HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors)
HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors)
This test is used to guide change of antiretroviral therapy for HIV-1-infected and virologically suppressed patients.
Test Summary
HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors)
Test Code: 94807
Clinical Use
- Guide change of antiretroviral therapy for virally suppressed individuals with HIV-1
Clinical Background
For people with HIV, combination antiretroviral therapy (cART) can reduce viral replication, reduce HIV transmission, and improve clinical outcomes.1,2 However, incomplete viral 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 viral RNA in plasma and are appropriate for viremic individuals. However, standard tests may not be appropriate for individuals with viral suppression, as viral levels may be too low for accurate genotyping. Individuals with viral suppression may be candidates for a regimen switch due to drug toxicity, regimen simplification, or other reasons. When considering a regimen switch, guidelines recommend reviewing an individual'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.1,2 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 virally suppressed individuals, proviral DNA genotypic testing is 75% to 89% concordant with plasma viral 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 viral RNA.6–9
As part of the HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors) test (test code 94807), Quest Diagnostics offers HIV-1 proviral DNA testing for multiple cART classes, including nucleoside and non-nucleoside reverse transcriptase inhibitors (RTIs), protease inhibitors (PIs), and integrase inhibitors. RTI and PI testing and Integrase Inhibitor testing are separately available:
- HIV-1 Resistance, Proviral DNA (RTI, PI Inhibitors): test code 94808
- HIV-1 Resistance, Proviral DNA (Integrase Inhibitors): test code 94809
In addition, Quest offers HIV-1 Resistance and Coreceptor Tropism, Proviral DNA (test code 94810), which includes RTI, PI, integrase inhibitors, and tropism. This panel also provides tropism testing that may be considered for screening virologically suppressed patients prior to prescribing a CCR5 antagonist.
Individuals Suitable for Testing
- Virally suppressed individuals with HIV-1 who are being considered for a regimen change whose treatment history and/or prior plasma HIV-1 RNA genotype are unavailable1,2
- Individuals with HIV-1 with low-level viremia (<1,000 copies/mL) whose genotype could not be determined by plasma viral RNA methods1,2
Methods
- 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 ≥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 (A, B, BF, C, D, AE, AG, or H)
Interpretive Information
- A result of “predicted resistance” indicates detection of mutations associated with drug resistance to the indicated drug.
- A result of “probable resistance” indicates detection of mutations likely to confer drug resistance to the indicated drug.
- 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
References
- Gandhi RT, Bedimo R, Hoy JF, et al. Antiretroviral drugs for treatment and prevention of HIV infection in adults. 2022 Recommendations of the International Antiviral Society – USA Panel. JAMA. 2023;329(1):63-84. doi:10.1001/jama.2022.22246
- Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in adults and adolescents with HIV. Department of Health and Human Services. Updated September 12, 2024. Accessed February 13, 2025. https://clinicalinfo.hiv.gov/en/guidelines/hiv-clinical-guidelines-adult-and-adolescent-arv/whats-new
- Tang MW, Shafer RW. HIV-1 antiretroviral resistance. Drugs. 2012;72(9):e1-e25. doi:10.2165/11633630-000000000-00000
- Arts EJ, Hazuda DJ. HIV-1 antiretroviral drug therapy. Cold Spring Harb Perspect Med. 2012;2(4):a007161. doi:10.1101/cshperspect.a007161
- Clutter DS, Jordan MR, Bertagnolio S, et al. HIV-1 drug resistance and resistance testing. Infect, Genet Evol. 2016;46:292-307. doi:10.1016/j.meegid.2016.08.031
- 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. doi:10.1016/j.jviromet.2017.10.016
- Lübke N, DiCristanziano V, Sierra S, et al. Proviral DNA as a target for HIV-1 resistance analysis. Intervirology. 2015;58(3):184-189. doi:10.1159/000431093
- Porter DP, Daeumer M, Thielen A, et al. Emergent HIV-1 drug resistance mutations were not present at low-frequency at baseline in non-nucleoside reverse transcriptase inhibitor-treated subjects in the STaR study. Viruses. 2015;7(12):6360-6370. doi:10.3390/v7122943
- 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. doi:10.1016/j.jcv.2016.07.007
Content reviewed 03/2025
This test is used to guide change of antiretroviral therapy for HIV-1-infected and virologically suppressed patients.
Test Summary
HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors)
Test Code: 94807
Clinical Use
- Guide change of antiretroviral therapy for virally suppressed individuals with HIV-1
Clinical Background
For people with HIV, combination antiretroviral therapy (cART) can reduce viral replication, reduce HIV transmission, and improve clinical outcomes.1,2 However, incomplete viral 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 viral RNA in plasma and are appropriate for viremic individuals. However, standard tests may not be appropriate for individuals with viral suppression, as viral levels may be too low for accurate genotyping. Individuals with viral suppression may be candidates for a regimen switch due to drug toxicity, regimen simplification, or other reasons. When considering a regimen switch, guidelines recommend reviewing an individual'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.1,2 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 virally suppressed individuals, proviral DNA genotypic testing is 75% to 89% concordant with plasma viral 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 viral RNA.6–9
As part of the HIV-1 Resistance, Proviral DNA (RTI, PI, Integrase Inhibitors) test (test code 94807), Quest Diagnostics offers HIV-1 proviral DNA testing for multiple cART classes, including nucleoside and non-nucleoside reverse transcriptase inhibitors (RTIs), protease inhibitors (PIs), and integrase inhibitors. RTI and PI testing and Integrase Inhibitor testing are separately available:
- HIV-1 Resistance, Proviral DNA (RTI, PI Inhibitors): test code 94808
- HIV-1 Resistance, Proviral DNA (Integrase Inhibitors): test code 94809
In addition, Quest offers HIV-1 Resistance and Coreceptor Tropism, Proviral DNA (test code 94810), which includes RTI, PI, integrase inhibitors, and tropism. This panel also provides tropism testing that may be considered for screening virologically suppressed patients prior to prescribing a CCR5 antagonist.
Individuals Suitable for Testing
- Virally suppressed individuals with HIV-1 who are being considered for a regimen change whose treatment history and/or prior plasma HIV-1 RNA genotype are unavailable1,2
- Individuals with HIV-1 with low-level viremia (<1,000 copies/mL) whose genotype could not be determined by plasma viral RNA methods1,2
Methods
- 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 ≥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 (A, B, BF, C, D, AE, AG, or H)
Interpretive Information
- A result of “predicted resistance” indicates detection of mutations associated with drug resistance to the indicated drug.
- A result of “probable resistance” indicates detection of mutations likely to confer drug resistance to the indicated drug.
- 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
References
- Gandhi RT, Bedimo R, Hoy JF, et al. Antiretroviral drugs for treatment and prevention of HIV infection in adults. 2022 Recommendations of the International Antiviral Society – USA Panel. JAMA. 2023;329(1):63-84. doi:10.1001/jama.2022.22246
- Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in adults and adolescents with HIV. Department of Health and Human Services. Updated September 12, 2024. Accessed February 13, 2025. https://clinicalinfo.hiv.gov/en/guidelines/hiv-clinical-guidelines-adult-and-adolescent-arv/whats-new
- Tang MW, Shafer RW. HIV-1 antiretroviral resistance. Drugs. 2012;72(9):e1-e25. doi:10.2165/11633630-000000000-00000
- Arts EJ, Hazuda DJ. HIV-1 antiretroviral drug therapy. Cold Spring Harb Perspect Med. 2012;2(4):a007161. doi:10.1101/cshperspect.a007161
- Clutter DS, Jordan MR, Bertagnolio S, et al. HIV-1 drug resistance and resistance testing. Infect, Genet Evol. 2016;46:292-307. doi:10.1016/j.meegid.2016.08.031
- 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. doi:10.1016/j.jviromet.2017.10.016
- Lübke N, DiCristanziano V, Sierra S, et al. Proviral DNA as a target for HIV-1 resistance analysis. Intervirology. 2015;58(3):184-189. doi:10.1159/000431093
- Porter DP, Daeumer M, Thielen A, et al. Emergent HIV-1 drug resistance mutations were not present at low-frequency at baseline in non-nucleoside reverse transcriptase inhibitor-treated subjects in the STaR study. Viruses. 2015;7(12):6360-6370. doi:10.3390/v7122943
- 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. doi:10.1016/j.jcv.2016.07.007
Content reviewed 03/2025