Human immunodeficiency virus (HIV) has been known to replicate rapidly, particularly in response to antiretroviral (ARV) therapies. These replications are a result of substitutions in the viral protease, reverse transcriptase, or integrase enzymes among other regions of the infectious agents, such as the location of fusion, which are targeted by various ARV drugs that can lead to drug-resistant mutations (quasi species). The end result is virologic treatment failure. Because of the rapidity of these replications, highly active antiretroviral therapy (HAART) has been designed to employ different mechanisms to reduce mutations to drug-resistant variants including, but not limited to, nucleoside reverse transcriptase inhibitors (NRTIs), nonnucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), integrase inhibitors, and fusion inhibitors. Examples of US Food and Drug Administration (FDA)--approved ARV drug classes include Fuzeon© (enfuviritide), the first FDA-approved HIV-1 fusion inhibitor, and Isentress® (raltegravir), an integrase inhibitor.
The effectiveness of HAART in suppressing HIV replication for prolonged periods has allowed HIV to be considered a chronic, rather than a fatal, disease. However, drug failure continues to occur because HAART regimens do not completely suppress replication in all cases. Other factors, such as nonadherence, inadequate potency, or suboptimal levels of drugs may play a part in drug failure. Historically, the initiation of, or a change in, antiretroviral therapy has been based on HIV ribonucleic acid (RNA) levels and CD4 cell counts, both of which are essential components of the clinical management of HIV. Because treatment decisions can irrevocably alter an individual's response to future therapy, clinicians can also utilize genotypic or phenotypic assays as additional clinical tools for selecting safe and efficacious treatment regimens.
Genotypic resistance assays look for mutations that are present in HIV genes (eg, reverse transcriptase [RT], protease, fusion, integrase). Some assays sequence the entire gene, while others use probes to detect mutations that are known to accord drug resistance. Phenotypic resistance assays measure the ability of the virus to replicate in vitro in the presence of an antiviral drug. The medical literature, the Department of Health and Human Services (DHHS) Guidelines, and the International AIDS Society--US Panel support the use of HIV genotyping and/or phenotyping to identify drug-resistant viruses and assist with selecting the most appropriate antiretroviral drugs for an individual.
Virtual phenotyping is a modified genotypic test that looks for mutations in the genetic structure of the HIV virus. When mutations are found, the information is entered into a database that contains data on thousands of HIV samples. If the genotype of the virus being studied matches a genotype in the database, the assumption is that the phenotype will also match. Virtual phenotyping is not a direct measure; rather, it is a prediction based on genotypic analysis and database matches. An example of a virtual phenotype assay is the VircoType™ (Virco NV, Belgium). Current clinical practice guidelines do not provide specific guidance about the role of virtual phenotyping in HIV resistance testing. However, based on current clinical practice, it appears there is correlation between genotypic interpretation and virtual phenotypic results, particularly when the drug(s) used in ART have been on the market long enough for the correlative database to garner enough matching genotypes and phenotypes to provide accurate phenotypic results. As a result, a limitation of virtual phenotyping is with respect to newer and experimental drugs because there are fewer matching genotypes and phenotypes in the correlative database.
