective studies are needed to evaluate the clinical interest of HIV DNA genotyping.
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Affiliation(s)
- Stéphanie Raymond
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France.
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Florence Abravanel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Luce Minier
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Caroline Lefebvre
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Guillaume Martin-Blondel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Pierre Delobel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Jacques Izopet
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
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18
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Weber J, Volkova I, Sahoo MK, Tzou PL, Shafer RW, Pinsky BA. Prospective Evaluation of the Vela Diagnostics Next-Generation Sequencing Platform for HIV-1 Genotypic Resistance Testing. J Mol Diagn 2019; 21:961-970. [PMID: 31382033 PMCID: PMC7152740 DOI: 10.1016/j.jmoldx.2019.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/16/2019] [Accepted: 06/05/2019] [Indexed: 11/30/2022] Open
Abstract
Genotypic antiretroviral drug resistance testing is a critical component of the global efforts to control the HIV-1 epidemic. This study investigates the semiautomated, next-generation sequencing (NGS)-based Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay in a prospective cohort of HIV-1-infected patients. Two-hundred sixty-nine samples were successfully sequenced by both NGS and Sanger sequencing. Among the 261 protease/reverse transcriptase (PR/RT) sequences, a mean of 0.37 drug resistance mutations were identified by both Sanger and NGS, 0.08 by NGS alone, and 0.03 by Sanger alone. Among the 50 integrase sequences, a mean of 0.3 drug resistance mutations were detected by both Sanger and NGS, and 0.08 by NGS alone. NGS estimated higher levels of drug resistance to one or more antiretroviral drugs for 6.5% of PR/RT sequences and 4.0% of integrase sequences, whereas Sanger estimated higher levels of drug resistance for 3.8% of PR/RT sequences. Although the samples successfully sequenced by the Sentosa SQ HIV Genotyping Assay demonstrated similar predicted resistance compared with Sanger, 44% of Sentosa runs failed quality control requiring 17 additional runs. This semi-automated NGS-based assay may aid in HIV-1 genotypic drug resistance testing, though numerous quality control issues were observed when this platform was used in a clinical laboratory setting. With additional refinement, the Sentosa SQ HIV-1 Genotyping Assay may contribute to the global efforts to control HIV-1.
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Affiliation(s)
- Jenna Weber
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Ilona Volkova
- Clinical Virology Laboratory, Stanford Health Care, Stanford, California
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Philip L Tzou
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Robert W Shafer
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California; Clinical Virology Laboratory, Stanford Health Care, Stanford, California; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California.
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19
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Facente SN, Busch MP, Grebe E, Pilcher CD, Welte A, Rice B, Murphy G. Challenges to the performance of current HIV diagnostic assays and the need for centralized specimen archives: a review of the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA) repository. Gates Open Res 2019; 3:1511. [PMID: 31460496 PMCID: PMC6706958 DOI: 10.12688/gatesopenres.13048.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 11/20/2022] Open
Abstract
Background: New challenges for diagnosis of HIV infection abound, including the impact on key viral and immunological markers of HIV vaccine studies, pre-exposure prophylaxis usage and breakthrough infections, and very early initiation of anti-retroviral treatment. These challenges impact the performance of current diagnostic assays, and require suitable specimens for development and evaluation. In this article we review and describe an archive developed by the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA), in order to identify the critical features required to create a centralized specimen archive to support these current and future developments. Review and Findings: We review and describe the CEPHIA repository, a large, consolidated repository comprised of over 31,000 highly-selected plasma samples and other body fluid specimen types, with over 50 purposely designed specimen panels distributed to 19 groups since 2012. The CEPHIA repository provided financial return on investment, supported the standardization of HIV incidence assays, and informed guidance and standards set by the World Health Organization and UNAIDS. Unified data from extensively characterized specimens has allowed this resource to support biomarker discovery, assay optimization, and development of new strategies for estimating duration of HIV infection. Critical features of a high-value repository include 1) extensively-characterized samples, 2) high-quality clinical background data, 3) multiple collaborations facilitating ongoing sample replenishment, and 4) sustained history of high-level specimen utilization. Conclusion: With strong governance and leadership, a large consolidated archive of samples from multiple studies provides investigators and assay developers with easy access to diverse samples designed to address challenges associated with HIV diagnosis, helping to enable improvements to HIV diagnostic assays and ultimately elimination of HIV. Its creation and ongoing utilization should compel funders, institutions and researchers to address and improve upon current approaches to sharing specimens.
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Affiliation(s)
- Shelley N. Facente
- University of California, San Francisco, San Francisco, CA, 94110, USA
- Vitalant Research Institute (formerly Blood Systems Research Institute), San Francisco, CA, 94118, USA
- Facente Consulting, Richmond, CA, 94804, USA
| | - Michael P. Busch
- University of California, San Francisco, San Francisco, CA, 94110, USA
- Vitalant Research Institute (formerly Blood Systems Research Institute), San Francisco, CA, 94118, USA
| | - Eduard Grebe
- University of California, San Francisco, San Francisco, CA, 94110, USA
- Vitalant Research Institute (formerly Blood Systems Research Institute), San Francisco, CA, 94118, USA
- The South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | | | - Alex Welte
- The South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Brian Rice
- London School of Hygiene and Tropical Medicine, London, UK
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20
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Correction: First evaluation of the Next-Generation Sequencing platform for the detection of HIV-1 drug resistance mutations in Belgium. PLoS One 2019; 14:e0211587. [PMID: 30682153 PMCID: PMC6347154 DOI: 10.1371/journal.pone.0211587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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