Drugs 2012; 72 (9): e1-e25 REVIEW ARTICLE 0012-6667/12/0009-0001 Adis ª 2012 Tang & Shafer, publisher and licensee Springer International Publishing AG. This is an open access article published under the terms of the Creative Commons License ‘‘Attribution-NonCommercial-NoDerivative 3.0’’ (http://creativecommons.org/licenses/by-nc-nd/3.0/) which permits non-commercial use, distribution, and reproduction, provided the original work is properly cited and not altered. HIV-1 Antiretroviral Resistance Scientific Principles and Clinical Applications Michele W. Tang and Robert W. Shafer Stanford University, Division of Infectious Diseases, Stanford, CA, USA Contents Abstract..................................................................................e1 1. Introduction . e2 2. Biological Basis of Drug Resistance . e3 3. Phenotypic and Genotypic Resistance Testing . e4 3.1 Phenotypic Resistance Testing. e4 3.2 Genotypic Resistance Testing . e5 3.3 Resistance Testing in Clinical Practice . e6 3.4 Minority Drug-Resistance Variants . e6 4. Drug Resistance by Antiretroviral (ARV) Classes. e7 4.1 Nucleoside/Nucleotide Reverse Transcriptase Inhibitors (NRTIs) . e7 4.2 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) . e8 4.3 Protease Inhibitors (PIs) . e9 4.4 Integrase Inhibitors (INIs) . e11 4.5 CC Chemokine Receptor 5 (CCR5) Antagonists . e12 4.6 Fusion Inhibitors . e12 5. Non-Subtype B Viruses . e13 6. Transmitted Drug Resistance. e13 7. First-Line ARV Therapy Failure . e14 8. Salvage Therapy . e15 8.1 Previously Unused ARV Class . e16 8.2 ARVs Belonging to Previously Used Drug Classes. e17 8.3 NRTI Combinations . e17 8.4 ReuseofARVsThatWerePreviouslyAssociatedwithVirologicalFailureandDrugResistance....e18 9. Summary . e18 Abstract The efficacy of an antiretroviral (ARV) treatment regimen depends on the activity of the regimen’s individual ARV drugs and the number of HIV-1 mutations required for the development of resistance to each ARV – the genetic barrier to resistance. ARV resistance impairs the response to therapy in patients with transmitted resistance, unsuccessful initial ARV therapy and multiple virological failures. Genotypic resistance testing is used to identify transmitted drug resistance, provide insight into the reasons for virological failure in treated patients, and help guide second-line and salvage therapies. In patients with transmitted drug resistance, the virological response to a regimen selected on the basis of standard genotypic testing approaches the responses observed in patients with wild-type viruses. However, because such patients are at a higher risk of harbouring minority drug-resistant variants, e2 Tang & Shafer initial ARV therapy in this population should contain a boosted protease inhibitor (PI) – the drug class with the highest genetic barrier to resistance. In patients receiving an initial ARV regimen with a high genetic barrier to resistance, the most common reasons for virological failure are nonadherence and, potentially, pharmacokinetic factors or minority transmitted drug- resistant variants. Among patients in whom first-line ARVs have failed, the patterns of drug-resistance mutations and cross-resistance are often pre- dictable. However, the extent of drug resistance correlates with the duration of uncontrolled virological replication. Second-line therapy should include the continued use of a dual nucleoside/nucleotide reverse transcriptase in- hibitor (NRTI)-containing backbone, together with a change in the non- NRTI component, most often to an ARV belonging to a new drug class. The number of available fully active ARVs is often diminished with each successive treatment failure. Therefore, a salvage regimen is likely to be more complicated in that it may require multiple ARVs with partial residual activity and compromised genetic barriers of resistance to attain complete virological suppression. A thorough examination of the patient’s ARV his- tory and prior resistance tests should be performed because genotypic and/or phenotypic susceptibility testing is often not sufficient to identify drug- resistant variants that emerged during past therapies and may still pose a threat to a new regimen. Phenotypic testing is also often helpful in this subset of patients. ARVs used for salvage therapy can be placed into the following hierarchy: (i) ARVs belonging to a previously unused drug class; (ii) ARVs belonging to a previously used drug class that maintain significant residual antiviral activity; (iii) NRTI combinations, as these often appear to retain in vivo virological activity, even in the presence of reduced in vitro NRTI susceptibility; and rarely (iv) ARVs associated with previous virological fail- ure and drug resistance that appear to have possibly regained their activity as a result of viral reversion to wild type. Understanding the basic principles of HIV drug resistance is helpful in guiding individual clinical decisions and the development of ARV treatment guidelines. 1. Introduction one nucleotide reverse transcriptase inhibitors (NRTIs), five non-nucleoside reverse transcriptase The development of antiretroviral (ARV) com- inhibitors (NNRTIs), nine protease inhibitors binations potent enough to prevent the emergence (PIs), one fusion inhibitor, one CC chemokine re- of HIV-1 drug resistance was central to the devel- ceptor 5 (CCR5) antagonist and one integrase in- opment of successful ARV therapy (ART). None- hibitor (table I). Due to a recent expansion in the theless, the acquisition and transmission of HIV-1 number of ARVs and ARV classes, virological drug resistance loom as continuing obstacles suppression has become achievable in most patients to successful ART. Patients who acquire or are in whom numerous prior ARV regimens have primarily infected with HIV-1 drug-resistant failed. Identifying and understanding HIV-1 drug viruses have fewer treatment options and are at resistance can therefore help clinicians avoid increased risk of morbidity and mortality, partic- minimally active ARVs in favour of newer ARVs ularly in developing countries where choices for that are fully or nearly fully active. ART are limited.[1,2] Whereas the principles of drug resistance are There are 24 ARV drugs in six classes licensed the same in all populations, approaches to drug- for the treatment of HIV-1: six nucleoside and resistance testing and regimen switching may Adis ª 2012 Tang & Shafer, publisher and licensee Springer International Publishing AG. Drugs 2012; 72 (9) HIV-1 Antiretroviral Resistance e3 Table I. List of currently available US FDA-approved antiretro- cases of HIV drug resistance with fewer ARV viral drugs options than those available to their peers in other Generic name Abbreviation Brand name (US)a parts of the world. Nucleoside reverse transcriptase inhibitors (NRTIs) In this review, we summarize the efficacy and Abacavir ABC Ziagenâ genetic barriers to resistance associated with dif- Didanosine ddI Videxâ ferent ART regimens, the extent of cross-resistance Emtricitabine FTC Emtrivaâ within each drug class, and approaches to drug- Lamivudine 3TC Epivirâ resistance testing. We then show how these prin- Stavudine d4T Zeritâ ciples can be used by clinicians to guide the design Tenofovir TDF Vireadâ of ART regimens for patients with a wide range of Zidovudine AZT, ZDV Retrovirâ treatment histories. Non-nucleoside reverse transcriptase inhibitors (NNRTIs) Delavirdine DLV Rescriptorâ 2. Biological Basis of Drug Resistance Efavirenz EFV Sustivaâ Etravirine ETR Intelenceâ HIV-1 has a high mutation rate, accumulating Nevirapine NVP Viramuneâ nearly one nucleotide mutation per replication Nevirapine extended release NVP XR Viramuneâ XRä cycle.[3,4] Although individuals are usually infected Rilpivirine RPV Edurantâ with only a single or few original clones,[5] an es- Protease inhibitors (PIs) timated 1010 virions are produced each day in Atazanavir ATV Reyatazâ untreated individuals, resulting in innumerable Darunavir DRV Prezistaâ virus variants, often called a quasispecies.[6,7] The Fosamprenavir FPV Lexivaâ complexity of the HIV-1 quasispecies is also in- Indinavir IDV Crixivanâ creased by the high recombination rate that oc- Lopinavir/ritonavir LPV/r Kaletraâ curs whenever more than one viral variant infects Nelfinavir NFV Viraceptâ the same cell.[8,9] In addition, latent virus variants Ritonavir RTV, /r Norvirâ archived in the chromosomes of infected cells Saquinavir hard gel caps SQV Inviraseâ may periodically reactivate, further complicating Tipranavir TPV Aptivusâ the spectrum of virus variants within infected Integrase inhibitors (INIs) patients. Raltegravir RAL Isentressâ The ability to rapidly generate new variants CCR5 antagonist allows HIV-1 to evade the immune system and Maraviroc MVC Selzentryâ fosters the development of ARV drug resistance. Fusion inhibitor In fact, the development of antiviral resistance is Enfuvirtide (T20) ENF Fuzeonâ considered essential to proving that an ARV a Many ARVs may have multiple brand names, depending upon candidate compound inhibits HIV-1 directly, rather the company and location in which they are manufactured. Examples include efavirenz, which is also known as Stocrinâ in than the host cells in which the virus replicates. Europe; fosamprenavir, which is also known as Telzirâ in Europe; HIV-1 drug-resistance mutations occur at the lopinavir/ritonavir, which is also known as Aluviaä in the develop- target of therapy and, almost without exception, ing world; and maraviroc, which is also known as Celsentriâ in decrease viral