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Case Files From Stanford University Medical Center: Drug Resistance Testing in Previously Untreated Patients With HIV -- Knowing What to Look for and Choosing Appropriate Therapy

Robert W. Shafer, MD; Dong Phuong Nguyen, PharmD; W. Jeffrey Fessel, MD 

Medscape General Medicine.  2006;8(3):32.  ©2006 Medscape
Posted 08/07/2006

Editor's Note

This is the second in a series of case studies from the Division of Infectious Diseases at Stanford University Medical Center. This series examines optimization of antiretroviral therapy in a treatment-experienced patient with HIV, or in a treatment-naive patient with a particularly challenging initial presentation. Robert W. Shafer, MD, is the editor of this series. He is an Associate Professor in the Division of Infectious Diseases at Stanford University Medical Center and an expert on the management of HIV infection, with a particular focus on antiretroviral drug resistance mechanisms and testing.

Case Patient and Discussion

Case Patient

A 29-year-old bisexual man was hospitalized in 2003 with Pneumocystis jiroveci pneumonia. Serologic testing for HIV-1 was positive. The patient's CD4+ cell count was 35 cells/mcL and a plasma HIV-1 RNA level was > 500,000 copies/mL (VERSANT bDNA; Bayer Diagnostics). An HIV-1 genotype resistance assay revealed the reverse transcriptase (RT) mutations M41M/L and T215C. The patient completed a 3-week course of treatment for P jiroveci pneumonia and was started on stavudine (d4T)/lamivudine (3TC)/lopinavir (coformulated with low-dose ritonavir). Plasma HIV-1 RNA levels decreased over the ensuing weeks and within 4 months were < 75 copies/mL. The HIV RNA levels have remained < 75 copies/mL until the present time. CD4+ cells increased to > 300 cells/mcL during the first 6 months of therapy and eventually stabilized at about 500 cells/mcL (Figure 1).

Figure 1. 

Plasma HIV-1 RNA levels, CD4+ cell counts, genotypic resistance tests results, and antiretroviral therapy in a patient with primary HIV-1 resistance.



This case raises several timely HIV-1 treatment issues. First, the delay in HIV-1 diagnosis caused the patient to present with a life-threatening illness rather than at a presymptomatic stage of infection -- a topic discussed in the first report in this series.[1] Second, this patient had genotypic evidence of transmitted HIV-1 drug resistance. A discussion of this issue is timely because primary or transmitted drug resistance has been increasing over the past 5-10 years and drug resistance testing is now recommended for previously untreated persons as well as for persons failing a treatment regimen. Third, the patient had a marked increase in CD4+ cells with treatment. Not all patients have such a recovery and the factors contributing to immune reconstitution and CD4+ cell recovery are still being studied.

Management of Persons With Primary Genotypic Resistance. This year, the US Department of Health and Human Services (DHHS) recommended that drug resistance testing be performed prior to the initiation of antiretroviral (ARV) therapy, ideally at the time of initial diagnosis.[2] The timing of this recommendation stems from the recent publication of 4 types of data. First, the frequency of transmitted or primary HIV-1 resistance has been increasing, and, in the United States and Europe, 5% to 15% of newly diagnosed persons and 10% to 25% of acutely infected individuals have genotypic evidence of drug resistance (reviewed in Pillay[3]). Second, transmitted drug resistance is clinically relevant. Retrospective studies have shown that persons infected with drug-resistant strains have an increased risk for virologic failure when treated with drugs to which their virus was resistant (for an example, see Figure 2[4]). Third, transmitted drug resistance often persists for 3 or more years, allaying concerns that transmitted resistant variants would be rapidly overgrown by wild-type variants and therefore no longer detectable if transmission had occurred more than several months earlier.[5] Fourth, genotypic resistance testing prior to choosing initial therapy is likely to be cost-effective.[6]

Figure 2. 

Clinical significance of baseline genotypic resistance in FTC-301A. Note: Statistically significant increased rates of virologic failure occurred in patients with baseline RT inhibitor-resistance mutations. Seven patients in each arm had viruses with K103N. Rates of virologic failure among those with wild-type and drug-resistant viruses were higher in the ddI/d4T/efavirenz arm (the ddI/d4T combination is no longer recommended because of its increased toxicity and decreased efficacy). Genotypic resistance testing was done only after the study was completed. Adapted from Borroto-Esoda.[4]


The DHHS has excellent guidelines for initial highly active antiretroviral therapy (HAART). However, these guidelines are designed for persons with wild-type viruses. As drug resistance testing is now increasingly performed in previously untreated patients, how should patients infected with drug-resistant viruses be treated? Although prospective randomized controlled studies have not been done to answer this question, data from several retrospective studies are available from which recommendations can be derived for 2 common scenarios: (1) transmission of viruses with nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistance mutations and (2) transmission of viruses with thymidine analog mutations (TAMs) including mutations such as T215C also known as a "T215 revertant" (see Sidebar 1).

Few clinicians would use an NNRTI-based initial ARV regimen in persons whose viruses contain 1 or more NNRTI resistance mutations. Indeed, a retrospective analysis of baseline samples from a Gilead Sciences trial (FTC-301A), which compared didanosine (ddI) + emtricitabine (FTC) + efavirenz (EFV) with ddI + d4T + EFV showed that the presence of an NNRTI resistance mutation, particularly K103N, prior to the start of therapy was significantly associated with virologic failure (resistance testing was done only after the study had been completed; Figure 2).[4]

Whereas standard sequencing reliably detects only those minor variants that are present in about 30% of a patient's plasma virus population, several experimental real-time point mutation polymerase chain reaction (PCR) assays can detect variants present in as low as 1% of a patient's plasma virus population. At the XV International HIV Drug Resistance Workshop in Sitges, Spain, in June 2006, a group from the US Centers for Disease Control and Prevention described the results of a study in which a real-time PCR assay for M184V, K103N, and Y181C was applied to the baseline samples of 138 previously untreated persons enrolling in 2001 in a study of abacavir plus lamivudine (3TC) plus EFV, including 69 patients who had developed virologic failure with this regimen and 69 matched control patients who had maintained virologic suppression. Of 10 persons infected with a virus having at least 1 of the 3 mutations targeted (including 3 in whom mutations were detected only by real-time PCR), all developed virologic failures by month 6. The reason for the worse outcome associated with resistance in this study compared with FTC-301A is not known.

Neither M41L alone, a T215 revertant alone, nor the combination of M41L and a T215 revertant reduces susceptibility to any of the nucleoside reverse transcriptase inhibitors (NRTIs). However, the presence of any of these mutations in a previously untreated individual strongly suggests that the individual was infected with a drug-resistant virus. In at least one study, the presence of T215 revertants has been associated with an increased risk for virologic failure during initial ARV therapy.[7] Moreover, even if the revertant (rather than one of the fully resistant variants) were transmitted, only a single mutation is required for the emergence of T215F or Y (rather than the 2 mutations required for viruses with the wild-type threonine at position 215[8]).

Therefore, even though NNRTI resistance mutations were not detected in the virus sample from the patient described in this report, it seems prudent to have used a ritonavir-boosted protease inhibitor (lopinavir/r)-containing regimen rather than an NNRTI, because the success of an NNRTI-based regimen is more highly contingent on the presence of active NRTIs than is the success of lopinavir/r, which has a higher genetic barrier to resistance and which is usually highly effective for initial ARV therapy even in the absence of accompanying NRTIs.[9] Although the extremely high plasma HIV-1 RNA level may not interfere with the success of an efavirenz-based dual NRTI/NNRTI regimen for treating a wild-type virus,[10] such a high virus load may present an added risk in a patient whose virus population contains drug-resistant variants. Sidebar 2 summarizes several principles of treatment in patients with primary HIV-1 drug resistance.

CD4+ Cell Recovery During Initial ARV Therapy. Large studies in the United States, United Kingdom, Switzerland, France, and Spain have characterized the CD4+ response to complete virologic suppression in patients beginning their first HAART regimen.[11-19] These studies show that there is a biphasic response to therapy with a more rapid increase in CD4+ cells during the first 3-4 months of therapy (approximately 20 cells/microliter [mcL] per month) followed by a slower increase in CD4+ cells (approximately 5 cells/mcL per month) during the subsequent months of therapy. However, about 10% to 15% of patients have CD4+ cell count increases < 100 cells/mcL. The factors most strongly associated with a poorer CD4+ increase are age > 40 years and incomplete virologic suppression. Higher levels of baseline HIV RNA levels appear to be associated with greater CD4+ cell recovery.[13,19] Although slightly greater increases in CD4+ cell count may occur in patients with lower baseline CD4+ cell counts, the increase is not enough to compensate for the lower starting point.[16,17]

In addition to preventing acute illness and death caused by opportunistic infections, another rationale for diagnosing HIV-1 at an earlier stage of immunosuppression is that persons with complete plasma HIV-1 RNA suppression do not necessarily experience the marked immune reconstitution observed in the patient reported here. Therefore, the earlier a patient is diagnosed, the greater the probability that CD4+ cell count will either be above 200 cells/mcL or will increase above this level, thereby decreasing the risk for opportunistic infection and obviating the need for long-term prophylaxis for P jiroveci and other opportunistic infections.


  1. Liu M, Holodniy M, Zolopa AR, Shafer RW. The initial presentation of HIV-1 Infection: Where public and personal health meet. MedGenMed HIV/AIDS. 2006;8(1):24. Available at: Accessed July 25, 2006.
  2. US Department of Health and Human Services Panel on Clinical Practices for Treatment of HIV Infection A. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. May 4, 2006. Available at: Accessed July 25, 2006.
  3. Pillay D. Current patterns in the epidemiology of primary HIV drug resistance in North America and Europe. Antivir Ther. 2004;9:695-702. Abstract
  4. Borroto-Esoda K, Harris J, Waters J, et al. Baseline genotype as a predictor of virological failure in patients receiving emtricitabine once daily or stavudine twice daily in combination with didanosine and efavirenz. Program and abstracts of the 11th Conference on Retroviruses and Opportunistic Infections; February 8-11, 2004; San Francisco, California. Abstract 672.
  5. Brenner BG, Routy JP, Petrella M, et al. Persistence and fitness of multidrug-resistant human immunodeficiency virus type 1 acquired in primary infection. J Virol. 2002;76:1753-1761. Abstract
  6. Sax PE, Islam R, Walensky RP, et al. Should resistance testing be performed for treatment-naive HIV-infected patients? A cost-effectiveness analysis. Clin Infect Dis. 2005;41:1316-1323. Abstract
  7. Violin M, Cozzi-Lepri A, Velleca R, et al. Risk of failure in patients with 215 HIV-1 revertants starting their first thymidine analog-containing highly active antiretroviral therapy. AIDS. 2004;18:227-235. Abstract
  8. Garcia-Lerma JG, Nidtha S, Blumoff K, Weinstock H, Heneine W. Increased ability for selection of zidovudine resistance in a distinct class of wild-type HIV-1 from drug-naive persons. Proc Natl Acad Sci U S A. 2001;98:13907-13912 Abstract
  9. Norton M, Delaugerre C, Batot G, Delfraissey J, Rouzioux C. Drug resistance outcomes in a trial comparing lopinavir/ritonavir (LPV/r) monotherapy to LPV/r + zidovudine / lamivudine (MONARK Trial). Antiviral Ther. 2006;11:S84 [abstract 74].
  10. Robbins GK, De Gruttola V, Shafer RW, et al. Comparison of sequential three-drug regimens as initial therapy for HIV-1 infection. N Engl J Med. 2003;349:2293-2303. Abstract
  11. Le Moing V, Thiebaut R, Chene G, et al. Predictors of long-term increase in CD4(+) cell counts in human immunodeficiency virus-infected patients receiving a protease inhibitor-containing antiretroviral regimen. J Infect Dis. 2002;185:471-480. Abstract
  12. Dronda F, Moreno S, Moreno A, Casado JL, Perez-Elias MJ, Antela A. Long-term outcomes among antiretroviral-naive human immunodeficiency virus-infected patients with small increases in CD4+ cell counts after successful virologic suppression. Clin Infect Dis. 2002;35:1005-1009. Abstract
  13. Kaufmann GR, Perrin L, Pantaleo G, et al. CD4 T-lymphocyte recovery in individuals with advanced HIV-1 infection receiving potent antiretroviral therapy for 4 years: the Swiss HIV Cohort Study. Arch Intern Med. 2003;163:2187-2195. Abstract
  14. Hunt P, Martin J, Sinclair E, et al. Drug-resistant phenotype is associated with decreased in vivo T-cell activation independent of changes in viral replication among patients discontinuing antiretroviral therapy. Antivir Ther. 2003;8:S82.
  15. Hunt PW, Martin JN, Sinclair E, et al. T cell activation is associated with lower CD4+ T cell gains in human immunodeficiency virus-infected patients with sustained viral suppression during antiretroviral therapy. J Infect Dis. 2003;187:1534-1543. Abstract
  16. Smith CJ, Sabin CA, Youle MS, et al. Factors influencing increases in CD4 cell counts of HIV-positive persons receiving long-term highly active antiretroviral therapy. J Infect Dis. 2004;190:1860-1868. Abstract
  17. Kaufmann GR, Furrer H, Ledergerber B, et al. Characteristics, determinants, and clinical relevance of CD4 T cell recovery to <500 cells/microL in HIV type 1-infected individuals receiving potent antiretroviral therapy. Clin Infect Dis. 2005;41:361-372. Abstract
  18. Goicoechea M, Smith DM, Liu L, et al. Determinants of CD4+ T Cell Recovery during suppressive antiretroviral therapy: association of immune activation, T cell maturation markers, and cellular HIV-1 DNA. J Infect Dis. 2006;194:29-37. Abstract
  19. Gandhi RT, Spritzler J, Chan E, et al. Effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy in HIV-1-positive subjects: Results From ACTG 384. J Acquir Immune Defic Syndr. 2006;42:426-434. Abstract
  20. Yerly S, Rakik A, De Loes SK, et al. Switch to unusual amino acids at codon 215 of the human immunodeficiency virus type 1 reverse transcriptase gene in seroconvertors infected with zidovudine-resistant variants. J Virol. 1998;72:3520-3523. Abstract
  21. de Ronde A, van Dooren M, van Der Hoek L, et al. Establishment of new transmissible and drug-sensitive human immunodeficiency virus type 1 wild types due to transmission of nucleoside analogue-resistant virus. J Virol. 2001;75:595-602. Abstract
  22. Oette M, Kaiser R, Daumer M, et al. Primary HIV drug resistance and efficacy of first-line antiretroviral therapy guided by resistance testing. J Acquir Immune Defic Syndr. 2006;41:573-581. Abstract
  23. Perno CF, Cozzi-Lepri A, Balotta C, et al. Impact of mutations conferring reduced susceptibility to lamivudine on the response to antiretroviral therapy. Antivir Ther. 2001;6:195-198. Abstract
  24. Perno CF, Cozzi-Lepri A, Balotta C, et al. Secondary mutations in the protease region of human immunodeficiency virus and virologic failure in drug-naive patients treated with protease inhibitor-based therapy. J Infect Dis. 2001;184:983-991. Abstract

Sidebar 1

Codon 215 Revertants: Footprints of a Drug-resistant Virus

  1. Substitution of the amino acid tyrosine (Tyr; Y) or phenylalanine (Phe; F) for the wild-type amino acid threonine (Thr; T) at position of 215 of HIV-1 RT reduces zidovudine and stavudine susceptibility. When present with other amino acid substitutions (particularly M41L and L210W), these mutations also reduce abacavir, tenofovir, and didanosine susceptibility.

  2. In contrast to the vast majority of drug-resistance mutations, both T215Y and T215F require 2 nucleotide mutations: ACT (Thr; T) ≥ TAT (Tyr; Y) or TTT (Phe; F). Occasionally, a virus containing a single substitution is observed during the early stages of virologic rebound: ACT ≥ TCT (serine, S).

  3. In the late 1990s, several groups reported that patients who were primarily infected with strains containing T215Y were observed over time to have viruses that developed novel mutations at this position such as T215C/D/E/I/S/V.[20,21] Viruses with these mutations evolve from those with a Y or an F at position 215, usually by the development of a single "back mutation" or "revertant." This evolution contrasts with what is observed in treated persons who discontinue therapy in whom archived viruses with wild-type T at position 215 rapidly reemerge.

  4. Multiple studies have reported that T215 revertants are among the most common changes observed in chronically infected newly diagnosed persons, occurring in about 3% of such individuals.[7,8,22]

Sidebar 2

Treatment of Patients With Primary HIV-1 Drug Resistance

  1. Genotypic resistance testing underestimates the extent of resistance that may be present as minor plasma virus variants or within cellular reservoirs, particularly if infection occurred several years prior to testing or if the initial infection was polyclonal. Although experimental assays for detecting minor variants are commonly used in research settings, they are not yet available or validated for use in clinical settings.

  2. Information on the source of infection should be sought, as the extent of resistance in the source patient provides a worst-case scenario for the extent of resistance in the recipient.

  3. Genotypic rather than phenotypic testing should be obtained in previously untreated patients because mixtures of wild-type and mutant viruses (which are particularly common, as back mutants compete with the originally transmitted virus) are more likely to be detected by genotypic tests and as T215 revertants do not cause phenotypic resistance.

  4. One of the most commonly observed patterns of primary HIV-1 resistance is the presence of isolated NNRTI resistance. Patients with baseline NNRTI resistance mutations should be treated with a ritonavir-boosted PI with a high genetic barrier to resistance (eg, lopinavir/r) in combination with 2 or 3 NRTIs.

  5. Although the majority of patients with just 1 or 2 TAMs or with a T215 revertant may respond to a standard NNRTI-containing regimen, the risk for virologic failure appears to be increased. Therefore, treatment with a boosted PI-containing regimen in this population is also prudent.

  6. Patients infected with viruses containing minor drug-resistance mutations that are also known polymorphisms (eg, V118I in RT; L10I/V, K20R, M36I, L63P, A71V/T, V77I, and I93L in protease) appear to do as well with standard NNRTI or boosted PI-containing treatment regimens.[23,24]

  7. Expert assistance should be sought when selecting therapy for patients with viruses containing more complicated patterns of drug-resistance mutations.

Robert W. Shafer, MD, Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California

Dong Phuong Nguyen, PharmD, Kaiser Permanente Medical Care Program - Northern California, San Francisco, California

W. Jeffrey Fessel, MD, Kaiser Permanente Medical Care Program - Northern California, San Francisco, California

Disclosure: Robert W. Shafer, MD, has disclosed that he has received grants for clinical research from Abbott Laboratories, Bristol-Myers Squibb, Celera Diagnostics, Gilead Sciences, GlaxoSmithKline, and Hoffman-LaRoche; has served as an advisor or consultant for Bayer Diagnostics, Bristol-Myers Squibb, and Celera Diagnostics; and has received honoraria from Tibotec.

Disclosure: Dong Phuong Nguyen, PharmD, has disclosed no relevant financial relationships.

Disclosure: W. Jeffrey Fessel, MD, has disclosed no relevant financial relationships.