Sensitive HIV-1 DNA Pol Next-Generation Sequencing for the Characterisation of Archived Antiretroviral Drug Resistance

被引：1
|
作者：
Botha, Johannes C. [1 ,2 ]
Byott, Matthew [1 ,2 ]
Spyer, Moira J. [1 ,2 ]
Grant, Paul R. [3 ]
Gaertner, Kathleen [1 ]
Chen, Wilson X. [4 ]
Burton, James [5 ]
Bamford, Alasdair [1 ,5 ,6 ]
Waters, Laura J. [7 ]
Giaquinto, Carlo [8 ,9 ]
Turkova, Anna [5 ,6 ]
Vavro, Cindy L. [4 ]
Nastouli, Eleni [1 ,2 ]
机构：
[1] UCL, Great Ormond St Inst Child Hlth, London WC1N 1EH, England
[2] Univ Coll London Hosp NHS Trust, Adv Pathogen Diagnost Unit, London NW1 2PG, England
[3] Hlth Serv Labs, London WC1H 9AX, England
[4] ViiV Healthcare, Durham, NC 27709 USA
[5] Great Ormond St Hosp Children NHS Fdn Trust, London WC1N 3JH, England
[6] UCL, Med Res Council, Clin Trials Unit, London WC1E 6BT, England
[7] Cent & North West London NHS Fdn Trust, Mortimer Market, London WC1E 6JB, England
[8] Univ Padua, Dept Women & Child Hlth, I-35122 Padua, Italy
[9] Fdn Penta ETS, I-35127 Padua, Italy
来源：
VIRUSES-BASEL | 2023年 / 15卷 / 09期
基金：
芬兰科学院; 英国医学研究理事会;
关键词：
HIV-1; DNA; drug resistance; provirus; NGS; sanger; BLOOD; DIVERSITY; RESERVOIR; THERAPY; ASSAY;
D O I：
10.3390/v15091811
中图分类号：
Q93 [微生物学];
学科分类号：
071005 ; 100705 ;
摘要：
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.
引用
收藏
页数：12
相关论文
共 50 条
  • [41] Quality Control of Next-Generation Sequencing-Based HIV-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework
    Capina, Rupert
    Li, Katherine
    Kearney, Levon
    Vandamme, Anne-Mieke
    Harrigan, P. Richard
    Van Laethem, Kristel
    VIRUSES-BASEL, 2020, 12 (06):
  • [42] Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences
    Tzou, Philip L.
    Pond, Sergei L. Kosakovsky
    Avila-Rios, Santiago
    Holmes, Susan P.
    Kantor, Rami
    Shafer, Robert W.
    PLOS ONE, 2020, 15 (02):
  • [43] Added Value of Next Generation Sequencing in Characterizing the Evolution of HIV-1 Drug Resistance in Kenyan Youth
    Novitsky, Vlad
    Nyandiko, Winstone
    Vreeman, Rachel
    DeLong, Allison K.
    Howison, Mark
    Manne, Akarsh
    Aluoch, Josephine
    Chory, Ashley
    Sang, Festus
    Ashimosi, Celestine
    Jepkemboi, Eslyne
    Orido, Millicent
    Hogan, Joseph W.
    Kantor, Rami
    VIRUSES-BASEL, 2023, 15 (07):
  • [44] Use of next-generation sequencing on HIV-1 DNA to assess archived resistance in highly treatment-experienced people with multidrug-resistant HIV under virological control: data from the PRESTIGIO Registry
    Armenia, Daniele
    Spagnuolo, Vincenzo
    Bellocchi, Maria C.
    Galli, Laura
    Duca, Leonardo
    Marchegiani, Greta
    Clemente, Tommaso
    Carioti, Luca
    Lolatto, Riccardo
    Calza, Leonardo
    Celesia, Benedetto M.
    Cascio, Antonio
    Francisci, Daniela
    Saracino, Annalisa
    Torti, Carlo
    Zazzi, Maurizio
    Castagna, Antonella
    Santoro, Maria M.
    JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2024, 79 (09) : 2354 - 2363
  • [45] First evaluation of the Next-Generation Sequencing platform for the detection of HIV-1-drug resistance mutations in Belgium
    Dessilly, Geraldine
    Goeminne, Leonie
    Vandenbroucke, Anne-Therese
    Dufrasne, Francois E.
    Martin, Anandi
    Kabamba-Mukabi, Benoit
    PLOS ONE, 2018, 13 (12):
  • [46] Detection of Cytomegalovirus Drug Resistance Mutations by Next-Generation Sequencing
    Sahoo, Malaya K.
    Lefterova, Martina I.
    Yamamoto, Fumiko
    Waggoner, Jesse J.
    Chou, Sunwen
    Holmes, Susan P.
    Anderson, Matthew W.
    Pinsky, Benjamin A.
    JOURNAL OF CLINICAL MICROBIOLOGY, 2013, 51 (11) : 3700 - 3710
  • [47] Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain
    Keys, Jessica R.
    Zhou, Shuntai
    Anderson, Jeffrey A.
    Eron, Joseph J., Jr.
    Rackoff, Lauren A.
    Jabara, Cassandra
    Swanstrom, Ronald
    AIDS RESEARCH AND HUMAN RETROVIRUSES, 2015, 31 (06) : 658 - 668
  • [48] Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use
    Stéphanie Raymond
    Florence Nicot
    Nicolas Jeanne
    Olivier Delfour
    Romain Carcenac
    Caroline Lefebvre
    Michelle Cazabat
    Karine Sauné
    Pierre Delobel
    Jacques Izopet
    Scientific Reports, 7
  • [49] Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use
    Raymond, Stephanie
    Nicot, Florence
    Jeanne, Nicolas
    Delfour, Olivier
    Carcenac, Romain
    Lefebvre, Caroline
    Cazabat, Michelle
    Saune, Karine
    Delobel, Pierre
    Izopet, Jacques
    SCIENTIFIC REPORTS, 2017, 7
  • [50] Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
    Hiener, Bonnie
    Eden, John-Sebastian
    Horsburgh, Bethany A.
    Palmer, Sarah
    JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, 2018, (140):
12345