Acquired resistance of HIV to available antiretroviral agents (ARVs) remains a worldwide concern. Soon after zidovudine (AZT, ZDV) received approval by the FDA in 1987 for the treatment of HIV infection, patients began experiencing treatment failure related to HIV resistance to this agent.¹³

Early-generation resistance tests, developed in 1989, identified the dose for individual ARVs necessary to inhibit 50% of HIV growth.⁷ Technology ultimately advanced with the use of polymerase chain reaction (PCR) to identify mutations within the HIV genome responsible for resistance to specific ARVs.

HIV genome sequencing uncovered additional complexities related to HIV resistance. For example, although HIV encodes only nine genes, mutations were identified that confer resistance to one drug or an entire class of drugs or that actually increase HIV sensitivity to ARVs.

HIV-1 subtype B predominates in the developed world and is the focus of the majority of susceptibility studies, though it accounts for only 12% of all HIV subtypes worldwide.¹²

Results of HIV resistance testing are best interpreted by experienced HIV providers in the context of many factors that may influence drug resistance, including compliance and the results of laboratory determinants of successful therapy.

The genome sequence of HIV recovered prior to initiation of highly active antiretroviral therapy (HAART) is referred to as the “wild-type” (WT) sequence. This “WT virus” does not reflect the genetic code of a single viral “clone,” but rather the most replication-competent viral clones (or “species”) within the patient’s circulation. In other words, it reflects many species (referred to as “quasispecies”), all of which replicate billions of times per day. WT virus exhibits drug resistance in 15% to 20% of patients.⁹

Intrinsic drug resistance may occur due to errors in viral transcription in the absence of exposure to HAART.⁶

Fully suppressive HAART was not available to patients until the mid-1990s (with the advent of protease inhibitors [PIs]). Therefore, many patients diagnosed with HIV early in the epidemic were receiving ARVs that did not fully suppress HIV replication, facilitating the development of drug resistance mutations.⁸

Suboptimal medication adherence, AVR interactions with other medications that increase or decrease effective blood levels (i.e., P450 inducers), and transmission of
drug resistance from person to person (intravenous drug abuse and mother-to-child transmission) also contribute to the prevalence of HIV drug resistance.

Resistant quasispecies are often not identified until the predominant WT virus is suppressed during HAART therapy. Drug-resistant quasispecies are typically present in insufficient quantities (>10% of all circulating species in the presence of the more replication-competent WT virus) to permit their detection. Therefore, for treatment-experienced patients, HIV resistance testing should be performed in the presence of HAART therapy.

Commercial assays, referred to as “genotypes,” sequence the HIV genome to identify mutations associated with drug resistance for HIV.

An individual patient’s collective HIV species, isolated from whole blood following venipuncture, is typically labeled as “susceptible,” “possibly resistant,” or “resistant” to each ARV tested based on the presence or absence of well-characterized mutations in the HIV genome.

Reports include mutations that confer resistance of HIV to ARVs in vitro (cell culture) and that have been associated with treatment failure for HIV patients.

Mutations are reported as a letter-number-letter sequence. The first letter represents the wild-type amino acid; the number represents the position of the mutation within the genome, and the second letter represents the amino acid substituted that confers resistance. Some mutations have not exhibited significant individual or synergistic contributions to HIV drug resistance, and we will not discuss these further.

Some drug classes exhibit a high barrier to resistance (e.g., HIV PIs), requiring the presence of several mutations before partial or complete drug resistance occurs.^4,5 Other classes exhibiting a low barrier to resistance (e.g., nucleoside and nonnucleoside reverse transcriptase inhibitors) may require only one mutation to render drugs in these classes inactive.¹⁰

Some mutations occur in a predictable pattern when HIV is only partially suppressed, as with thymidine analogue-associated mutations (TAMs) arising with inadequate treatment using nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs).

Several genotype assays are available involving allele-specific PCR, multiplex primer extension, and so-called deep sequencing. Frequently utilized assays employ some variation of these protocols to identify specific mutations within the most prevalent quasispecies (comprising >10% of all species).

Indications for performing the genotype assay include the following scenarios: (i) after HIV diagnosis and before HAART administration, (ii) during HAART therapy with repeatedly detectable HIV viral load (typically >1,000 copies/mL to allow for optimal genome sequencing), (iii) pregnancy, and (iv) postexposure prophylaxis (we recommend genotype testing for the source individual in cases of high-risk exposure if possible in order to help guide therapy in the event of eventual HIV infection of the exposed patient).⁷