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Clinical Evaluation of a Novel NGS-Based HIV-1 Drug Resistance Monitoring Test
EP25836
Poster Title: Clinical Evaluation of a Novel NGS-Based HIV-1 Drug Resistance Monitoring Test
Submitted on 05 Jun 2017
Author(s): 1Elian Rakhmanaliev, 2Wasun Chantratita, 2Pornpimon Nimitsuntiwong, 2Chortip Wathtphan, 2Ekawat Passomsub, 1Raymond Luo, 1Pramila Ariyaratne, 1Charlie Lee, 1Gerd Michel
Affiliations: 1Vela Research Pte. Ltd., Singapore; 2Department of Pathology, Faculty of Medicine, Ramathibodi Hospital Mahidol University, Bangkok, Thailand
This poster was presented at AMP Global 2017 Congress on Molecular Pathology, Berlin, Germany, April 3-5, 2017
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Poster Information
Abstract: Introduction: The worldwide scale-up of antiretroviral therapy has decreased HIV mortality and improved clinical outcomes. However, incomplete suppression is known to be a risk factor for developing Drug Resistance Mutations (DRMs). The objective of this study was to evaluate a novel Next Generation Sequencing (NGS)-based HIV-1 drug resistance monitoring test (Sentosa SQ HIV-1 Genotyping Assay).
Methods: In this study we used an automated NGS-based integrated workflow, comprised of 1) a robotic liquid handling system for RNA extraction and NGS library preparation (Sentosa SX101); 2) Ion Torrent’s instruments for deep sequencing; 3) kits for RNA extraction, HIV NGS library preparation and sequencing, and 4) data analysis and reporting software. Reporting includes 276 amino acid (AA) mutations in 103 AA positions across the Reverse Transcriptase (RT), Protease (PR) and Integrase HIV genes.
Results: 3330 prospective clinical samples from patents infected with HIV-1 were tested on Vela’s Sentosa SQ NGS system. 91.9% (3061) of the samples were subtyped as CRF01_AE, 3.7% (124) as recombinant form BC, 2.5% (83) as subtype B, <0.4% (12) as other subtypes. 50 samples (1.5%) were infected with 2 or more HIV-1 strains belonging to different subtypes. In total, 33,439 DRMs were detected in 3330 samples (15,789, 17,226 and 424 in the RT, PR and Integrase genes respectively). These DRMs were distributed across the target genes as follows: 94 AA variants in 31 AA positions of the RT gene, 78 AA variants in 38 AA positions of the PR gene and 32 AA variants in 23 AA positions of the Integrase gene. The most prevalent DRMs in the RT gene were: K238R(53.1%), M184V(47.5%), K103N(35.9%), Y181C(26.8%), V179I(25.1%), G190A(18.4%), D67N(14.5%), K65R(14.4%), K103E(13.8%), H221Y(12.5%), K101E(12.0%), N348I(11.0%), T69N(10.6%), V106I(10.0%). In the PR gene: M36I(94.2%), H69K(93.6%), L89M(85.5%), G16E(35.2%), L63P(30.8%), K20R(27.9%), L10I(22.3%), I93L(21.9%), L10V(16.5%), I62V(13.4%), V82I(11.5%), and in the Integrase gene: S230N(2.7%), V151I(2.3%), E157Q(1.6%), L74M(1.2%).
Conclusions: To our knowledge this is the first large clinical data set employing automated Ion Torrent based NGS as the analytical method for detection of DRMs in HIV-1. NGS has demonstrated clinical utility by providing results in a comparatively short period of time with increased sensitivity compared to conventional sequencing approaches. The new NGS workflow thus appears as a promising new tool for detecting clinically relevant variants in HIV-1.
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