1
|
Raymond S, Jeanne N, Vellas C, Nicot F, Saune K, Ranger N, Latour J, Carcenac R, Harter A, Delobel P, Izopet J. HIV-1 genotypic resistance testing using single molecule real-time sequencing. J Clin Virol 2024; 174:105717. [PMID: 39068746 DOI: 10.1016/j.jcv.2024.105717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND HIV-1 resistance testing is recommended in clinical management and next-generation sequencing (NGS) methods are now available in many virology laboratories. OBJECTIVES To evaluate the diagnostic performance of Long-Read Single Molecule Real-time (SMRT) sequencing (Sequel, PacBio) for HIV-1 polymerase genotyping. STUDY DESIGN 111 prospective clinical samples (83 plasma and 28 leukocyte-enriched blood fraction) were analyzed for routine HIV-1 resistance genotyping using Sanger sequencing, Vela NGS, and SMRT sequencing. We developed a SMRT sequencing protocol and a bio-informatics pipeline to infer antiretroviral resistance on both haplotype and variant calling approaches. RESULTS The polymerase was successfully sequenced by the three platforms in 98 % of plasma RNA samples for viral loads above 4 log copies/mL. The success rate decreased to 83 % using Sanger or Vela sequencing and to 67 % using SMRT sequencing for viral loads of 3 to 4 log copies/mL. Sensitivities of 50 %, 54 % and 61 % were obtained using SMRT, Vela, and Sanger sequencing, respectively, in cellular DNA from patients with prolonged undetectable plasma HIV-1 RNA. Ninety-eight percent of resistance-associated mutations (RAMs) identified with Sanger sequencing were detected using SMRT sequencing. Furthermore, 91 % of RAMs (> 5 % threshold) identified with Vela NGS were detected using SMRT sequencing. RAM quantification using Vela and SMRT sequencing was well correlated (Spearman correlation ρ = 0.82; P < 0.0001). CONCLUSIONS SMRT sequencing of the full-length HIV-1 polymerase appeared performant for characterizing HIV-1 genotypic resistance on both RNA and DNA clinical samples. Long-read sequencing is a new tool for mutation haplotyping and resistance analysis.
Collapse
Affiliation(s)
- Stéphanie Raymond
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France.
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Camille Vellas
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Karine Saune
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Noémie Ranger
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Justine Latour
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Pierre Delobel
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Jacques Izopet
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| |
Collapse
|
2
|
Papa Mze N, Fernand-Laurent C, Daugabel S, Zanzouri O, Juillet SM. Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform. Genes (Basel) 2024; 15:259. [PMID: 38397248 PMCID: PMC10887851 DOI: 10.3390/genes15020259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Genotypic testing is often recommended to improve the management of patients infected with human immunodeficiency virus (HIV). To help combat this major pandemic, next-generation sequencing (NGS) techniques are widely used to analyse resistance to antiretroviral drugs. In this study, we used a Vela Sentosa kit (Vela Diagnostics, Kendall, Singapore), which is usually used for the Ion Torrent personal genome machine (PGM) platform, to sequence HIV using the Illumina Miseq platform. After RNA extraction and reverse transcriptase-polymerase chain reaction (RT-PCR), minor modifications were applied to the Vela Sentosa kit to adapt it to the Illumina Miseq platform. Analysis of the results showed the same mutations present in the samples using both sequencing platforms. The total number of reads varied from 185,069 to 752,343 and from 642,162 to 2,074,028 in the Ion Torrent PGM platform and the Illumina Miseq platform, respectively. The average depth was 21,955 and 46,856 for Ion Torrent PGM and Illumina Miseq platforms, respectively. The cost of sequencing a run of eight samples was quite similar between the two platforms (about USD 1790 for Illumina Miseq and about USD 1833 for Ion Torrent PGM platform). We have shown for the first time that it is possible to adapt and use the Vela Sentosa kit for the Illumina Miseq platform to obtain high-quality results with a similar cost.
Collapse
Affiliation(s)
- Nasserdine Papa Mze
- Service de Biologie, Unité de Microbiologie, Hôpital Mignot, Centre Hospitalier de Versailles, 177 rue de Versailles, 78150 Le Chesnay, France (O.Z.); (S.M.J.)
| | | | | | | | | |
Collapse
|
3
|
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.
Collapse
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
| | | |
Collapse
|
4
|
Botha JC, Byott M, Spyer MJ, Grant PR, Gärtner K, Chen WX, Burton J, Bamford A, Waters LJ, Giaquinto C, Turkova A, Vavro CL, Nastouli E. Sensitive HIV-1 DNA Pol Next-Generation Sequencing for the Characterisation of Archived Antiretroviral Drug Resistance. Viruses 2023; 15:1811. [PMID: 37766218 PMCID: PMC10536450 DOI: 10.3390/v15091811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Modern HIV-1 treatment effectively suppresses viral amplification in people living with HIV. However, the persistence of HIV-1 DNA as proviruses integrated into the human genome remains the main barrier to achieving a cure. Next-generation sequencing (NGS) offers increased sensitivity for characterising archived drug resistance mutations (DRMs) in HIV-1 DNA for improved treatment options. In this study, we present an ultra-sensitive targeted PCR assay coupled with NGS and a robust pipeline to characterise HIV-1 DNA DRMs from buffy coat samples. Our evaluation supports the use of this assay for Pan-HIV-1 analyses with reliable detection of DRMs across the HIV-1 Pol region. We propose this assay as a new valuable tool for monitoring archived HIV-1 drug resistance in virologically suppressed individuals, especially in clinical trials investigating novel therapeutic approaches.
Collapse
Affiliation(s)
- Johannes C. Botha
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK (E.N.)
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Trust, London NW1 2PG, UK
| | - Matthew Byott
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK (E.N.)
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Trust, London NW1 2PG, UK
| | - Moira J. Spyer
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK (E.N.)
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Trust, London NW1 2PG, UK
| | | | - Kathleen Gärtner
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK (E.N.)
| | | | - James Burton
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Alasdair Bamford
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK (E.N.)
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- Medical Research Council Clinical Trials Unit, University College London, London WC1E 6BT, UK
| | - Laura J. Waters
- Central and North West London NHS Foundation Trust, Mortimer Market, London WC1E 6JB, UK
| | - Carlo Giaquinto
- Department of Women and Child Health, University of Padova, 35122 Padova, Italy
- Fondazione Penta ETS, 35127 Padova, Italy
| | - Anna Turkova
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- Medical Research Council Clinical Trials Unit, University College London, London WC1E 6BT, UK
| | | | - Eleni Nastouli
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK (E.N.)
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Trust, London NW1 2PG, UK
| |
Collapse
|
5
|
Cao B, Liu M, Jiang T, Yu Q, Yuan T, Ding P, Zhou X, Huang F, Huang Y, Jiang J. HIV-1 RNA and DNA genotyping drug resistance detection in patients with low-level viremia in Liangshan, China. AIDS Res Hum Retroviruses 2023. [PMID: 37183411 DOI: 10.1089/aid.2022.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
In this study, we characterized HIV-1 RNA and HIV-1 DNA genotyping drug resistance detection in patients with low-level viremia in Liangshan, China. Whole blood samples were collected from HIV/AIDS patients who had received anti-retroviral therapy for more than six months and whose HIV-1 RNA loads were 50-1000 copies/mL for two consecutive times at least one month apart. The patients were enrolled from a county in Liangshan Yi Autonomous Prefecture, Sichuan Province between May 2021 and May 2022. Plasma and blood cells were separated. Plasma samples were tested for HIV-1 RNA genotyping drug resistance, while blood cell samples were tested for HIV-1 DNA genotyping drug resistance. Then, HIV-1 RNA and HIV-1 DNA genotyping drug resistance outcomes were compared. Among the 32 participants, 16 were males while 16 were females; with the median age of 34.5 years. The main HIV-1 infection route was heterosexual transmission. The median anti-retroviral therapy duration was 3.9 years. Two types of nucleoside reverse transcriptase inhibitors (NRTIs) + one non-nucleoside reverse transcriptase inhibitors (NNRTIs) were the main antiviral therapeutic options. Pol region genes for 28 HIV-1 DNA samples and 10 HIV-1 RNA samples were successfully amplified. The success rate of pol region genes amplification for HIV-1 DNA was significantly higher than that of HIV-1 RNA (χ2 = 20.988, P < 0.05). In HIV-1 RNA and HIV-1 DNA samples, M184 (4/8) and K103 (3/8) were the most frequent drug resistance mutation sites. Among the NNRTIs, the rates of drug resistance were highest to EFV (6/8) and NVP (6/8) while among the NRTIs, the rates of drug resistance were highest to ABC (4/8), FTC (4/8) and 3TC (4/8). In conclusion, detection of HIV-1 RNA genotyping drug resistance combined with HIV-1 DNA genotyping drug resistance can improve the success rate of drug resistance detection in patients with low-level viremia.
Collapse
Affiliation(s)
- Bianchuan Cao
- Guangxi Medical University First Affiliated Hospital, 117742, Department of Infectious Disease, Nanning, China
- The Affiliated Hospital of Southwest Medical University, 556508, Department of Infectious Disease, Luzhou, Sichuan, China;
| | - Mei Liu
- First People's Hospital of Yuexi County, Antiviral Therapy Center, Liangshan, China;
| | - Tao Jiang
- First People's Hospital of Yuexi County, Antiviral Therapy Center, Liangshan, China;
| | - Qinghua Yu
- First People's Hospital of Yuexi County, Antiviral Therapy Center, Liangshan, China;
| | - Tianru Yuan
- First People's Hospital of Yuexi County, Antiviral Therapy Center, Liangshan, China;
| | - Ping Ding
- First People's Hospital of Yuexi County, Antiviral Therapy Center, Liangshan, China;
| | - Xian Zhou
- First People's Hospital of Yuexi County, Antiviral Therapy Center, Liangshan, China;
| | - Fuli Huang
- The Affiliated Hospital of Southwest Medical University, 556508, Department of Infectious Disease, Luzhou, Sichuan, China;
| | - Yongmao Huang
- The Affiliated Hospital of Southwest Medical University, 556508, Department of Infectious Disease, Luzhou, Sichuan, China;
| | - Jianning Jiang
- Guangxi Medical University First Affiliated Hospital, 117742, No.6 Shuangyong Road, Nanning, China, 530021;
| |
Collapse
|
6
|
Yu D, Liang B, Yang Y, Liu J, Liang H, Zhang F, Jiang J, Huang J, Zhong S, Qin C, Jiang J, Liang H, Ye L. Prevalence of Drug Resistance and Genetic Transmission Networks Among Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome Patients with Antiretroviral Therapy Failure in Guangxi, China. AIDS Res Hum Retroviruses 2022; 38:822-830. [PMID: 35972723 DOI: 10.1089/aid.2021.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Prevalence of drug resistance (DR) challenges the epidemic control of human immunodeficiency virus (HIV)-1. However, little is known about DR among patients with antiretroviral therapy (ART) failure in Guangxi province, China. This cross-sectional study was aimed to investigate the prevalence of DR and the characteristics of DR sequences in the genetic transmission network among HIV-1 patients with ART failure in Guangxi. We enrolled 358 eligible patients between 2012 and 2018. Blood samples were subjected to reverse transcription polymerase chain reaction, followed by sequencing of the HIV-1 polymerase (pol) gene. An online subtyping tool and neighbor-joining phylogenetic tree were used to determine the genotype. HIV-TRACE tool was used to constructed transmission network with a pairwise genetic distance of 0.013. DR was analyzed using the Stanford University HIV Drug Resistance Database. We obtained 293 pol-sequences from participants; CRF01_AE (75.4%), CRF 08_BC (15.7%), and CRF07_BC (8.5%) were the main subtypes, and an A1 subtype was detected in Guangxi for the first time. The overall prevalence of DR was 32.4% (95/293). Among those with identified DR, 25.6% were against non-nucleoside analog reverse-transcriptase inhibitors (NNRTIs), 17.7% were against nucleoside analog reverse-transcriptase inhibitors (NRTIs), and 14.3% were against both NRTIs and NNRTIs. The common drug-resistant mutations were M184V (10.2%), K103N (10.6%) and V179D (6.1%). The patients located in the southern Guangxi [adjust odds ratio (AOR) = 10.87], or whose blood plasma were taken in 2017-2018 (AOR = 3.98) had an increased risk of DR. Of the CRF01_AE, CRF07_BC, and CRF08_BC sequences, 18.6%, 8.0%, and 13.0% fell into clusters, respectively. Nine (9.7%) sequences from patients with DR fell into three clusters. The largest cluster containing 11 individuals was the CRF01_AE subtype, 27.3% of whom were DR patients. Although the prevalence of DR among ART failure patients in Guangxi was at a low level, the continuous surveillance of DR in ART patients is necessary.
Collapse
Affiliation(s)
- Dee Yu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Yuan Yang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Jie Liu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Huayue Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Fei Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jiaxiao Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Shanmei Zhong
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Cai Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Sciences Institute, Guangxi Medical University, Nanning, China
| |
Collapse
|
7
|
HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
Collapse
|
8
|
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: 2] [Impact Index Per Article: 1.0] [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.
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
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
|
12
|
Noguera-Julian M, Lee ER, Shafer RW, Kantor R, Ji H. Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing. Viruses 2020; 12:v12060666. [PMID: 32575676 PMCID: PMC7354622 DOI: 10.3390/v12060666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
External quality assessment (EQA) is a keystone element in the validation and implementation of next generation sequencing (NGS)-based HIV drug resistance testing (DRT). Software validation and evaluation is a critical element in NGS EQA programs. While the development, sharing, and adoption of wet lab protocols is coupled with the increasing access to NGS technology worldwide, rendering it easy to produce NGS data for HIV-DRT, bioinformatic data analysis remains a bottleneck for most of the diagnostic laboratories. Several computational tools have been made available, via free or commercial sources, to automate the conversion of raw NGS data into an actionable clinical report. Although different software platforms yield equivalent results when identical raw NGS datasets are analyzed for variations at higher abundance, discrepancies arise when variations at lower frequencies are considered. This implies that validation and performance assessment of the bioinformatics tools applied in NGS HIV-DRT is critical, and the origins of the observed discrepancies should be determined. Well-characterized reference NGS datasets with ground truth on the genotype composition at all examined loci and the exact frequencies of HIV variations they may harbor, so-called dry panels, would be essential in such cases. The strategic design and construction of such panels are challenging but imperative tasks in support of EQA programs for NGS-based HIV-DRT and the validation of relevant bioinformatics tools. Here, we present criteria that can guide the design of such dry panels, which were discussed in the Second International Winnipeg Symposium themed for EQA strategies for NGS HIVDR assays.
Collapse
Affiliation(s)
- Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, Catalonia, 08196 Badalona, Spain
- Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic, Central University of Catalonia, Can Baumann. Ctra. de Roda, 70, 08500 Vic, Spain
- Correspondence:
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (E.R.L.); (H.J.)
| | | | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02903, USA;
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (E.R.L.); (H.J.)
- Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| |
Collapse
|
13
|
Ji H, Sandstrom P, Paredes R, Harrigan PR, Brumme CJ, Avila Rios S, Noguera-Julian M, Parkin N, Kantor R. Are We Ready for NGS HIV Drug Resistance Testing? The Second "Winnipeg Consensus" Symposium. Viruses 2020; 12:E586. [PMID: 32471096 PMCID: PMC7354487 DOI: 10.3390/v12060586] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/13/2020] [Accepted: 05/25/2020] [Indexed: 12/31/2022] Open
Abstract
HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. While NGS is likely to become the new standard for routine HIVDR testing, many technical and knowledge gaps remain to be resolved before its generalized adoption in regular clinical care, public health, and research. Recognizing this, we conceived and launched an international symposium series on NGS HIVDR, to bring together leading experts in the field to address these issues through in-depth discussions and brainstorming. Following the first symposium in 2018 (Winnipeg, MB Canada, 21-22 February, 2018), a second "Winnipeg Consensus" symposium was held in September 2019 in Winnipeg, Canada, and was focused on external quality assurance strategies for NGS HIVDR assays. In this paper, we summarize this second symposium's goals and highlights.
Collapse
Affiliation(s)
- Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, 08916 Badalona, Catalonia, Spain; (R.P.); (M.N.-J.)
- Infectious Diseases Department, Hospital Germans Trias i Pujol, 08916 Badalona, Catalonia, Spain
| | - P. Richard Harrigan
- Division of AIDS, Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada;
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada;
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Santiago Avila Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City 14080, Mexico;
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, 08916 Badalona, Catalonia, Spain; (R.P.); (M.N.-J.)
- Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic–Central University of Catalonia (UVic–UCC), Can Baumann, Ctra. de Roda, 70, 08500 Vic, Spain
| | - Neil Parkin
- Data First Consulting Inc., Sebastopol, CA 95472, USA;
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA;
| |
Collapse
|
14
|
Chrysostomou AC, Topcu C, Stylianou DC, Hezka J, Kostrikis LG. Development of a new comprehensive HIV-1 genotypic drug resistance assay for all commercially available reverse transcriptase, protease and integrase inhibitors in patients infected with group M HIV-1 strains. INFECTION GENETICS AND EVOLUTION 2020; 81:104243. [PMID: 32061896 DOI: 10.1016/j.meegid.2020.104243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/28/2022]
Abstract
Comprehensive PCR assays for the genotypic drug resistance analysis of all HIV-1 antiretroviral agents (reverse transcriptase, protease and integrase inhibitors) are increasingly in demand due to introduction of integrase inhibitors in the first line regimens and the increasing presence of non-B HIV-1 clades around the world. This study focused on the development and evaluation of a new PCR-based assay for the amplification and sequencing of the entire HIV-1 pol region of major circulating group M HIV-1 strains in Europe for genotypic drug resistance analysis. The comprehensive touchdown PCR assay developed in this study utilized HIV-1 RNA extracted from the plasma of blood samples of consenting HIV-1 infected patients in Cyprus, collected from 2017 to 2019. The HIV-1 pol region was amplified by touchdown PCR for both the primary RT-PCR and the secondary PCR steps. Successful PCR amplicons were determined by population DNA sequencing, using the Sanger method and the genotypic drug resistance analysis was performed with the Stanford University HIV Drug Resistance Database Program. The newly developed assay successfully amplified the entire HIV-1 pol region (2844 nucleotides long) of 141 out of 144 samples of group M HIV-1 subtypes and recombinant strains of the Cyprus HIV-1 Transmission Cohort Study (CHICS) isolated from 2017 to 2019 and genotypic analyses were conducted for all currently available HIV-1 reverse transcriptase, protease and integrase inhibitors. The drug resistance, epidemiological and demographic data of these study subjects will be expanded upon in the CHICS (L.G. Kostrikis et al., manuscript in preparation for publication). The newly developed HIV-1 genotypic drug resistance assay would benefit clinical settings, and research focusing on the world-wide spread of HIV-1 drug-resistant strains, especially in geographic regions characterized by polyphyletic HIV-1 infections.
Collapse
Affiliation(s)
- Andreas C Chrysostomou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Cicek Topcu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Dora C Stylianou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Johana Hezka
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Leondios G Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus.
| |
Collapse
|