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Sequencing Technology Comparison for Detection of HIV-1 Mutations in the Protease and Reverse Transcriptase Regions
Poster Title: Sequencing Technology Comparison for Detection of HIV-1 Mutations in the Protease and Reverse Transcriptase Regions
Submitted on 13 Jan 2017
Author(s): Elian Rakhmanaliev1, Pramila Ariyaratne1, Alex Yeo1, Charlie Lee1, Pornpimon Nimitsuntiwong2, Chortip Wathtphan2, Zhang Rui1, Ekawat Passomsub2, Wasun Chantratita2, Gerd Michel1
Affiliations: 1Vela Research Pte. Ltd., Singapore; 2Department of Pathology, Faculty of Medicine, Ramathibodi Hospital Mahidol University, Bangkok, Thailand
This poster was presented at AMP 2016 Annual Meeting, Charlotte, North Carolina, USA, 10-12 Nov 2016
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Poster Information
Abstract: Resistance of HIV to antiretroviral drugs is the most common cause for therapeutic failure in people infected with Human Immunodeficiency Virus (HIV). Objective of this study was to compare two sequencing-based HIV-1 drug resistance monitoring systems: an CLIP-based system (TruGene HIV-1 Genotyping Kit) and a novel Next Generation Sequencing (NGS)-based test (Sentosa SQ HIV-1 Genotyping Assay). We used an automated NGS-based integrated workflow, comprised of 1) a robotic liquid handling system for nucleic acid extraction and NGS library preparation ((Sentosa SX101); 2) Ion Torrent instruments for deep sequencing; 3) kits for RNA extraction, HIV NGS library preparation and deep sequencing, and 4) data analysis and reporting software. Reporting includes 86 Drug Resistance Mutations (DRMs) across the Reverse Transcriptase (RT), Protease (PR) and Integrase genes. 111 prospective EDTA plasma clinical samples from patents infected with HIV-1 were tested for this study. All samples were tested on both systems. 97.3% (108/111) samples were subtyped as CRF01_AE. In total, 647 DRMs were detected (435 in the RT gene, 199 in the PR gene and 13 in the Integrase gene). The (Sentosa HIV Assay detected 100% (199/199) of all DRMs in the PR gene and more that 98% DRMs (427/435) in the RT gene. In total, 130 DRMs were detected by the (Sentosa HIV Assay, that were not found by TruGene and 8 DRMs were missed by the (Sentosa HIV Assay (but detected by TruGene). Mutation detection rate for the HIV PR gene was 100% (95%CI: 98.11-100%) for the (Sentosa HIV Assay and 90.45% (95%CI: 85.57-93.80%) for the TruGene system. In the RT gene 98.16% (95%CI: 96.41-99.07%) of DRMs were recorded by the (Sentosa HIV Assay and 74.48% (95%CI: 70.18-78.35%) by TruGene. Overall DRM detection rates aggregated were 98.74% (95%CI: 97.53-99.36%) for the (Sentosa HIV Assay and 79.5% (95%CI: 79.02-79.62%) for the TruGene HIV Kit. All HIV strains were carrying 1 or multiple DRMs in 61, 16 and 9 AA positions of the RT, PR and Integrase genes respectively. The most prevalent DRMs in the RT gene were: M184V 48,7%(54/111), K103N 29.7%(33/11), Y181C 27,9%(31/111), G190A and D67N (both 18.9%(21/111)). In the PR gene: M36I 91.9%(102/111), K20R 21.6%(24/111) and L10I 20.7%(23/111). Although DRMs are automatically reported by the system the software does not provide interpretation of the data with regard to usage in patient management. Detection and reporting of DRMs is critical for drug regiment and can minimize the development of resistance to antiviral drugs. High sensitivity (up to 5% mutation frequency) and the comparatively short turnaround time of 2.5 days make this NGS-based workflow a promising new tool for detecting relevant mutations in HIV-1 treatment targets.Summary: Sequencing Technology Comparison for Detection of HIV-1 Mutations in the Protease and Reverse Transcriptase Regions.Report abuse »
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