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HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors)

HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors)

Test Summary

HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors)


Clinical Use

  • Guide change of antiretroviral therapy for HIV-1-infected and virologically suppressed patients

Clinical Background

In HIV-1-infected patients, combination antiretroviral therapy (cART) can reduce viral replication, reduce HIV transmission, and improve clinical outcomes.1,2 However, incomplete virologic suppression can lead to drug-resistant virus and therapeutic failure.3-5 Genotypic resistance testing is recommended for selection of antiretroviral regimens before initiating cART, to assess for transmitted resistant virus, and at the time of treatment failure.1,2

Standard genotypic resistance tests measure plasma RNA and are appropriate for viremic patients, but they may not be appropriate for individuals with viral suppression, as viral levels may be too low for accurate genotyping. Patients with viral suppression may be candidates for a regimen switch for reasons such as drug toxicity or regimen simplification, among others. When considering a regimen switch, guidelines recommend reviewing a patient's cART history and prior resistance testing results.1,2

When viral RNA levels are low and cART treatment history and prior resistance testing results are unavailable, proviral DNA genotypic testing may be useful.1 Proviral DNA is viral DNA that is integrated into the host genome; thus, it can be assessed when plasma RNA levels are low or undetectable. It also represents an archive of viral mutations that can differ from plasma RNA.

Although the clinical utility of proviral DNA genotypic testing has not yet been established, resistance mutations present in plasma viral RNA prior to virologic suppression can often be identified in proviral DNA. For virologically suppressed patients, proviral DNA genotypic testing is 75% to 89% concordant with plasma RNA testing for protease and reverse transcriptase mutations.6-8 In addition, proviral DNA testing may detect resistance mutations that may be archived and, thus, not detected in plasma RNA.6-9

Quest Diagnostics offers HIV-1 proviral DNA testing for multiple cART classes: nucleoside reverse transcriptase inhibitors (RTIs), non-nucleoside RTIs, protease inhibitors (PIs), and integrase inhibitors. The following tests include HIV-1 proviral DNA testing:

  • HIV-1 Proviral DNA (RTI, PI, Integrase Inhibitors): test code 94807

  • HIV-1 Proviral DNA (RTI, PI, Integrase Inhibitors + Tropism): test code 94810

  • HIV-1 Proviral DNA (RTI, PI Inhibitors): test code 94808

  • HIV-1 Proviral DNA (Integrase Inhibitors): test code 94809

Individuals Suitable for Testing

  • Virologically suppressed HIV-1-infected individuals being considered for a regimen change whose treatment history and/or prior plasma HIV-1 RNA genotype are unavailable1

  • HIV-1-infected individuals with low-level viremia (<1,000 copies/mL) whose genotype could not be determined by plasma RNA methods1


  • Next-generation sequencing of protease (codons 1-99), reverse transcriptase (codons 1-560), and integrase (codons 1-288) regions of the HIV-1 pol gene
  • Bioinformatic analysis: filter sequences and identify resistance-associated mutations present in ‚Č•10% of the proviral DNA species
  • Proviral DNA limit of detection (LOD95): 83 DNA copies/mL (whole blood)
  • Reported results

    –  Resistance status: predicted resistance or probable resistance

    –  Specific mutations: eg, M184V in reverse transcriptase

    –  HIV-1 subtype, including A, B, BF, C, D, AE, AG, or H

Interpretive Information

  • A result of "predicted resistance" indicates that mutations associated with drug resistance to the indicated drug were detected.

  • A result of "probable resistance" indicates that mutations likely to confer drug resistance to the indicated drug were detected.

  • A result of "no resistance predicted" indicates that drug resistance is unlikely for the indicated drug.

Although the proviral DNA is an archive of many resistance mutations that emerged throughout the course of infection, this archive should not be considered comprehensive; some resistance mutations detected in plasma viral RNA may not be detected in proviral DNA.6-9


  1. Gunthard 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;316:191-210.

  2. Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in adults and adolescents living with HIV. Department of Health and Human Services. http://www.aidsinfo.nih.gov/ContentFiles/AdultandAdolescentGL.pdf. Updated October 17, 2017. Accessed December 27, 2017.

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

  4. Arts EJ, Hazuda DJ. HIV-1 antiretroviral drug therapy. Cold Spring Harb Perspect Med. 2012;2:a007161.

  5. Tang MW, Shafer RW. HIV-1 antiretroviral resistance: scientific principles and clinical applications. Drugs. 2012;72:e1-25.

  6. Allavena C, Rodallec A, Leplat A, et al. Interest of proviral HIV-1 DNA genotypic resistance testing in virologically suppressed patients candidate for maintenance therapy. J Virol Methods. 2018;251:106-110.

  7. Lubke N, Di Cristanziano V, Sierra S, et al. Proviral DNA as a target for HIV-1 resistance analysis. Intervirology. 2015;58:184-189.

  8. Porter D, Toma J, Tan Y, et al. Clinical outcomes of virologically-suppressed patients with pre-existing HIV-1 drug resistance mutations switching to rilpivirine/emtricitabine/tenofovir disoproxil fumarate in the SPIRIT Study. HIV Clin Trials. 2016;17:29-37.

  9. Zaccarelli M, Santoro MM, Armenia D, et al. Genotypic resistance test in proviral DNA can identify resistance mutations never detected in historical genotypic test in patients with low level or undetectable HIV-RNA. J Clin Virol. 2016;82:94-100.

Content reviewed 01/2018


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