Overview of HIV drug resistance testing assays
- Michael J Kozal, MD
Michael J Kozal, MD
- Professor of Medicine
- Yale University School of Medicine
- Section Editors
- Martin S Hirsch, MD
Martin S Hirsch, MD
- Editor-in-Chief — Infectious Diseases
- Section Editor — Viral Infections
- Professor of Medicine
- Harvard Medical School
- Paul E Sax, MD
Paul E Sax, MD
- Section Editor — HIV
- Clinical Director, Division of Infectious Diseases
- Brigham and Women's Hospital
- Professor of Medicine
- Harvard Medical School
The use of drug resistance testing has become an integral part of HIV clinical care. The first clinical description of HIV resistance to an antiretroviral agent was published in 1989, when patients taking zidovudine monotherapy accumulated mutations within the reverse transcriptase gene, resulting in a marked increase in drug resistance . Subsequently, HIV variants resistant to every available antiretroviral agent have been identified. The evolution of drug resistance has significant clinical implications for choosing effective antiretroviral regimens.
This topic will provide an overview of HIV drug resistance testing. The interpretation of these tests and the approach to selecting an antiretroviral therapy regimen for patients with drug resistance mutations are discussed elsewhere. (See "Interpretation of HIV drug resistance testing" and "Selecting an antiretroviral regimen for treatment-experienced HIV-infected patients who are failing therapy" and "Evaluation of the treatment-experienced patient failing HIV therapy".)
RATIONALE FOR HIV SUSCEPTIBILITY TESTING
The use of HIV susceptibility testing to guide therapy leads to better viral suppression and has been associated with improved survival [2,3]. As an example, in an observational study of more than 2699 HIV-infected patients who were eligible for genotypic and phenotypic testing between 1999 and 2005, resistance testing was associated with improved survival (adjusted hazard ratio, 0.69 [95% CI 0.51-0.94]) after controlling for demographics, CD4 cell count, HIV RNA level, and intensity of clinical follow-up .
GENOTYPIC VERSUS PHENOTYPIC ASSAYS
This section will provide an overview of the commonly used resistance assays. The use of resistance testing when selecting an antiretroviral regimen is discussed elsewhere. (See "Selecting antiretroviral regimens for the treatment-naïve HIV-infected patient", section on 'Considerations prior to initiating treatment' and "Evaluation of the treatment-experienced patient failing HIV therapy".)
Overview of the assays — Resistance assays can be categorized as either genotypic or phenotypic. These assays detect resistance in fundamentally different ways, although the results generally correlate with each other.To continue reading this article, you must log in with your personal, hospital, or group practice subscription. For more information on subscription options, click below on the option that best describes you:
- Larder BA, Darby G, Richman DD. HIV with reduced sensitivity to zidovudine (AZT) isolated during prolonged therapy. Science 1989; 243:1731.
- Baxter JD, Mayers DL, Wentworth DN, et al. A randomized study of antiretroviral management based on plasma genotypic antiretroviral resistance testing in patients failing therapy. CPCRA 046 Study Team for the Terry Beirn Community Programs for Clinical Research on AIDS. AIDS 2000; 14:F83.
- Palella FJ Jr, Armon C, Buchacz K, et al. The association of HIV susceptibility testing with survival among HIV-infected patients receiving antiretroviral therapy: a cohort study. Ann Intern Med 2009; 151:73.
- Kuritzkes DR. Preventing and managing antiretroviral drug resistance. AIDS Patient Care STDS 2004; 18:259.
- Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. Department of Health and Human Services. Available at http://aidsinfo.nih.gov/contentfiles/lvguidelines/AdultandAdolescentGL.pdf (Accessed on September 13, 2017).
- Günthard HF, Saag MS, Benson CA, et al. Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2016 Recommendations of the International Antiviral Society-USA Panel. JAMA 2016; 316:191.
- Metzner KJ, Giulieri SG, Knoepfel SA, et al. Minority quasispecies of drug-resistant HIV-1 that lead to early therapy failure in treatment-naive and -adherent patients. Clin Infect Dis 2009; 48:239.
- Simen BB, Simons JF, Hullsiek KH, et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009; 199:693.
- Fox ZV, Geretti AM, Kjaer J, et al. The ability of four genotypic interpretation systems to predict virological response to ritonavir-boosted protease inhibitors. AIDS 2007; 21:2033.
- Rhee SY, Fessel WJ, Liu TF, et al. Predictive value of HIV-1 genotypic resistance test interpretation algorithms. J Infect Dis 2009; 200:453.
- Frentz D, Boucher CA, Assel M, et al. Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time. PLoS One 2010; 5:e11505.
- De Luca A, Cingolani A, Di Giambenedetto S, et al. Variable prediction of antiretroviral treatment outcome by different systems for interpreting genotypic human immunodeficiency virus type 1 drug resistance. J Infect Dis 2003; 187:1934.
- Van Laethem K, De Luca A, Antinori A, et al. A genotypic drug resistance interpretation algorithm that significantly predicts therapy response in HIV-1-infected patients. Antivir Ther 2002; 7:123.
- Liu TF, Shafer RW. Web resources for HIV type 1 genotypic-resistance test interpretation. Clin Infect Dis 2006; 42:1608.
- Desai S, Kyriakides T, Holodniy M, et al. Evolution of genotypic resistance algorithms and their impact on the interpretation of clinical trials: an OPTIMA trial substudy. HIV Clin Trials 2007; 8:293.
- Kellam P, Larder BA. Recombinant virus assay: a rapid, phenotypic assay for assessment of drug susceptibility of human immunodeficiency virus type 1 isolates. Antimicrob Agents Chemother 1994; 38:23.
- Japour AJ, Mayers DL, Johnson VA, et al. Standardized peripheral blood mononuclear cell culture assay for determination of drug susceptibilities of clinical human immunodeficiency virus type 1 isolates. The RV-43 Study Group, the AIDS Clinical Trials Group Virology Committee Resistance Working Group. Antimicrob Agents Chemother 1993; 37:1095.
- Abstracts of the 3rd International Workshop on Adverse Drug Reactions and Lipodystrophy in HIV. 23-26 October 2001. Athens, Greece. Antivir Ther 2001; 6 Suppl 4:3.
- Wrin T, Huang W, Yap J, et al. Evaluating HIV-1 co-receptor usage and inhibitors of virus entry using recombinant virus assays. Antivir Ther 2001; 6:3.
- Limoli K, Huang W, Toma S, et al. Validation and performance characteristics of the PhenoSense HIV fusion inhibitor susceptibility assay. 45th Annual ICAAC, Washington DC, 2005. Abstract H-1076.
- Underwood MR, Ross LL, Irlbeck DM, et al. Sensitivity of phenotypic susceptibility analyses for nonthymidine nucleoside analogues conferred by K65R or M184V in mixtures with wild-type HIV-1. J Infect Dis 2009; 199:84.
- Demeter L, Haubrich R. International perspectives on antiretroviral resistance. Phenotypic and genotypic resistance assays: methodology, reliability, and interpretations. J Acquir Immune Defic Syndr 2001; 26 Suppl 1:S3.
- Flandre P, Chappey C, Marcelin AG, et al. Phenotypic susceptibility to didanosine is associated with antiviral activity in treatment-experienced patients with HIV-1 infection. J Infect Dis 2007; 195:392.
- Harrigan PR, Montaner JS, Wegner SA, et al. World-wide variation in HIV-1 phenotypic susceptibility in untreated individuals: biologically relevant values for resistance testing. AIDS 2001; 15:1671.
- Shafer RW. Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. J Infect Dis 2009; 199:610.
- Halvas EK, Wiegand A, Boltz VF, et al. Low frequency nonnucleoside reverse-transcriptase inhibitor-resistant variants contribute to failure of efavirenz-containing regimens in treatment- experienced patients. J Infect Dis 2010; 201:672.
- Paredes R, Lalama CM, Ribaudo HJ, et al. Pre-existing minority drug-resistant HIV-1 variants, adherence, and risk of antiretroviral treatment failure. J Infect Dis 2010; 201:662.
- Kuritzkes DR, Lalama CM, Ribaudo HJ, et al. Preexisting resistance to nonnucleoside reverse-transcriptase inhibitors predicts virologic failure of an efavirenz-based regimen in treatment-naive HIV-1-infected subjects. J Infect Dis 2008; 197:867.
- Johnson JA, Li JF, Wei X, et al. Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naïve populations and associate with reduced treatment efficacy. PLoS Med 2008; 5:e158.
- Garcia-Diaz A, Lok CB, Madge S, et al. Detection of low-frequency K103N mutants after unstructured discontinuation of efavirenz in the presence of the CYP2B6 516 TT polymorphism. J Antimicrob Chemother 2008; 62:1188.
- Chabria SB, Gupta S, Kozal MJ. Deep sequencing of HIV: clinical and research applications. Annu Rev Genomics Hum Genet 2014; 15:295.
- Lataillade M, Chiarella J, Yang R, et al. Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study. PLoS One 2010; 5:e10952.
- Le T, Chiarella J, Simen BB, et al. Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use. PLoS One 2009; 4:e6079.
- Bonjoch A, Pou C, Pérez-Álvarez N, et al. Switching the third drug of antiretroviral therapy to maraviroc in aviraemic subjects: a pilot, prospective, randomized clinical trial. J Antimicrob Chemother 2013; 68:1382.
- Vitiello P, Brudney D, MacCartney M, et al. Responses to switching to maraviroc-based antiretroviral therapy in treated patients with suppressed plasma HIV-1-RNA load. Intervirology 2012; 55:172.
- Hammer SM, Eron JJ Jr, Reiss P, et al. Antiretroviral treatment of adult HIV infection: 2008 recommendations of the International AIDS Society-USA panel. JAMA 2008; 300:555.
- Moyle GJ, Wildfire A, Mandalia S, et al. Epidemiology and predictive factors for chemokine receptor use in HIV-1 infection. J Infect Dis 2005; 191:866.
- Brumme ZL, Goodrich J, Mayer HB, et al. Molecular and clinical epidemiology of CXCR4-using HIV-1 in a large population of antiretroviral-naive individuals. J Infect Dis 2005; 192:466.
- Wilkin TJ, Su Z, Kuritzkes DR, et al. HIV type 1 chemokine coreceptor use among antiretroviral-experienced patients screened for a clinical trial of a CCR5 inhibitor: AIDS Clinical Trial Group A5211. Clin Infect Dis 2007; 44:591.
- Coakley E. HIV tropism testing in the clinic. J Viral Entry 2007; 3:10.
- Koot M, Keet IP, Vos AH, et al. Prognostic value of HIV-1 syncytium-inducing phenotype for rate of CD4+ cell depletion and progression to AIDS. Ann Intern Med 1993; 118:681.
- Hosoya N, Su Z, Wilkin T, et al. Assessing human immunodeficiency virus type 1 tropism: Comparison of assays using replication-competent virus versus plasma-derived pseudotyped virions. J Clin Microbiol 2009; 47:2604.
- Lin NH, Kuritzkes DR. Tropism testing in the clinical management of HIV-1 infection. Curr Opin HIV AIDS 2009; 4:481.
- Whitcomb JM, Huang W, Fransen S, et al. Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism. Antimicrob Agents Chemother 2007; 51:566.
- Reeves JD, Coakley E, Petropoulos CJ, Whitcomb JM. An enhanced sensitivity Trofile HIV coreceptor tropism assay for selecting patients for therapy with entry inhibitors targeting CCR5: a review of analytical and clinical studies. J Viral Entry 2009; 3:94.
- Raymond S, Delobel P, Mavigner M, et al. Correlation between genotypic predictions based on V3 sequences and phenotypic determination of HIV-1 tropism. AIDS 2008; 22:F11.
- Coakley E, Reeves JD, Huang W, et al. Comparison of human immunodeficiency virus type 1 tropism profiles in clinical samples by the Trofile and MT-2 assays. Antimicrob Agents Chemother 2009; 53:4686.
- Su Z, Gulick RM, Krambrink A, et al. Response to vicriviroc in treatment-experienced subjects, as determined by an enhanced-sensitivity coreceptor tropism assay: reanalysis of AIDS clinical trials group A5211. J Infect Dis 2009; 200:1724.
- Trouplin V, Salvatori F, Cappello F, et al. Determination of coreceptor usage of human immunodeficiency virus type 1 from patient plasma samples by using a recombinant phenotypic assay. J Virol 2001; 75:251.
- Collin G, Descamps D, Telles F, et al. Differences in protease and reverse transcriptase sequences between the TruGene HIV-1 genotyping kit (Visible Genetics) and the ViroSeq genotyping system (PE Applied biosystems). Antivir Ther 2000; 5:53.
- Kagan RM, Johnson EP, Siaw M, et al. A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients. PLoS One 2012; 7:e46334.
- McGovern RA, Thielen A, Mo T, et al. Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies. AIDS 2010; 24:2517.
- McGovern RA, Thielen A, Portsmouth S, et al. Population-based sequencing of the V3-loop can predict the virological response to maraviroc in treatment-naive patients of the MERIT trial. J Acquir Immune Defic Syndr 2012; 61:279.
- Swenson LC, Mo T, Dong WW, et al. Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis 2011; 203:237.
- Swenson LC, Mo T, Dong WW, et al. Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc. Clin Infect Dis 2011; 53:732.
- RATIONALE FOR HIV SUSCEPTIBILITY TESTING
- GENOTYPIC VERSUS PHENOTYPIC ASSAYS
- Overview of the assays
- Advantages and limitations
- Genotypic resistance assays
- - Available assays
- - Genotypic definitions of resistance
- - Interpreting genotypic assays
- Phenotypic resistance assays
- - Recombinant virus assay
- - Phenotypic definitions of resistance
- Assay variability
- Biologic variability
- Virologic outcome
- ADDITIONAL RESISTANCE ASSAYS
- Low-abundance drug-resistant variants
- - Point mutation assays
- - Clonal sequencing assays
- - Deep sequencing
- HIV-1 proviral DNA assays
- Tropism assays
- - General background
- - Types of tropism assays
- Phenotypic tropism assays
- Genotypic tropism assays
- SUMMARY AND RECOMMENDATIONS