Preexisting Resistance to Nonnucleoside
Predicts Virologic Failure of an
Efavirenz-Based Regimen in Treatment-
Naive HIV-1–Infected Subjects
Daniel R. Kuritzkes,1Christina M. Lalama,2Heather J. Ribaudo,2
Michelle Marcial,1William A. Meyer III,3Cecilia Shikuma,4
Victoria A. Johnson,5,6Susan A. Fiscus,7Richard T. D’Aquila,8
Bruce R. Schackman,9Edward P. Acosta,6and Roy M. Gulick9
1Brigham and Women’s Hospital, Harvard Medical School, and2Harvard School of
Public Health, Boston, Massachusetts;3Quest Diagnostics, Inc., Baltimore, Maryland;
4University of Hawaii, Honolulu;5Birmingham Veterans Affairs Medical Center and
6University of Alabama at Birmingham School of Medicine, Birmingham;7University
of North Carolina, Chapel Hill;8Vanderbilt University, Nashville, Tennessee;9Weill
Medical College, Cornell University, New York, New York
A case-cohort study was used to determine the effect of base-
line nonnucleoside reverse-transcriptase inhibitor (NNRTI)
resistance, as assessed by viral genotyping, on the response to
efavirenz-containing regimens in AIDS Clinical Trials Group
A5095. The sample included a random cohort of efavirenz-
treated subjects plus unselected subjects who experienced vi-
tance was 5%. The risk of virologic failure for subjects with
baseline NNRTI resistance was higher than that for subjects
terval],1.15–4.49;P ? .018).Theseresultssupportresistance
Treatment guidelines recommend efavirenz (a nonnucleoside
reverse-transcriptase inhibitor [NNRTI]) or a ritonavir-boosted
(or nucleotide) reverse-transcriptase inhibitors (NRTIs) for initial
anti-HIV therapy . The efficacy of NNRTI-based regimens is
that the prevalence of drug-resistant HIV-1 is increasing among
newly infected or newly diagnosed persons who have not received
in NNRTI resistance, which rose from 0.4% to 8.4% from 1998 to
effective , data on the impact of primary resistance on the re-
sponse to NNRTI-based regimens in chronically infected patients
The AIDS Clinical Trials Group (ACTG) A5095 study was a
randomized, controlled trial comparing the efficacy of efavirenz
plus a fixed-dose combination of zidovudine/lamivudine (3-
drug arm) or zidovudine/lamivudine/abacavir (4-drug arm) in
previously untreated HIV-1–infected subjects . With a me-
dian 144 weeks of follow-up, time to virologic failure was not
significantly different between the 3- and 4-drug arms. Black
non-Hispanic race/ethnicity and recent nonadherence were as-
sociated with a significantly increased risk of virologic failure
. Genotypic testing of stored baseline plasma samples from
a case-cohort study to determine the prevalence of NNRTI re-
sistance and its impact on treatment outcome. A case-cohort
study design uses a subsampling technique in survival data for
estimating the relative risk of disease in a cohort study without
collecting data from the entire cohort. This design is an efficient
and economical way to study risk factors for infrequent disease
disease cases observed in the entire cohort and for the members
of a random subcohort. In addition to ascertaining the relative
risk of disease in relation to the risk factors of interest, the ran-
dom subcohort also offers the ability to assess the prevalence of
with plasma HIV-1 RNA levels ?400 copies/mL into the
efavirenz-containing arms between March 2001 and November
2002 at 33 AIDS Clinical Trials Units (ClinicalTrials.gov identi-
Received 23 September 2007; accepted 15 October 2007; electronically published 12
Potential conflicts of interest: D.R.K. is a consultant to and has received honoraria and
research grant support from Bayer, Boehringer-Ingleheim (BI), Bristol-Myers Squibb (BMS), and
GlaxoSmithKline (GSK). E.P.A. is a consultant to BMS. R.T.D. has received grant support from
BMS and is a consultant to BI and GSK. R.M.G. is a consultant to BMS and GSK. V.A.J. is a
consultant to and/or has received grant support from Bayer, BMS, and GSK. C.S. has received
research grant support from BMS. All other authors report no potential conflicts.
Presented in part: 14th Conference on Retroviruses and Opportunistic Infections, Los
Angeles 25–28 February 2007 (abstract 665).
Financial support: National Institutes of Health (NIH; grants AI38858, AI068636 [AIDS Clinical
Trials Group Central Grant], AI069419, AI051966, AI069472, AI069452, and RR024996); subcon-
tracts from NIH grants AI38858 and AI06836 with the Virology Support Laboratories at Massa-
chusetts General Hospital, the University of Alabama, the University of Colorado Health Sciences
Center, the University of North Carolina, and Vanderbilt University; Birmingham Veterans Affairs
Medical Center; Harvard University and University of Alabama at Birmingham Centers for AIDS
Research (grants AI060354 and AI027767). Bristol-Myers Squibb and GlaxoSmithKline provided
drug for this study as well as financial support for plasma HIV-1 RNA determinations.
Reprints or correspondence: Dr. Daniel R. Kuritzkes, Section of Retroviral Therapeutics,
Brigham and Women’s Hospital, 65 Landsdowne St., Rm. 449, Cambridge, MA 02139
The Journal of Infectious Diseases
© 2008 by the Infectious Diseases Society of America. All rights reserved.
B R I E F R E P O R T
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fier NCT00013520). A total of 193 subjects (25%) experienced
virologic failure (2 consecutive measurements of HIV-1 RNA
level ?200 copies/mL, with the first measurement at least 16
weeks after study entry) . Genotyping of HIV-1 protease and
reverse trancriptase was performed on stored plasma samples
obtained at study entry by use of the HIV-1 TRUGENE assay
study, the primary outcome measure was the occurrence of vi-
ence or absence of mutations associated with resistance to efa-
virenz or nevirapine (NNRTI resistance). In the case of the PIs,
samples were considered to be resistant if categorized by the
cohort sample consisted of a random sample (subcohort) strat-
plus the case subjects (those who experienced virologic failure)
who were not selected to be in the subcohort. Assuming a 25%
failure rate and 5% prevalence of NNRTI resistance, it was esti-
mated that a subcohort size of 220 subjects would give 80%
power to detect a hazard ratio (HR) for virologic failure of 3.56
between subjects with and without NNRTI-resistant virus.
On the basis of the random sample, the prevalence of baseline
or without preexisting NNRTI resistance were compared by Fish-
er’s exact and Wilcoxon tests for categorical and continuous vari-
race/ethnicity and recent self-reported adherence. The presence of
a different impact of recent adherence dependent on the presence
presented from intent-to-treat or as-treated analyses as described.
All P values and confidence intervals (CIs) presented are nominal,
case patients (subjects with virologic failure) and 163 (74%) were
control subjects (those without virological failure). The additional
136 subjects with virologic failure were added to the subcohort to
163 without virologic failure). Viral genotypes could not be ob-
hort and for 2 subjects from the additional subjects with virologic
not have reached protocol-defined virologic failure; these subjects
Of the 219 subjects in the randomly sampled subcohort with
NRTIs, and 6 (3%) to PIs. Table 1 summarizes the baseline de-
mographics of the random subcohort by presence or absence of
preexisting NNRTI resistance. Subjects with NNRTI-resistant
virus were somewhat more likely to be previous or current in-
jection drug users (P ? .091) and to have higher median base-
line CD4 cell counts (P ? .048). Demographics are also pre-
sented for the additional subjects with virologic failure.
follow-up, 16 (8%) who had experienced virologic failure and 3
(2%) who had not carried NNRTI-resistant virus at baseline. By
contrast, virus samples from 6 (3%) with virologic failure and 3
the 3-drug arm, baseline NNRTI resistance was detected in 13
72 of those without failure. By comparison, in the 4-drug arm,
baseline NNRTI resistance was detected in 3 (3%) of 94 subjects
with virologic failure and in 3 (4%) of 79 without.
The K103N mutation was present in samples from 12 of the 16
Y188L, and G190A mutations were each present individually in
these mutations have been associated with resistance to efavirenz
Time to first virologic failure in the subcohort was substantially
els including baseline NNRTI resistance showed a significantly in-
creased risk of virologic failure for subjects with NNRTI-resistant
2.27 [95% CI, 1.15–4.49]; P ? .018) (as-treated: HR, 2.61 [95%
CI, 1.30–5.20]; P ? .007). The above results persisted after ad-
treated:adjustedHR,3.13[95%CI,1.36–7.22];P ? .007).The
estimated effects of race/ethnicity and recent adherence were
consistent with those previously reported . There was no sig-
nificant evidence of an interaction between recent self-reported
adherence and baseline NNRTI resistance (P ? .46).
We used a case-cohort design to compare the
who started receiving an efavirenz-containing regimen in a ran-
was 5%. Resistance to NNRTI was present at baseline in samples
than doubled the risk of virologic failure. In this study, all subjects
with genotypic evidence of NNRTI resistance at baseline who re-
perienced virologic failure, although a few subjects maintained vi-
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provide a strong rationale for performing resistance testing before
selecting a regimen for initial antiretroviral therapy. Moreover,
in our study are the most commonly used regimens for the initial
Although most current guidelines for the treatment of HIV-1
call for resistance testing before the initiation of antiretroviral
therapy, few published reports document the impact of trans-
found a longer time to virologic suppression and a shorter time
to virologic failure among recently infected patients whose reg-
. Another study found a nearly 3-fold increased risk of viro-
logic failure in chronically infected patients with evidence of
transmitted zidovudine resistance . By contrast, a third study
3-drug regimen . None of these studies specifically investi-
gated the issue of transmitted NNRTI resistance.
Similarly, few randomized clinical trials of initial antiretrovi-
ral therapy in treatment-naive patients have considered the ef-
fect of preexisting drug resistance on treatment outcome. In
ure among subjects in the randomly selected subcohort with and without
virus resistant to nonnucleoside reverse-transcriptase inhibitors at base-
line. Virologic failure was defined as a confirmed plasma HIV-1 RNA level
?200 copies/mL at week 16 or later.
Kaplan-Meier plot of time to protocol-defined virologic fail-
Table 1.Baseline characteristics of the study sample.
failure (n ? 136)
(n ? 12)
(n ? 207)
Age, median (IQR), years
Injection drug use
HIV-1 RNA level, median
CD4 cell count, median
Hepatitis B seropositive
Hepatitis C seropositive
4.53 (4.34–5.04)4.77 (4.37–5.38)4.81 (4.50–5.63)
the efavirenz-containing arms of ACTG A5095 . Case patients were those who met the protocol-defined
virologic failure end point; control subjects were those who did not experience virologic failure. Additional
subjects were those who met the virologic failure end point but were not selected for the random subcohort. IQR,
interquartile range; NNRTI, nonnucleoside reverse-transcriptase inhibitor.
aOn the basis of Fisher’s exact test comparing NNRTI resistance with NNRTI nonresistance in the subcohort,
all categorical variables had P ? .25, except for history of injection drug use (P ? .091). On the basis of the
Wilcoxon test comparing NNRTI resistance with NNRTI nonresistance in the subcohort, HIV-1 RNA level had
P ? .26, and CD4 cell count had P ? .048.
Data are no. (%) of subjects, unless otherwise indicated. The subcohort was randomly selected from
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ples from subjects who experience treatment failure, it has not
been possible to determine the risk of treatment failure associ-
ated with baseline drug resistance. For example, one study de-
jects with virologic failure receiving an initial regimen of
emtricitabine or stavudine plus didanosine and efavirenz .
No data were available, however, on the prevalence of NNRTI
resistance in subjects classified as virologic responders.
In the absence of antiretroviral therapy, most transmitted
drug-resistance mutations revert to wild type over time [8, 12].
Certain NNRTI resistance mutations (e.g., K103N) remain de-
tectable by routine genotypic resistance tests for at least 2 to 3
of these mutations are limited. An earlier study of chronically
infected antiretroviral-naive patients with a median CD4 cell
count of 0.296 ? 109cells/L found an overall prevalence of re-
sistance of 9%, suggesting persistence of transmitted drug-
resistance mutations . Although we do not have data on the
duration of HIV-1 infection in the subjects we studied, the rela-
tivelylowmedianbaselineCD4cellcount(0.203 ? 109cells/L)
suggests that they had been infected for many years before entry
into ACTG A5095. Our results therefore support current guide-
lines that recommend performing baseline drug-resistance test-
ing even in patients who have been infected for ?2 years.
In the present study, detection of NNRTI resistance relied on a
standard genotyping assay (TRUGENE) that is commonly used in
clinical practice. This approach may have failed to detect the pres-
ence of NNRTI resistance when such variants made up a minority
of the virus population. Although other methods such as allele-
fer greater sensitivity in detecting drug-resistance mutations, at
Three subjects maintained virologic suppression despite the
presence of NNRTI-resistant virus at study entry. Of note, all 3 re-
nent of the regimen. However, triple-NRTI regimens have been
retroviral therapy . The optimal choice of initial regimen for
We thank the 33 participating AIDS Clinical Trials Units and the additional
AIDS Clinical Trials Group (ACTG) A5095 study team members, including:
sity of California, Los Angeles), study laboratory technologists; Valery Hughes
(Weill Medical College of Cornell University), study field representative; Anne
data managers; Ana Martinez (Division of AIDS, National Institute of Allergy
and Infectious Disease), study pharmacist; Monica Murphy and Nancy Webb
(Frontier Science and Technology Foundation), laboratory data coordinators;
Vinny Parillo (AIDS Clinical Trials Group Community Constituency Group),
Systems, Inc.), clinical trials specialists; Kirk Ryan and Shulin Wang (Bristol-
Smith (Massachusetts General Hospital), Russell Young (University of Colo-
rado Health Sciences Center), Lorraine Sutton (Vanderbilt University), J. Dar-
sity of North Carolina at Chapel Hill) performed HIV-1 genotyping assays for
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