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Session 10 Oral Abstracts and Mini-Lecture
Transmission, Selection, and Persistence of Drug-Resistant Virus
Monday, 10 am - 12:15 pm
Presentation Time: 11:00 am
Room 3000


39
Low-frequency NNRTI-resistant Variants Contribute to Failure of Efavirenz-containing Regimens
J Mellors*1, S Palmer2, D Nissley2, M Kearney2, E Halvas1, C Bixby1, L Demeter3, S Eshleman4, K Bennett5, S Hart6, F Vaida5, M Wantman5, J Coffin2, and S Hammer for the ACTG 398 Study Group7
1Univ. of Pittsburgh, PA, USA; 2Drug Resistance Prgm., NCI, NIH, DHHS, Frederick, MD, USA; 3Univ. of Rochester, NY, USA; 4Johns Hopkins Univ., Baltimore, MD, USA; 5Harvard Sch. of Publ. Hlth., Boston, MA, USA; 6Frontier Sci. and Technology Res. Fndn., Amherst, NY, USA; and 7Columbia Univ., New York, NY, USA

Background:  The role of minor (low-frequency) drug-resistant variants in failure of antiretroviral therapy is not defined. In ACTG 398, 212 NNRTI-experienced and 269 NNRTI-naïve patients were randomized to efavirenz (EFV), abacavir, adefovir, and amprenavir plus a second PI or placebo. This allowed us to examine relations between NNRTI experience, NNRTI resistance, virologic response, and emergence of EFV resistance.

Methods:   Baseline genotypes were obtained in 452/481 patients by a standard (ViroSeq v2.0). Minor NNRTI-resistant variants were sought with single genome RT-PCR and sequencing (SGS) and a Ty1/HIV-1 RT yeast system that detects EFV-resistant colonies. Phylogenetic analyses were performed with the neighbor joining method.

Results:  Virologic failure was associated with NNRTI experience (p <0.001), baseline NNRTI mutations (p <0.001), and development of EFV resistance (p <0.001). Standard genotype did not identify NNRTI mutations in baseline samples from 48 (22%) NNRTI-experienced patients. Virologic response in this group was no better than in the experienced group with baseline NNRTI mutations (n = 166), suggesting that standard genotype was insensitive for NNRTI-resistant variants. Baseline plasma from a random sample of 11 NNRTI-experienced and 12 NNRTI-naïve patients experiencing virologic failure despite negative standard genotypes for NNRTI mutations were assayed for NNRTI-resistant variants. Such variants were identified by SGS in 6/11 NNRTI-experienced patients with the following frequencies per positive patient: 181C and 190A (5/15 sequences); 181C (3/19); 181C (3/22); 108I (2/35); 103N (1/33); and 103N (1/34). By comparison, NNRTI-resistant variants were found in 2/12 NNRTI-naïve patients: 100I and 225L (1/33 sequences each) and 103N (1/41 sequences). The Ty1/HIV-1 RT assay detected EFV-resistant colonies in 8/10 NNRTI-experienced patients with the following frequencies: 7.2, 3.3, 2.8, 1.7, 1.7, 0.9, 0.8, and 0.6%. In NNRTI-naïve patients, resistant colonies were found in only 2/12 patients with frequencies of 0.6% and 0.4%. Phylogenetic analyses showed clustering of the baseline NNRTI-resistant variants identified by SGS with the genotype at virologic failure in 5/6 NNRTI-experienced patients. In the 2 NNRTI-naïve patients, the 103N variant clustered with the failure genotype but the 100I/225L variants did not.

Conclusions:  Prior NNRTI expsoure can select minor NNRTI-resistant variants that are missed by standard genotyping and can contribute to failure of EFV-based regimens.

Keywords: NNRTI Resistance; Minor Variants; Treatment Failure