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Antiretroviral resistance: is there a solution?

Giampero Carosi
Director of the Institute of Infectious and Tropical Diseases

Carlo Torti
Clinical Researcher HIV Unit, Institute of Infectious and Tropical Diseases University of Brescia

Eugenia Quiros-Roldan
Consultant Physician
Department of Infectious Diseases
Spedali Civili General Hospital Brescia

It has been said that “New medicines, and new methods of cure, always work miracles for a while” (William Heberden, 1802). As we have learnt for other infectious diseases, HIV is no exception to this rule since there are now reasons to believe that all antiretroviral regimens available today will ultimately fail if they are used for long enough.

The risk of failure increases dramatically from first to subsequent treatment lines. The median time to failure of a first regimen is 10.6 months, while that of a second regimen is 8.1 months, and that of subsequent regimens is 6.4 months.(1) The most common reason for these failures is the development of HIV pharmacoresistance. Estimates of resistance to antiretroviral drugs among newly infected patients range from 3%(2) to 16.3%,(3) rising as high as 95%(4) among those in whom multiple regimens have failed.

What is HIV pharmacoresistance?
HIV pharmacoresistance can be defined as reduced susceptibility of HIV to antiretroviral drugs. This property of HIV can be assayed in vitro by phenotypic or genotypic tests (laboratory resistance) and determines an impaired response of HIV to antiretroviral drugs in vivo (clinical resistance).(5)

Phenotypic assays measure the ability of HIV to grow in the presence of antiretroviral agents over a fixed period of time. They represent a direct measure of the susceptibility of HIV to antiretroviral drugs in vitro. The amount of drug required to inhibit viral replication by 50% relative to a no-drug control of a reference strain of HIV-1 is used to measure phenotypic resistance (ie, fold-resistance). Phenotypic assays are more expensive and labour-intensive than the genotypic ones. In addition, phenotypic cutoffs that are relevant for the clinical outcome are currently unknown for most of the drugs.

Genotypic assays are based on determination of the nucleotide sequence of regions that confer phenotypic resistance. They are an indirect measure of HIV susceptibility to antiretroviral drugs in vitro. Results of a genotype assay can be complex, since mutations can interact between each other, either increasing or decreasing their effect on drug susceptibility.

Thus, a major challenge with both genotypic and phenotypic tests is to develop clinically relevant definitions of resistance.

How does pharmacoresistance emerge?
The genesis of HIV pharmacoresistance is summarised in Figure 1. HIV has an enormous replication rate (10(10) new viral particles are produced per day).(6) Since the HIV reverse transcriptase enzyme is error-prone and lacks proofreading ability, broad virus diversity is continuously produced. The rapid generation of variants implies the ability of the HIV to escape selective pressure such as that exerted by antiretroviral drugs. In theory this mechanism is controlled or suppressed when HIV replication is minimal or null. However, it has been demonstrated using ultrasensitive methods that HIV replication continues in leukocyte polymorphonuclear cells(7) and in compartments other than plasma,(8) even though plasma viral load is undetectable (ie, below the cutoffs currently available for quantifying plasma viral load). It has also been demonstrated that resistance mutations can be present during apparent suppressive therapy and emerge during overt antiretroviral failure.(9,10) Moreover, drug-resistance mutations have been detected during transient reactivation of plasma viral load (“blips”), with a potential effect on promoting subsequent treatment failure.(11–15)


Poor adherence to antiretroviral drugs is frequent, mainly due to the complexity and poor tolerability of antiretroviral regimens. This promotes HIV replication and thus the emergence of HIV pharmacoresistance.(16) Similarly, poor pharmacokinetics (absorption, distribution, metabolism and excretion), which is common with some drugs such as protease inhibitors, can decrease plasma drug concentrations, again leading to drug resistance.(17)

The fact that HIV drug-resistant strains or strains that contain a genetic background able to promote the emergence of HIV pharmacoresistance may be transmitted should also be considered. Indeed, these strains are reported increasingly frequently in patients naive for antiretroviral drugs, with a potentially negative impact either on the achievement of an initial treatment response or on the durability of the antiviral effect.(18)

What are the consequences of HIV pharmacoresistance?
HIV pharmacoresistance results in a number of worrying consequences, as shown in Figure 1. Once antiretroviral treatment failure occurs, drug options may be severely limited. In fact, resistance-associated mutations confer resistance not only to drugs that have been used, but also to drugs not yet experienced by patients (cross-resistance). If viral replication is sustained under conditions of persistent drug-selective pressure, resistance mutations can accumulate, resulting in further extension of cross- resistance and exhaustion of the available drug options. Moreover, HIV has a memory for drug-resistance mutations – they are archived in the proviral DNA, ready to re-emerge under the resumption of drug-selective pressure. This prevents the recycling of drugs even when resistance mutations are not detected in the plasma viral load.(15)

More importantly, although drug resistance mutations can decrease both HIV pathogenicity and replication capacity (so-called “fitness”), they are eventually restored by the accumulation of compensatory mutations, which leads to immune deterioration and clinical progression.(19) For these reasons, the maximum achievable suppression of the plasma viral load continues to be an important goal of antiretroviral therapy.(20) Undetectable plasma viral load is the primary goal, but this is not always achievable in treatment-experienced patients. Stabilisation of CD4 cell numbers and the absence of clinical progression have been demonstrated when viral load is sustained at a level threefold (0.5 Log(10)) below the patient’s natural set point (pretreatment value).(19)

What to do in case of HIV pharmacoresistance and how to prevent it?
Several retrospective and prospective studies have indicated that both genotypic and phenotypic HIV-1 drug resistance testing are associated with a better treatment outcome (see Table 1). While some studies have indicated a clear benefit, others – those conducted in patients with a more heavy antiretroviral treatment history – have failed to demonstrate a clear benefit from either genotypic or phenotypic resistance tests.(21–28) This suggests that resistance testing should be performed early.


During early first virological failure, resistance mutations are present in limited numbers and only for some drugs,(29) which allows for more effective treatment switching, selective substitutions of drugs or treatment intensification,(30) even though these two last strategies have not yet been validated. By contrast, waiting until multiple failures have occurred and multiple mutations have accumulated may run the risk of resistance and unresponsiveness to all the available drugs. As archived resistance mutations may emerge and promote treatment failure, it is very important to consider the patient’s treatment history and available results of previous resistance testing before devising a new drug regimen.(15)

Recent pharmacoeconomic analyses have suggested a favourable cost-effectiveness ratio for HIV drug resistance testing. In the prospective VIRADAPT study,(31) the cost of one genotypic assay was estimated to be US$500 (e. 508). Analysis at one year showed no significant difference in the mean cost of care between the no-genotype arm and the genotype arm of the study. Thus, the short-term resistance testing costs were offset by the reduced use of protease inhibitors. This conclusion was also supported by a pharmacoeconomic simulation model conducted by the National Institute of Allergy and Infectious Diseases (NIAID) and Centers for Disease Control and Prevention (CDC), which showed that genotypic antiretroviral testing following antiretroviral failure is cost-effective as well as resistance testing in patients who are naive for antiretrovirals, especially as far as the prevalence of primary resistance increases.(32)

Another important consideration is that HIV pharmacoresistance is not a black-or-white phenomenon. In fact, incomplete levels of resistance can be overcome by drug exposure, a concept usually referred to as inhibitory quotient (IQ). IQ is defined as the ratio between the trough drug concentration measured in the individual patient and the susceptibility of the virus to that drug isolated from the same patient. The higher the IQ, the better the treatment response should be. In practice, this concept applies only to protease inhibitors, as their concentrations are substantially variable between patients and a concentration-dependent activity between plasma drug concentration and treatment response has been demonstrated.(17)

Therapeutic drug monitoring (TDM) is a promising means of individualising and optimising existing treatment options for HIV management. Straightforward application is dose adjustments to maintain drug concentrations within the therapeutic index by means of either dose reduction to overcome toxic effects or dose increase to overcome drug resistance. Indeed, a preliminary analysis of the ATHENA study(33) has demonstrated a lower rate of discontinuation for toxicity in a subgroup of patients on indinavir-containing regimens who were randomised to TDM intervention, while in another subgroup of patients taking nelfinavir the application of TDM enabled a higher percentage of undetectable viral load to be achieved after 12 months of treatment. By contrast, two studies conducted in France in experienced patients (PharmAdapt(34) and GENOPHAR(35) failed to demonstrate any significant clinical benefit deriving from TDM.

An important application of IQ that increases the potency of antiretroviral drugs is the use of low ritonavir dosages to enhance the pharmacokinetics of other protease inhibitors. Ritonavir is a potent inhibitor of the cytochrome P450–CYP3A4, which is involved in the metabolism of protease inhibitors in the liver and, possibly, in the intestinal mucosal epithelium. The results are profound increases in the parameters of systemic exposure of protease inhibitors such as saquinavir and lopinavir (C(max) increase) or indinavir and amprenavir (half-life prolongation). Lopinavir coformulated with low-dose ritonavir (Kaletra”; Abbott) has recently been demonstrated to be superior to nelfinavir in HIV patients naive for antiretroviral therapy.(36)

How to manage HIV pharmacoresistance is a crucial topic, and key interventions are listed in Table 2. HIV drug resistance testing with or without TDM is not enough, and efforts should be directed towards the prevention of HIV pharmacoresistance if possible. In the absence of drug-selective pressure, the emergence of HIV pharmacoresistance does not happen; however, treatment delay is not recommended when CD4+ T-cell count is <-200 cells/mm(3).


When treatment is initiated, the best way to prevent resistance is to give the most effective treatment possible. To achieve this objective, treatment should be individualised according to: the intrinsic potency of the regimen, ease of consumption, optimisation of pharmacokinetics, and toxicity and tolerability profiles, in order to ensure the highest degree of adherence possible.

HIV pharmacoresistance is an emerging issue in antiretroviral therapy that needs to be appropriately addressed in current clinical practice. Resistance tests are important, and their cost-effectiveness will be improved when other factors that can have an impact on clinical outcome are optimised, particularly adherence and pharmacokinetics. All the interventions discussed are most successful when they are applied at the beginning of the therapeutic itinerary, clearly indicating that a more proactive approach is necessary, as stated unanimously by current guidelines (see Resources).


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