Human Immunodeficiency Virus 1, Antiretroviral Drug Resistance Testing - HIV Drug Resistance

  • Diagnosis
  • Monitoring
  • Background
  • Lab Tests
  • References
  • Related Topics

Indications for Testing

  • Newly diagnosed HIV patients prior to initiating therapy (Gunthard, 2016)
  • Previously diagnosed HIV patients who delayed antiretroviral therapy (ART)
  • Patients receiving ART but experiencing treatment failure

Laboratory Testing

  • Resistance testing
    • Genotyping for reverse transcriptase (RT) and protease resistance (PR) mutations – standard drug resistance testing should focus on testing for mutations in these genes
      • Recommended for all patients (Gunthard, 2016)
      • For patients experiencing treatment failure, genotype only if patient is highly adherent to antiretroviral therapy
      • Method
        • Standard genotype resistance testing uses Sanger sequencing on cDNA amplified by polymerase chain reaction (PCR) with a lower limit of detection of 20%
        • Point mutation assays and next generation deep sequencing allow for a lower limit of detection (below 20%)
          • Accuracy and clinical significance of these findings are still being investigated
      • Results
        • Some specific mutations can guide ART selection
          • Calculation of genotype susceptibility score can also be utilized (Rhee, 2009; Wittkop, 2011)
        • Stanford University HIV Drug Resistance Database
          • Can use provided mutation data to provide recommendations
      • Genotyping is cost prohibitive in low- and middle-income countries
        • Population-based testing may be helpful where cost is a factor to determine resistance patterns
        • Baseline genotypic testing in patients from areas with evidence of HIV drug resistance may help determine etiology of treatment failure
    • Phenotyping in combination with genotyping
      • Phenotyping measures in vitro susceptibility in cell culture
      • Indications
        • Patients with complex treatment failure history
        • Drug development and drug resistance research
      • Limitation
        • High cost and lengthy turnaround times
  • Specific drug resistance testing (Clutter, 2016)
    • Nucleoside/nucleotide reverse transcriptase inhibitors (NRTI)/nonnucleoside reverse transcriptase inhibitors (NNRTI)/protease inhibitor (PI) resistance mutations
    • Integrase strand transfer inhibitors (INSTIs)
      • Most recent antiretroviral drugs approved for therapy
      • If transmitted INSTI resistance is a concern, providers should also test for resistance mutations to this class of drugs
      • Raltegravir (RAL) and elvitegravir (EVG) – show high levels of cross-resistance
      • Dolutegravir (DTG) – high genetic barrier to resistance
    • HIV tropism assays for coreceptors
      • Guides use of maraviroc therapy in adult patients infected with CCR5-tropic HIV-1 virus strain resistant to multiple antiretroviral agents and who have evidence of viral replication and multidrug failure
      • Perform testing before initiating CCR5 antagonist or at time of virologic failure while patient is receiving CCR5 antagonist (Department of Health and Human Services [HHS], 2016)
      • Phenotyping and genotyping assays are available
        • Phenotyping recommended; however, newer genotyping assays may provide sufficient data
    • HLA-B*5701 testing (genotyping for abacavir resistance)  
      • Should be performed prior to abacavir use – those who test positive should not be given abacavir (Gunthard, 2016; HHS, 2016)
      • Required by FDA prior to the use of abacavir
      • ~50% of individuals who are positive for HLA-B*5701 allele experience hypersensitivity reaction to abacavir that may be life threatening
  • HIV retroviral therapy should be monitored (Department of Health and Human Services [HHS], 2016)
  • Resistance testing should be performed at the following points in a patient’s treatment (HHS, 2016)
    • Initial entry into care
    • After antiretroviral therapy (ART) initiation or modification – optional if changed for toxicity or convenience
    • After treatment failure
    • When clinically indicated
    • If ART initiation is delayed (optional)
  • Quantitative HIV-1 RNA viral load testing – monitored to determine efficacy of treatment
    • Successful therapy results in suppression to <20-75 copies/mL
    • Serial testing recommended by the International Antiviral Society – (USA Panel, 2016)
    • HIV-1 RNA should be measured ~4 weeks after initiation of testing and every 3-4 months the first year
    • Viral amplification is not possible for virologically suppressed patients switching therapy because of toxicity or for convenience – resistance testing should not be performed in those patients
      • Results from prior resistance testing may help in constructing a new regimen

Drug resistance develops to all classes of HIV antiretroviral drugs. The use of ≥3 highly active antiretroviral therapy (HAART) is used to counter this tendency.  In the U.S., the Department of Health and Human Services (HHS) Use of Antiretroviral Agents in HIV-1-Infected Adults and Adolescents lists recommendations for initiating drug regimens in antiretroviral-naive patients.  

Drug resistance testing is conducted prior to the start of therapy to assist with selection of optimal treatment regimens, and again when treatment failures occur. Drug resistance mutations can be determined using phenotypic and genotypic methods.


  • Prevalence – new mutations associated with drug resistance occur in 16-65% of patients


  • Histocompatibility – HLA-B*57:01 genotype associated with risk of abacavir hypersensitivity
    • Autosomal dominant inheritance
    • Most common in Indian and Thai individuals; less common in Caucasians; rare in East Asians


  • Acquired drug resistance occurs during therapy and is a result of drug pressure (selection) 
    • Stopping treatment causes reversion to wild type – resistance will persist and quickly manifest when restarting therapy
  • The high rate of transcriptional errors that occur during HIV viral duplication results in a high rate of mutations, which are selected by drug pressure
    • Transmitted drug resistance are mutations found in newly diagnosed HIV-1 infected individuals
  • Use of triple therapy delays development of drug resistance; however, interruption of therapy leads to development of drug resistance and treatment failure
    • Reasons for interruptions in therapy and/or treatment failure include
      • Lack of access to care
      • Patient noncompliance
      • Drug pharmacology issues – absorption, elimination, interactions
  • Highest resistance rates (lowest genetic barriers) – nucleoside reverse transcriptase inhibitors
  • Role of resistance testing in primary infection
    • Identify mutations present to guide initial treatment selection
    • Identify etiology of treatment failures
  • Role of resistance testing in established infections that are currently being treated
    • Failure of current therapy – decreasing CD4 count, increasing viral load
    • Patient noncompliance with HAART regimen
    • Increased risk of resistance to newly resumed therapy
    • Clinical failure
Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

Human Immunodeficiency Virus 1, Genotype by Sequencing 0055670
Method: Reverse Transcription Polymerase Chain Reaction/Sequencing


Treatment failure can be caused by factors other than drug resistance; interpretation of resistance genotyping results must be done in conjunction with other clinical and laboratory information 

Uses the Viroseq HIV-1 Genotyping System for sequencing; some insertions or deletions may be difficult to detect

Absence of resistance mutations does not rule out presence of reservoirs of resistant viruses that cannot be detected

May not detect HIV-1 populations <20% of the total population

Human Immunodeficiency Virus Type 1 (HIV-1) Drug Resistance (PhenoSense GT Plus Integrase) 2010808
Method: Phenotyping/Genotyping  

Human Immunodeficiency Virus (HIV) Phenotype Comprehensive 0092050
Method: Drug Susceptibility using HIV Culture
(Cell Culture)


Treatment failure can be caused by factors other than drug resistance; interpretation of resistance genotyping results must be done in conjunction with other clinical and laboratory information

Comparisons between assays performed in different laboratories are not recommended; no standardization exists among methods of HIV-1 drug resistance testing

Absence of resistance mutations does not rule out the presence of reservoirs of resistant viruses that cannot be detected

Human Immunodeficiency Virus Type 1 (HIV-1) Drug Resistance (GenoSURE PRIme) 2008438
Method: Polymerase Chain Reaction/Sequencing 

HIV1 Genotype and Integrase Inhibitor Resistance by Sequencing 2009256
Method: Polymerase Chain Reaction/Sequencing

Human Immunodeficiency Virus 1 (HIV-1) by Quantitative PCR with Reflex to HIV-1 Genotype by Sequencing 2002689
Method: Quantitative Polymerase Chain Reaction/Sequencing

PhenoSense Entry 2003237
Method: Phenotyping/Genotyping

PhenoSense Integrase Inhibitor 2003235
Method: Phenotyping

Human Immunodeficiency Virus 1 (HIV-1) by Quantitative PCR with Reflex to HIV PhenoSense GT 2010797
Method: Quantitative Polymerase Chain Reaction/Sequencing/Culture

Trofile Co-Receptor Tropism 0093370
Method: Recombinant virus, single replication

Trofile DNA Co-Receptor Tropism Assay 2004747
Method: CD4 Cell Culture Assay for Phenotypic Recombinant-virus Co-receptor Tropism

HIV-1 Genotyping and Tropism by Next Generation Sequencing (DEEPGEN) 2011279
Method: Massively Parallel Sequencing


This test should be used for patients with documented HIV-1 infection and a viral load greater than 1000 copies/mL

HIV-1 Co-Receptor Tropism by Next Generation Sequencing (DEEPGEN) 2011283
Method: Massively Parallel Sequencing

HLA-B*57:01 for Abacavir Sensitivity 2002429
Method: Polymerase Chain Reaction/Fluorescence Monitoring


Diagnostic errors can occur due to rare sequence variations

Rare recombination events between HCP5 SNP rs2395029 and HLA-B*57:01 may occur

Nongenetic factors that may affect drug sensitivity are not identified

Testing for a genetic variant associated with ABC HSR does not replace the need for therapeutic drug or other clinical monitoring


Günthard HF, Saag MS, Benson CA, del Rio C, Eron JJ, Gallant JE, Hoy JF, Mugavero MJ, Sax PE, Thompson MA, Gandhi RT, Landovitz RJ, Smith DM, Jacobsen DM, Volberding PA. Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2016 Recommendations of the International Antiviral Society-USA Panel. JAMA. 2016; 316(2): 191-210. PubMed

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.. [Last updated Jul 2016; Accessed: Apr 2017]

PENTA Steering Committee, Welch S, Sharland M, Lyall EG, Tudor-Williams G, Niehues T, Wintergerst U, Bunupuradah T, Hainaut M, Negra MD, Pena MJ, Amador JT, Gattinara GC, Compagnucci A, Faye A, Giaquinto C, Gibb DM, Gandhi K, Forcat S, Buckberry K, Harper L, Königs C, Patel D, Bastiaans D. PENTA 2009 guidelines for the use of antiretroviral therapy in paediatric HIV-1 infection. HIV Med. 2009; 10(10): 591-613. PubMed

Vandekerckhove LP, Wensing AM, Kaiser R, Brun-Vézinet F, Clotet B, De Luca A, Dressler S, Garcia F, Geretti AM, Klimkait T, Korn K, Masquelier B, Perno CF, Schapiro JM, Soriano V, Sönnerborg A, Vandamme A, Verhofstede C, Walter H, Zazzi M, Boucher CA, European Consensus Group on clinical management of tropism testing. European guidelines on the clinical management of HIV-1 tropism testing. Lancet Infect Dis. 2011; 11(5): 394-407. PubMed

General References

Clutter DS, Jordan MR, Bertagnolio S, Shafer RW. HIV-1 drug resistance and resistance testing. Infect Genet Evol. 2016; 46: 292-307. PubMed

Dunn DT, Coughlin K, Cane PA. Genotypic resistance testing in routine clinical care. Curr Opin HIV AIDS. 2011; 6(4): 251-7. PubMed

Geretti AM, Paredes R, Kozal MJ. Transmission of HIV drug resistance: lessons from sensitive screening assays. Curr Opin Infect Dis. 2015; 28(1): 23-30. PubMed

Grant PM, Zolopa AR. The use of resistance testing in the management of HIV-1-infected patients. Curr Opin HIV AIDS. 2009; 4(6): 474-80. PubMed

Llibre JM, Pulido F, García F, Deltoro MG, Blanco JL, Delgado R. Genetic barrier to resistance for dolutegravir. AIDS Rev. 2015; 17(1): 56-64. PubMed

Mesplède T, Wainberg MA. Resistance against Integrase Strand Transfer Inhibitors and Relevance to HIV Persistence. Viruses. 2015; 7(7): 3703-18. PubMed

Rhee S, Fessel J, Liu TF, Marlowe NM, Rowland CM, Rode RA, Vandamme A, Van Laethem K, Brun-Vezinet F, Calvez V, Taylor J, Hurley L, Horberg M, Shafer RW. Predictive value of HIV-1 genotypic resistance test interpretation algorithms. J Infect Dis. 2009; 200(3): 453-63. PubMed

Smit E. Antiviral resistance testing. Curr Opin Infect Dis. 2014; 27(6): 566-72. PubMed

Taylor S, Jayasuriya A, Smit E. Using HIV resistance tests in clinical practice. J Antimicrob Chemother. 2009; 64(2): 218-22. PubMed

Wittkop L, Günthard HF, de Wolf F, Dunn D, Cozzi-Lepri A, de Luca A, Kücherer C, Obel N, von Wyl V, Masquelier B, Stephan C, Torti C, Antinori A, García F, Judd A, Porter K, Thiébaut R, Castro H, van Sighem AI, Colin C, Kjaer J, Lundgren JD, Paredes R, Pozniak A, Clotet B, Phillips A, Pillay D, Chêne G, EuroCoord-CHAIN study group. Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): a European multicohort study. Lancet Infect Dis. 2011; 11(5): 363-71. PubMed

References from the ARUP Institute for Clinical and Experimental Pathology®

Melis R, Lewis T, Millson A, Lyon E, McMillin GA, Slev PR, Swensen J. Copy number variation and incomplete linkage disequilibrium interfere with the HCP5 genotyping assay for abacavir hypersensitivity. Genet Test Mol Biomarkers. 2012; 16(9): 1111-4. PubMed

Pyne MT, Wilson A, Hillyard DR. Large-scale comparison of Roche Cobas AmpliPrep/Cobas TaqMan and Abbott RealTime HIV assays. J Virol Methods. 2012; 184(1-2): 106-8. PubMed

Taborda NA, Cataño JC, Delgado JC, Rugeles MT, Montoya CJ. Higher SLPI expression, lower immune activation, and increased frequency of immune cells in a cohort of Colombian HIV-1 controllers. J Acquir Immune Defic Syndr. 2012; 60(1): 12-9. PubMed

Medical Reviewers

Content Reviewed: 
March 2017

Last Update: July 2017