HIV drug resistance testing


Drug resistance testing is used to determine whether a patient with the human immunodeficiency virus (HIV) has a mutated form of the virus that does not respond to antiretroviral therapy (ART).

HIV is a retrovirus that causes AIDS (acquire immune deficiency syndrome). The retrovirus primarily attacks the body's immune system, making the body extremely vulnerable to opportunistic infections, which occur in immunocompromised individuals.

HIV is transmitted from person to person via bodily fluids, including blood, semen, vaginal discharge, and breast milk. It can be spread by sexual contact with an infected person, by sharing needles/syringes with someone who is infected, or, less commonly (and rare in countries like the United States where blood is screened for HIV antibodies), through transfusions with infected blood. HIV has been found in saliva and tears in very low concentrations in some AIDS patients. However, contact with saliva, tears, or sweat has never been shown to result in HIV transmission.

Currently, there is no cure for HIV/AIDS. Although antiretroviral drugs can suppress the virus, even to undetectable levels, they are unable to completely eliminate HIV from the body.

When HIV reproduces, different strains (types) of the virus emerge. Mutations (changes) occur almost every time a new copy of the virus is produced. This is because HIV reproduces rapidly and does not contain the proteins that are needed to correct mistakes that are made during replication.

Some of the mutated (changed) HIV strains are resistant to antiretroviral drugs. This means that changes in the virus allow it to continue to multiply rapidly despite antiretroviral therapy (ART). Not every mutation leads to drug resistance.

If an HIV-infected patient becomes resistant to a drug and continues to take the same medication, HIV is able to multiply faster because the drug cannot stop it from replicating. When the new, mutated form is favored, it is called selective pressure. If the resistant virus makes enough copies of itself, it could eventually become the dominant type of HIV in the body. Once this happens, the medication is useless, and the patient will be resistant to the specific medication forever.

If the patient stops taking the medication, there is no selective pressure, and the normal form (called the wild type) of the virus will multiply faster than the mutated form. However, once an individual is resistant to a drug, the patient should not take it in the future because the resistant strain may reappear.

Resistance can happen for many reasons, including poor treatment adherence. When a patient takes medication irregularly or frequently misses doses, HIV can reproduce more quickly. When the viral load (amount of HIV in the body) increases, so does the amount of mutated HIV, including mutations that may be resistant to medications.

Testing HIV patients for drug resistance may help healthcare professionals make appropriate treatment decisions for their patients.


Poor treatment adherence: In order for anti-HIV drugs to work correctly, they must be taken exactly as prescribed. Skipping doses or not taking the medications correctly can cause the amount of an antiretroviral drug to decrease in the bloodstream. If the drug level becomes too low, HIV can begin reproducing more quickly. The faster HIV reproduces, the more mutations occur, including those that may be resistant to drugs.

According to several studies, HIV patients must be more than 95% adherent (missing less than one dose a month) to their treatment regimens in order for them to remain effective. Healthcare providers evaluate the effectiveness of treatment by measuring the patients' CD4 cell count. These immune cells are the primary targets of HIV. If the CD4 cell count is maintained, the likelihood of virus mutating into resistant strains is decreased.

Poor absorption: The antiretrovirals must be absorbed into the bloodstream properly in order for them to be effective. Once the drugs are taken by mouth, they must be absorbed by the small intestine and broken down by the liver before they enter the bloodstream. If the drugs are not absorbed properly this can result in low levels of antiretrovirals in the bloodstream, which ultimately allows HIV to multiply at increased rates, causing an accumulation of mutations.

Medication should be taken exactly as prescribed. Some drugs, such as Videx©, must be taken on an empty stomach in order to ensure proper absorption. Other antiretrovirals, such as darunavir (Prezista©) or ritonavir (Norvir©), must be taken with food.

In addition, HIV patients often experience diarrhea and vomiting, either as a side effect of medication or as a result of infections associated with the disease. Diarrhea and vomiting can cause antiretrovirals to be expelled from the stomach too quickly, reducing the amount of drugs in the bloodstream. HIV patients who experience diarrhea should consult their healthcare providers to promptly treat the cause. Treatment options range from over-the-counter (OTC) and prescription drugs to changes in diet.

Varying pharmacokinetics: Individuals absorb, breakdown, distribute, and remove drugs from the body differently. Even if two people receive the exact same treatment regimen, the amount of drug present in the bloodstream may be different in both patients. Some patients are able to metabolize (process) drugs faster or slower than average, which can speed up or slow down the rate at which drugs are expelled from the body. Factors such as body weight, height, and age can contribute to the different pharmacokinetic properties.


Currently, the U.S. Food and Drug Administration (FDA) has only approved one drug resistance test, TrueGene™. This is because the sensitivity, specificity, and reproducibility for many of the tests have not been well established. However, several tests are available, and many health insurance plans cover them.

There are two main types of drug resistance tests: genotypic and phenotypic resistance tests. Genotypic tests examine the genetic structure of a patient's HIV, while phenotypic tests examine the sensitivity of a patient's HIV to a specific drug.

Genotypic resistance testing: Genotypic resistance testing examines the genetic structure (genotype) of a patient's HIV. A blood sample is taken from the patient, and the HIV is analyzed for the presence of specific genetic mutations that are known to cause resistance to specific drugs. For instance, researchers have determined that lamivudine (Epivir©) and emtricitabine (Emtriva©) are not effective against forms of HIV that contain the mutation "M184V" in its reverse transcriptase gene. If a patient tests positive for this mutation, it is highly likely that he or she is resistant to both drugs, and alternative drugs should be prescribed.

To conduct a genotypic test, a sample of the patient's blood is sent to a testing laboratory. These laboratories use polymerase chain reaction (PCR) technology to produce many copies of the HIV's genetic material. Then, the genetic sequences of particular viral enzymes, such as protease and reverse transcriptase, can be analyzed for mutations.

There are two main types of genotypic tests: sequencing assays and point-mutation assays.

Sequencing assays: Sequencing assays are used to detect mutations in either the reverse transcriptase or protease genes. Both of these genes are involved in the replication of HIV.

Point-mutation assays: Point-mutation assays are used to detect mutations in the specific genes that are known to cause drug resistance. These tests are performed more often than sequencing assays because they are easier to perform, and the results are easier to interpret. The patient typically receives the test results in about one to two weeks after the blood is shipped to the laboratory.

In general, the results of genotypic tests are difficult to interpret because different mutations and different combinations of mutations can convey different meanings. Most laboratories that offer genotypic tests work with experts to develop rules based on algorithms. According to one study, healthcare providers who rely on HIV drug-resistance experts to interpret the results of genotypic tests were more likely to prescribe effective treatment than healthcare providers who relied on a computer software package (RetroGram, version 1.0). If the patient is shown to be resistant to a certain drug, the healthcare provider will prescribe HIV treatment with different antiretrovirals.

Current genotypic resistance tests include Bayer Health Diagnostics' HIV-1 TrueGene™, Celera Diagnostics/Abbott Laboratories' ViroSeq™, LabCorp's GenoSure (Plus)™, and Monogram Biosciences GeneSeq™. Currently, none of the available genotypic drug resistance tests can detect mutations in HIV's envelope gene, which can cause resistance to fusion inhibitors like enfuvirtide (Fuzeon©).

Phenotypic testing: Phenotypic testing directly measures the sensitivity (phenotype) of a patient's HIV in response to specific antiretrovirals. Many experts believe that these tests are more accurate and comprehensive than genotypic tests. These tests can help a physician determine the amount or concentration of a drug that is needed to stop a specific strain of HIV from replicating in a patient.

During a phenotypic test, samples of an HIV patient's blood are placed inside test tubes that contain different antiretrovirals. The virus is exposed to varying strengths and/or concentrations of each antiretroviral drug. The scientist observes how the virus reacts to the drug. The results from the patient's sample are compared to a normal (wild-type) virus that is known to be 100% susceptible to all antiretroviral drugs.

The results tell healthcare providers how much of a specific antiretroviral is needed to stop the growth of HIV by 50% (compared to how much is needed to stop the wild-type virus by 50%). This is called inhibitory concentration (IC50).

The concentration of the drug that is needed to prevent virus replication is expressed in units called nanomoles (nM). For instance, if the IC50 of the wild-type virus is 100nM and the IC50 of the test virus is 500nM, the test virus is considered to be five times more resistant to the particular drug. In other words, the patient is five times less sensitive to the drug.

When phenotypic tests were first developed, the results were difficult to interpret. Today, researchers have developed clinical cutoffs to help healthcare providers interpret the results.

Clinical cutoffs are based on clinical studies of specific antiretrovirals. During these trials, researchers monitor the patients to see how their viral loads change when they are taking specific drugs in combination with other antiretrovirals. Phenotypic tests are used to determine the lower and upper clinical cutoffs. The lower clinical cutoff represents the point at which the drug's effect on the virus begins to decline and the virus is somewhat resistant. The upper cutoff represents the point at which the drug has little or no effect on the virus.

Clinical cutoffs are not available for some antiretrovirals because researchers have not yet determined them in studies. If a lab is conducting a phenotypic test on such antiretrovirals, biological cutoff will be used. Biological cutoffs are based on in vitro (test tube) studies of HIV.

There are two main phenotypic tests available: Virco Lab's Antivirogram© and Monogram Bioscience's PhenoSense™ assay. These tests measure the fold changes for antiretrovirals that fall into the drug categories of nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs). PhenoSense Entry© tests HIV's sensitivity to the fusion inhibitor enfuvirtide (Fuzeon©).

In addition, Virco Lab's virco© TYPE HIV-1 assay is used to determine the virus' phenotype without actually performing a phenotypic test. This is called a predictive phenotypic test. First, genotypic tests are performed to determine if an HIV sample has mutations that are known to cause drug resistance. After the genotype is identified, the laboratory searches a Virco database that contains thousands of HIV samples from other patients. The database locates the phenotypes that match these samples and then averages the information together to predict the drugs that the patient is likely to be more or less sensitive to.


The tests cannot detect minority mutations that occur in less than 20% of the HIV-infected population.

The results may not be accurate if the patient's viral load is very low. Tests usually cannot be conducted if the patient's viral load is less than 500 to 1,000 copies per milliliter of blood.

The test results can be difficult to interpret.

Some HIV mutations can reverse resistance to some medications. In other words, some patients may not be resistant to a drug, even if they were resistant to it in the past.

Sometimes genotypic and phenotypic tests provide conflicting results for the same patient. If the tests results are inconclusive, a viral load test can be conducted to determine how many viral particles are in the patient's blood.


This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (

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  • Stanford University HIV Drug Resistance Database. Accessed April 5, 2007.
  • Tural C, Ruiz L, Holtzer C, Schapiro J, Viciana P, Gonzalez J, Domingo P, Boucher C, rey-Joly C, Clotet B. Clinical utility of HIV-1 genotyping and expert advice: the Havana trial. AIDS. 2002 Jan 25;16(2):209-18. .View abstract

Copyright © 2011 Natural Standard (
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