OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories
Nuttada Panpradist,
Ingrid A. Beck,
Justin Vrana,
Nikki Higa,
David McIntyre,
Parker S. Ruth,
Isaac So,
Enos C. Kline,
Ruth Kanthula,
Annie Wong-On-Wing,
Jonathan Lim,
Daisy Ko,
Ross Milne,
Theresa Rossouw,
Ute D. Feucht,
Michael Chung,
Gonzague Jourdain,
Nicole Ngo-Giang-Huong,
Laddawan Laomanit,
Jaime Soria,
James Lai,
Eric D. Klavins,
Lisa M. Frenkel,
Barry R. Lutz
Affiliations
Nuttada Panpradist
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Global WACh Program, Department of Global Health, University of Washington, Seattle, WA 98104, USA
Ingrid A. Beck
Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
Justin Vrana
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
Nikki Higa
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
David McIntyre
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
Parker S. Ruth
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
Isaac So
Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
Enos C. Kline
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
Ruth Kanthula
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Medstar Georgetown University Hospital, DC, 20007, USA
Annie Wong-On-Wing
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
Jonathan Lim
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
Daisy Ko
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
Ross Milne
Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
Theresa Rossouw
Department of Immunology, University of Pretoria, Pretoria 0002, South Africa
Ute D. Feucht
Research Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, Department of Paediatrics, University of Pretoria, Pretoria 0002, South Africa; Research Unit for Maternal and Infant Health Care Strategies, South African Medical Research Council, Kalafong Hospital, Atteridgeville 0008, South Africa
Michael Chung
Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Medicine, Aga Khan University, Nairobi, Kenya
Gonzague Jourdain
Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
Nicole Ngo-Giang-Huong
Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
Laddawan Laomanit
Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
Jaime Soria
Department of Infectious Diseases, Hospital Nacional Dos de Mayo, Av. Miguel Grau 13, Cercado de Lima 15003, Peru
James Lai
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
Eric D. Klavins
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
Lisa M. Frenkel
Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Virology, Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Corresponding author at: Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA.
Barry R. Lutz
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Corresponding author.
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. Keywords: HIV genotyping assay, NNRTI, NRT, Resistance, Regimen switching
