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HIV-1 Genotype

HIV-1 Genotype

Test Summary

HIV-1 Genotype


Clinical Use

  • Guide selection of antiretroviral drugs

  • Detect HIV-1 mutations in the reverse transcriptase (RT) and protease (Pr) genes

Clinical Background

Despite continuing advances in treatment for HIV-1 infection, highly active antiretroviral therapy (HAART) often fails. The high replication rate of HIV-1 coupled with its rapid mutation rate drives the accumulation of mutations,1 some of which confer reduced susceptibility to antiretroviral agents. If viral replication is not adequately suppressed during HAART, HIV-1 variants containing resistance-associated mutations will emerge, increasing the likelihood of treatment failure.

This HIV-1 genotype assay identifies RT and Pr mutations associated with current or evolving drug resistance. Current guidelines support the use of resistance testing to help guide therapy decisions in treatment-naïve as well as treatment-experienced patients, and to document transmission of resistant virus.2,3 Because of its generally lower cost, faster turnaround time, and sensitivity for detecting variants in mixed viral populations, genotypic testing is recommended in most clinical settings where resistance testing is indicated.3 The addition of phenotypic resistance testing is recommended for patients with complex resistance patterns2,3 (eg, after failure of 3 or more regimens, or earlier in patients initially infected multidrug-resistant virus2).

Because wild-type virus tends to out-compete resistant virus in the absence of selective pressure, resistance testing is most reliable for drugs that the patient is taking at the time of testing and should be performed within 4 weeks after discontinuing therapy.3

Individuals Suitable for Testing2,3

  • Individuals with acute or established HIV-1 infection at entry into care (before therapy is initiated)

  • Individuals with chronic infection initiating their first antiretroviral regimen

  • Individuals experiencing antiretroviral regimen failure

  • Individuals experiencing suboptimal viral suppression

  • Pregnant women with HIV-1 infection


  • Reverse transcription and polymerase chain reaction (PCR) amplification of plasma HIV-1 RNA followed by automated DNA sequencing

   Amplification of the entire sequence of the Pr gene (to codon 99) and RT gene (to codon 319)

   Sequencing using an Applied Biosystems Model 3730 capillary automated sequencer

   Multiple control samples with known mutations are included in each assay run; because these are placed at different positions on each run, they also serve as plate identifiers.

  • Each sequence is compared with sequences obtained in the past 3 years in the Quest Diagnostics database to help ensure detection of rare cross-contamination events or sample mix-ups.

  • Associated drug resistance identified using the Quest Diagnostics rules-based algorithm.

  • Report includes detected mutations and predicted drug resistance.

  • Analytical sensitivity: 676 copies/mL viral load and viral populations accounting for >25% of the individual’s HIV-1 population

  • Synonyms: HIV-1 drug resistance, HIV-1 gene sequencing, HIV-1 mutations

Interpretive Information

The report form lists individual mutations in the RT and Pr genes, along with associated drug resistance for each antiretroviral drug. The HIV-1 subtype, or clade, is also reported. The interpretation algorithm used to associate mutations with drug resistance is updated regularly by a panel of HIV experts but is not reviewed by the FDA. Resistance may also be affected by as yet uncharacterized mutations and interactions among mutations. In addition, mutations in minor viral populations (25% of the viral population) may not be detected.

Therapeutic failure may be due to factors other than resistance, including poor adherence to the drug regimen, suboptimal therapy or drug bioavailability, and immunologic decline. Thus, in clinical practice, physicians select therapeutic regimens on the basis of the patient’s antiretroviral treatment history, viral load, clinical status, and potential metabolic toxicity as well as resistance information.


  1. Coffin JM. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science. 1995;267:483-489.

  2. Hirsch MS, Gunthard 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;47:266-285.

  3. 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. July 14, 2016. http://aidsinfo.nih.gov/contentfiles/lvguidelines/adultandadolescentgl.pdf. Accessed September 15, 2017

This test was developed and its analytical performance characteristics have been determined by Quest Diagnostics. It has not been cleared or approved by FDA. This assay has been validated pursuant to the CLIA regulations and is used for clinical purposes.

Content reviewed 09/2017

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