Interpretive Handbook

Test 62581 :
HIV-1 Ultrasensitive Genotypic Drug Resistance Mutation Analysis, Plasma

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Antiviral resistance may compromise highly active antiretroviral therapy (HAART) in HIV-infected patients receiving this therapy. When combination therapy fails, detection and analysis of HIV genotypic mutations can guide necessary changes to antiretroviral therapy and decrease HIV viral load, thereby improving patient outcome.


HIV-1 is an RNA virus that infects cells and is then converted to complementary DNA (cDNA) by the action of the viral reverse transcriptase (RT) gene product. RT has little proofreading capacity and therefore incorporates errors in the proviral DNA. These errors are transcribed into infectious viral particles when the proviral DNA is transcribed into RNA. Similarly, the enzyme protease catalyzes a polyprotein to produce peptides necessary for active viral replication. Although HAART (combination of nucleoside analog, nonnucleoside agent and/or protease inhibitor) may be effective in reducing the viral load, genotypic mutations arising in the drug-targeted HIV gene loci due to selective pressure from antiviral therapy result in antiviral resistance that may compromise such therapy.


Amplification and analysis of drug-targeted HIV-1-gene sequence allows identification of changes in nucleotide bases and associated amino acid codons that may cause antiviral drug resistance. Such genotypic changes are deemed as mutations by comparing the sequence data of the patient's HIV-1 strain to those of a wild-type HIV-1 strain. The significance of these genotypic mutations in relation to antiviral resistance is then determined by a set of interpretive rules developed by a consensus panel of leading experts in the field of HIV resistance. Relevant data presented at a recognized scientific conference or published in peer-reviewed journals are considered by the consensus panel in developing these rules. When necessary, reliable unpublished drug resistance data known to consensus panel members may be considered in the process. The interpretive rules are updated by the consensus panel annually after reviewing newly published data on HIV-1 genotypic drug resistance mutations.

Useful For Suggests clinical disorders or settings where the test may be helpful

Identification of HIV-1 genotypic mutations associated with resistance to nucleotide reverse-transcriptase inhibitors, nonnucleotide reverse-transcriptase inhibitors, and protease inhibitors in patients with HIV-1 viral loads between 200 and 1,000 copies/mL


Guiding change of anti-HIV-1 treatment regimens in patients with HIV-1 viral loads between 200 and 1,000 copies/mL

Interpretation Provides information to assist in interpretation of the test results

Detectable HIV-1 genotypic mutations conferring resistance to an antiviral drug are reported as amino acid codon changes (eg, M184V) resulting from mutations in the viral nucleotide sequence.


"Susceptible" indicates that the genotypic mutations present in patient's HIV-1 strain have not been associated with resistance to the specific drug in question.


"Resistant" indicates that genotypic mutations (see specific list in corresponding result comment) detected have been associated with maximum reduction in susceptibility to the specific drug.


"Possibly resistant" indicates that genotypic mutations detected have been associated with 1 or both of the following outcomes:

-Diminished virologic response in some, but not all, patients having virus with these mutations

-Intermediate decrease in susceptibility of the virus to the specific drug


"Insufficient evidence" indicates that there is inadequate direct or indirect evidence to determine susceptibility of the virus to the specific drug on the basis of the genotypic mutations present, according to the opinion of the consensus panel of leading experts in the field of HIV-1 resistance.


"Unable to genotype" indicates that the sequence data obtained are of poor quality to determine the presence or absence of genotypic resistant mutations in the patient's HIV-1 strain. Possible causes of such poor sequence data include low HIV-1 viral load (eg, <200 copies/mL) and polymorphisms in the region of the sequencing primers interfering with primer binding and subsequent sequencing reactions.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Due to the complexity of the results generated, the International AIDS Society-USA Panel recommends expert interpretation of genotyping and phenotype test results for patient care management. A patient's response to antiviral therapy depends on multiple factors, including the percentage of patient's viral populations that is drug resistant, patient compliance with the prescribed drug therapy, patient access to adequate care, drug pharmacokinetics, and drug interactions. Drug resistance test results should be interpreted only in conjunction with clinical presentation and other laboratory markers when making therapeutic decisions.


Absence of resistance to a drug does not rule out the presence of reservoirs of drug-resistant virus in the infected patient.

The HIV-1 genotypic test is not a direct measure of drug resistance. Although genotypic testing can detect mutations in the relevant HIV-1 genome, the significance of these mutations requires careful interpretation to predict drug susceptibility. This assay's ability to amplify the target and detect genotypic mutations is poor and unreliable when the plasma HIV-1 viral load is <200 copies/mL. Specimens submitted for this test should contain > or =200 copies/mL of HIV-1 RNA.


This assay has been optimized for genotypic analysis and interpretation of HIV-1 group M subtype B, which are the majority of HIV-1 isolates infecting patients in the United States and Europe. The protease and reverse transcriptase gene regions examined in this assay are not well correlated with the envelope gene, which is the defining gene sequence used for subtyping. Other subtypes of group M HIV-1 have been tested and validated to a limited extent by this assay. Therefore, genotypic mutations in groups N, O, and P, and some group M non-B subtype HIV-1 isolates may or may not be detected using this assay, and it is not known whether drug resistance mutation interpretation for group M subtype B isolates apply to these other groups and subtypes of HIV-1.


The genotypic mutation database and interpretive rules used by this commercial assay are updated periodically by the assay manufacturer. Therefore, the test results do not necessarily include all of the drug-related mutations described in the current medical literature.


Possible causes of treatment failure other than the development of drug resistance are poor adherence to medication regimen, drug potency, and individual variation in pharmacokinetics (eg, inadequate phosphorylation of nucleosides).

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Not applicable

Clinical References Provides recommendations for further in-depth reading of a clinical nature

1. Hirsch MS, Gunthard HF, Schapiro JM, et al: Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 Recommendations of the International AIDS Society-USA Panel. Clin Infect Dis 2008;47:266-285 Available from URL:

2. Wainberg MA, Zaharatos GJ, Brenner BG: Development of antiretroviral drug resistance. N Engl J Med 2011;365:637-646

3. Johnson VA, Calvez V, Gunthard HF, et al: Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med 2013;21:6-14 Available from URL: