Features of Genotypic and Phenotypic Resistance Assays

Last updated March 22, 2015
Case Authors: 
David H. Spach, MD's picture
David H. Spach, MD
Professor of Medicine
Division of Infectious Diseases
Clinical Director, Frontier AIDS Education and Training Center
University of Washington School of Medicine
Learning Objectives: 
  1. Describe the genotypic assays and the meaning of the letter and number notated for individual mutations.
  2. Discuss the principles of the phenotypic assay and what the fold change represents.

Display Group

  1. Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science. 1996;271:1582-6.
  2. O'Neil PK, Sun G, Yu H, Ron Y, Dougherty JP, Preston BD. Mutational analysis of HIV-1 long terminal repeats to explore the relative contribution of reverse transcriptase and RNA polymerase II to viral mutagenesis. J Biol Chem. 2002;277:38053-61.
  3. Hanna GJ, D'Aquila RT. Clinical use of genotypic and phenotypic drug resistance testing to monitor antiretroviral chemotherapy. Clin Infect Dis. 2001;32:774-82.
  4. Hirsch MS, Günthard HF, Schapiro JM, et al. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis. 2008;47:266-85.
  5. Wensing AM, Calvez V, Günthard HF, et al. 2014 Update of the drug resistance mutations in HIV-1. Top Antivir Med. 2014;22:642-50.
  6. Larder BA, Kemp SD, Harrigan PR. Potential mechanism for sustained antiretroviral efficacy of AZT-3TC combination therapy. Science. 1995;269:696-9.
  7. Durant J, Clevenbergh P, Halfon P, et al. Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet. 1999;353:2195-9.
  8. 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:F83-93.
  9. Tural C, Ruiz L, Holtzer C, et al. Clinical utility of HIV-1 genotyping and expert advice: the Havana trial. AIDS. 2002;16:209-18.
  10. Cingolani A, Antinori A, Rizzo MG, et al. Usefulness of monitoring HIV drug resistance and adherence in individuals failing highly active antiretroviral therapy: a randomized study (ARGENTA). AIDS. 2002;16:369-79.
  11. Meynard JL, Vray M, Morand-Joubert L, et al. Phenotypic or genotypic resistance testing for choosing antiretroviral therapy after treatment failure: a randomized trial. AIDS. 2002;16:727-36.
  12. Cohen CJ, Hunt S, Sension M, et al. A randomized trial assessing the impact of phenotypic resistance testing on antiretroviral therapy. AIDS. 2002;16:579-88.
  13. Haubrich RH, Kemper CA, Hellmann NS, et al. A randomized, prospective study of phenotype susceptibility testing versus standard of care to manage antiretroviral therapy: CCTG 575. AIDS. 2005;19:295-302.
  14. Deeks SG, Hellmann NS, Grant RM, et al. Novel four-drug salvage treatment regimens after failure of a human immunodeficiency virus type 1 protease inhibitor-containing regimen: antiviral activity and correlation of baseline phenotypic drug susceptibility with virologic outcome. J Infect Dis. 1999;179:1375-81.
  15. Walter H, Schmidt B, Rascu A, et al. Phenotypic HIV-1 resistance correlates with treatment outcome of nelfinavir salvage therapy. Antivir Ther. 2000;5:249-56.
  16. Deeks SG, Wrin T, Liegler T, et al. Virologic and immunologic consequences of discontinuing combination antiretroviral-drug therapy in HIV-infected patients with detectable viremia. N Engl J Med. 2001;344:472-80.
  17. Finzi D, Blankson J, Siliciano JD, et al. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat Med. 1999;5:512-7.