Performance evaluation of the Vela Dx Sentosa next-generation sequencing system for HIV-1 DNA genotypic resistance

Autor: Pierre Delobel, Caroline Lefebvre, Stéphanie Raymond, Jacques Izopet, Florence Nicot, Luce Minier, Guillaume Martin-Blondel, Romain Carcenac, Florence Abravanel, Agnès Harter
Přispěvatelé: Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Virologie [Toulouse], CHU Toulouse [Toulouse], Service des maladies infectieuses et tropicales [Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], Laboratoire Virologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Service Maladies infectieuses et tropicales [CHU Toulouse], Pôle Inflammation, infection, immunologie et loco-moteur [CHU Toulouse] (Pôle I3LM Toulouse), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), CCSD, Accord Elsevier
Rok vydání: 2019
Předmět:
0301 basic medicine
Genotyping Techniques
MESH: High-Throughput Nucleotide Sequencing / methods
[SDV]Life Sciences [q-bio]
MESH: Automation
Laboratory
Integrase inhibitor
HIV Infections
Integrase
0302 clinical medicine
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases
030212 general & internal medicine
Longitudinal Studies
MESH: Longitudinal Studies
Sanger sequencing
DNA genotyping
MESH: Genotyping Techniques / methods
High-Throughput Nucleotide Sequencing
Viral Load
MESH: Drug Resistance
Viral / genetics
MESH: HIV-1 / genetics
3. Good health
[SDV] Life Sciences [q-bio]
Infectious Diseases
[SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases
symbols
RNA
Viral
MESH: RNA
Viral / blood
MESH: Viral Load
Viral load
HIV drug resistance
MESH: Mutation
030106 microbiology
Biology
MESH: HIV-1 / drug effects
DNA sequencing
Deep sequencing
03 medical and health sciences
symbols.namesake
Virology
Drug Resistance
Viral
Reverse transcriptase
MESH: HIV Infections / virology
Humans
Genotyping
Automation
Laboratory
MESH: Humans
DNA extraction
Drug resistance
Mutation
Next-generation sequencing
HIV-1
Zdroj: Journal of Clinical Virology
Journal of Clinical Virology, Elsevier, 2020, 122, pp.104229-104233. ⟨10.1016/j.jcv.2019.104229⟩
Journal of Clinical Virology, 2020, 122, pp.104229. ⟨10.1016/j.jcv.2019.104229⟩
ISSN: 1873-5967
1386-6532
Popis: International audience; 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
Databáze: OpenAIRE
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