OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories

• Type of Material: Article
• Authors: Nuttada Panpradist, University of Washington; Ingrid A. Beck, Seattle Biomedical Research Institute; Justin Vrana, University of Washington; Nikki Higa, University of Washington; David McIntyre, University of Washington; Parker S. Ruth, University of Washington; Isaac So, Seattle Biomedical Research Institute; Enos C. Kline, University of Washington; Ruth Kanthula, University of Washington; Annie Wong-On-Wing, University of Washington; Jonathan Lim, University of Washington; Daisy Ko, University of Washington; Ross Milne, Seattle Biomedical Research Institute; Theresa Rossouw, University of Pretoria; Ute D. Feucht, University of Pretoria; Michael Chung, Emory University; Gonzague Jourdain, Institute of research for development, Thailand; Nicole Ngo-Giang-Huong, Institute of research for development, Thailand; Laddawan Laomanit, Division of Clinical Microbiology; Jaime Soria, Hospital Nacional Dos de Mayo; James Lai, University of Washington; Eric D. Klavins, University of Washington; Lisa M. Frenkel, Seattle Biomedical Research Institute; Barry R. Lutz, University of Washington
• Language: English
• Date: 2019-12-01
• Publisher: Lancet
• Publication Version: Final Published Version
• Copyright Statement: © 2019 The Author(s)
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1016/j.ebiom.2019.11.002
• Title of Journal or Parent Work: EBioMedicine
• Volume: 50
• Start Page: 34
• End Page: 44
• Grant/Funding Information: US National Institutes of Health R01 (AI110375) and the Clinical and Retrovirology Research Core and the Molecular Profiling and Computational Biology Core of the UW CFAR (P30 AI027757) funded the study; Feasibility testing was funded by the Office of Science-Industry Partnerships at Seattle Children's Research Institute, 2018 UW Holloman Innovation Challenge Award, and BRL's Pilcher Faculty Fellowship. NP thanks 2016 Ambulatory Practice for the Future Award. NH, DM, AW, and JL thank UW Mary Gates Undergraduate Research Scholarship (2014-16). The funders of the study did not have a role in study design, data collection, data analysis, data interpretation, or writing.
• Keywords: Resistance; Anti-HIV Agents; Computational Biology; Reagent Kits, Diagnostic; Research Design; HIV Infections; NNRTI; Genotyping Techniques; Mutation; Workflow; Genotype; Microbial Sensitivity Tests; HIV-1; Humans; Software; HIV genotyping assay; Drug Resistance, Viral; NRT; Regimen switching
• Research Categories: Biology, Genetics; Biology, Virology

Abstract

Background: HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels. Methods: The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated on 672 codons (168 specimens) from subtypes A, B, C, D, and AE. The kit uses dry reagents to facilitate assay setup, lateral flow devices for visual HIVDR detections, and in-house software with an interface for guiding users and analyzing results. Findings: HIVDR analysis of specimens by OLA-Simple compared to Sanger sequencing revealed 99.6 ± 0.3% specificity and 98.2 ± 0.9% sensitivity, and compared to high-sensitivity assays, 99.6 ± 0.6% specificity and 86.2 ± 2.5% sensitivity, with 2.6 ± 0.9% indeterminate results. OLA-Simple was performed more rapidly compared to Sanger sequencing (<4 h vs. 35–72 h). Forty-one untrained volunteers blindly tested two specimens each with 96.8 ± 0.8% accuracy. Interpretation: OLA-Simple compares favorably with HIVDR genotyping by Sanger and sensitive comparators. Instructional software enabled inexperienced, first-time users to perform the assay with high accuracy. The reduced complexity, cost, and training requirements of OLA-Simple could improve access to HIVDR testing in low-resource settings and potentially allow same-day selection of appropriate antiretroviral therapy. Fund: USA National Institutes of Health R01; the Clinical and Retrovirology Research Core and the Molecular Profiling and Computational Biology Core of the UW CFAR; Seattle Children's Research Institute; UW Holloman Innovation Challenge Award; Pilcher Faculty Fellowship.