Presence of Minor Populations of Y181C Mutants Detected by Allele-specific PCRand Risk of Efavirenz Failure in Treatment-naÔve Patients: Results of an ACTG 5095 Case-cohort Study
Roger Paredes*1,2, C Lalama3, H Ribaudo3, B Schackman4, C Shikuma5, W Meyer, III6, F Giguel1, K Squires7, R Gulick4, and D Kuritzkes1
1Brigham and Women`s Hosp, Harvard Med Sch, Boston, MA, US; 2Fndns irsiCaixa and Lluita contra la SIDA, Badalona, Spain; 3Harvard Sch of Publ Hlth, Boston, MA, US; 4Weill Med Coll of Cornell Univ, New York, NY, US; 5Univ of Hawaii, Honolulu, US; 6Quest Diagnostics, Baltimore, MD, US; and 7Jefferson Med Coll, Philadelphia, PA, US
Background: †The clinical role of assessing antiretroviral resistance in minor
variants of HIV-1 remains to be defined. We reanalyzed a case-cohort substudy
of AIDS Clinical Trials Group (ACTG) 5095, a randomized trial comparing the efficacy of efavirenz (EFV) + 2 or 3 NRTI, to determine the effect of minor
NNRTI-resistant populations on response among subjects without major resistance
to EFV-based regimens.
case-cohort sample included a randomly sampled cohort (n=220, 57
virologic failures, 163 non-failures) of the 765 EFV-randomized subjects, plus the
remaining 136 unsampled subjects with virologic failure (n = 356: 193 virologic
failures, 163 non-virologic failures). Bulk sequencing of HIV-1 protease and RT
(TRUGENE) was performed on stored baseline plasma samples. In subjects without
NNRTI resistance by bulk sequencing, presence of minority K103N or Y181C
populations was assayed by allele-specific polymerase chain reaction (ASPCR).
Prevalence of minority NNRTI-resistant variants (i.e., mutations detected by
ASPCR but not by bulk sequencing) in the random cohort was compared with
Fisherís exact test. Weighted Cox proportional hazards models estimated the
relative risk of virologic failure in the presence (yes/no) of baseline
minority Y181C by ASPCR for the case-cohort sample. Analyses were adjusted for
recent adherence. An interaction was evaluated.†
detection threshold of ASPCR was calculated at: †K103N (AAT) = 0.001%, K103N
(AAC) = 0.003%; Y181C = 0.04%. In the random cohort, median baseline plasma
HIV-1 RNA (viral load) and CD4 count were 4.77 log10 copies/mL and
206 cells/mm3, respectively. Of 345 subjects in the case-cohort
sample with follow-up ≥16 weeks, 19 had baseline NNRTI resistance by bulk
sequencing; 307 of the remaining 326 had at least 1 basaeline ASPCR result.
Minority Y181C was detected more frequently than minority K103N (125 [41%] vs
42 [14%], respectively); 29 samples (9.5%) were positive for both mutations. In
the random cohort, 25 of 43 (58%) with virologic failure vs 41 of 142 (29%) non-virologic
failure had detectable Y181C (p = 0.001), whereas 5 of 43 (12%) virologic
failure vs 14 of 142 (10%) non-virologic failure had detectable K103N (p
= 0.8). Weighted Cox analyses showed a significantly increased risk of virologic
failure for adherent and non-adherent subjects with detectable Y181C at baseline
(HR 3.57, 95%CI 1.98 to 6.42, p <0.001; HR 6.09, 95%CI 2.83 to 13.1, p
<0.001, respectively), compared to adherent subjects and no NNRTI
mutations by either assay (interaction p = 0.08).
†In antiretroviral-naive subjects without evidence of NNRTI resistance by bulk
sequencing, presence of minority Y181C mutants detected by ASPCR more than
tripled the risk of virologic failure of EFV-based regimens.