Testing for HIV resistance to antiretroviral medications has become an important component of the clinical care of HIV-infected persons. Resistance assays can assist the clinician in selecting a maximally effective antiretroviral regimen by identifying the level of resistance, if any, to antiretroviral agents. In most situation, genotypic resistance assays are used, not phenotypic, for resistance testing. The 2014 HHS guidelines for the use of antiretroviral therapy guidelines in adults and adolescents provides specific recommendations regarding HIV drug resistance testing (Figure 1). If genotypic resistance testing is performed, it is best if the patient's HIV RNA level is greater than 1,000 copies/ml. If the HIV RNA level between 500 and 1000 copies/ml, resistance testing should be considered, although at these levels the test may be unsuccessful because of inadequate viral amplification. Some experts attempt standard genotype resistance testing in patients with HIV levels lower than 500 copies/ml.[,]
Resistance Testing for Virologic Failure
The 2014 HHS antiretroviral therapy guidelines recommend resistance testing in the setting of virologic failure or suboptimal viral suppression in patients receiving antiretroviral therapy. The term "virologic failure" refers to the development of a detectabel and rising HIV RNA level in a patient on antiretroviral therapy who previously had virologic control (HIV RNA levels less than 50 copies/ml) (Figure 2). This scenario would not apply to a patient has abruptly stopped taking all antiretroviral medications. Several randomized controlled trials have demonstrated the clinical benefit of resistance testing among patients with virologic failure.[,,]
Resistance Testing for Suboptimal Viral Load Reduction
"Suboptimal viral load reduction" or "failure to suppress" describes a situation in which a patient initially shows a favorable initial response to antiretroviral therapy with a decrease in HIV RNA level, but is not able to drive the HIV RNA level below the level of detection (less than 50 copies/ml) (Figure 3). Suboptimal viral suppression can result from the rapid development of resistance, inadequate potency of the regimen, or both.
Resistance Testing with Acute HIV Infection
In the setting of acute HIV infection, the 2014 HHS antiretroviral therapy guidelines recommend obtaining genotypic resistance testing, regardless of whether the decision is made to initiate antiretroviral therapy. Obtaining a resistance test in acute or early HIV provides the greatest likelihood of detecting transmitted drug-resistant HIV. If therapy is deferred, the guidelines suggest considering repeat resistance testing prior to initiating antiretroviral therapy, since the patient may possibly acquire resistant HIV in the interim. Multiple studies have suggested that 6 to 21% of newly infected patients acquire drug-resistant HIV (with resistance to at least one antiretroviral drug).[,,,,,,] In a study that involved 373 patients diagnosed with acute HIV infection in the San Francisco Bay Area from 2002 to 2009, drug resistance among newly HIV-infected individuals increased overall during 2002 to 2007, but remained stable at 15% in 2008 and 2009 (Figure 4). Studies have also shown that patients infected with drug-resistant HIV have a longer time to viral suppression and shorter time to virologic failure when compared with patients who did not have evidence of acquired drug-resistant HIV.[,,]
Resistance Testing in Antiretroviral-Naive Patients with Chronic Infection
Because most HIV-infected individuals are diagnosed with HIV long after their acute HIV illness, the first opportunity for resistance testing typically occurs years after initial HIV infection. The 2014 HHS antiretroviral therapy guidelines recommend performing resistance testing in the setting of chronic HIV infection at the time a patient enters into care for their HIV disease, even if the patient is not planning to start on antiretroviral in the near future.. Among those with acute HIV infection who acquire drug-resistant HIV strains and who do not receive antiretroviral therapy, several possible scenarios exist regarding subsequent detection of resistant HIV strains: (1) resistant strains of HIV may back-mutate to more fit wild-type strains, or be overgrown by wild-type virus (Figure 5); (2) if resistant stains do not cause a loss in viral fitness, the strains could persist indefinitely (Figure 6); and (3) some resistant mutations may revert to more fit wild-type whereas others that do not cause a significant loss in fitness could persist (Figure 7). One study with a limited number of patients found that some multi-drug resistant strains acquired during initial infection persisted for up to 5 years as the dominant quasispecies, despite these strains having lower fitness than wild type strains. Regardless of whether or not resistance testing detects transmitted strains of resistant HIV, most experts would agree that transmitted drug-resistant variants persist in cellular reservoirs, such as latently infected CD4 cells, and thus could reemerge upon antiretroviral therapy selective pressure. Several studies have shown that presence of baseline drug-resistant HIV in persons with chronic HIV infection can negatively impact response to antiretroviral therapy and thus detection of drug-resistant mutations could help guide the choice for an initial antiretroviral therapy regimen.[,]
Resistance Testing after Discontinuation of Therapy
The 2014 HHS antiretroviral therapy guidelines state that drug resistant assays are usually not recommended when patients who have taken antiretroviral agents in the past, but have been off antiretrovial therapy for more than 4 weeks. When HIV drug resistance develops in response to antiretroviral therapy, populations of wild-type and resistant strains of HIV may co-exist, but upon discontinuation of antiretroviral therapy, replication of the more fit wild type strain generally outpaces that of the resistant strain (Figure 9). Accordingly, the resistant strain will likely become a minority species in the overall viral population. Because currently available resistance assays do not reliably identify strains of HIV that constitute a low percentage (generally defined as less than 10 to 20%) of the overall viral population, the "minority resistant" strains often evade detection by resistance assays in chronically infected persons who discontinue therapy. The speed at which resistant strains become overgrown by wild type strains will likely vary from patient to patient, but this typically occurs within 12 weeks of stopping antiretroviral therapy (Figure 9).[,,] Although drug-resistant strains may not be evident on resistance testing in this situation, they remain archived in the host and thus would presumably play a role if the patient reinitiated antiretroviral therapy that included medications to which the patient had previously developed resistance.
Resistance Testing with Low HIV RNA Levels
The 2014 HHS antiretroviral therapy guidelines does not recommend resistance testing in the setting of a patient experiencing apparent virologic breakthrough with an HIV RNA level less than 1,000 copies/ml. This recommendation exists because most currently commerically-available resistance assays require HIV viral levels of approximately 1,000 copies/ml or more to adequately amplify and accurately identify drug-resistant HIV. The guidelines also state that f the HIV RNA level between 500 and 1000 copies/ml, resistance testing should be considered, although at these levels the test may be unsuccessful because of inadequate viral amplification. As the technology of genotypic resistance assays improves, testing may become more accurate at detecting resistance at HIV RNA levels less than 500 copies/ml. New next generation sequencing techniques that amplify HIV proviral DNA allow for performance of HIV drug-resistance testing in samples from patients with very low or even undetectable HIV RNA levels; although these new proviral resistance assays are commercially available, their utility in clinical practice remains uncertain.