Article Figures & Data
Figures
- FIG 1
Prevalence of NNRTI resistance-associated amino acid substitutions among first-line treatment failures. Sequences from 1,433 HIV-1 subtype C-infected patients failing first-line therapy with NNRTI resistance-associated mutations were obtained from the SATuRN (n = 766; light gray bars) and Stanford (n = 667; dark gray bars) databases. Amino acid substitutions are grouped according to prevalence: >10%, 5% to 10%, 1% to 5%, and <1%.
- FIG 2
Phenotypic resistance of viruses with single amino acid substitutions associated with resistance to the NNRTIs ETR, RPV, EFV, and NVP. Single NNRTI resistance-associated mutations (n = 34) were introduced into the p8.MJ4 subtype C HIV-1 expression plasmid by site-directed mutagenesis. Phenotypic susceptibilities to ETR (A), RPV (B), EFV (C), and NVP (D) were determined using a single-cycle nonreplicative phenotypic assay. The lower cutoff values determined for this assay are indicated for each drug. Columns indicate mean values, while error bars indicate the standard errors of the means (SEMs). Each mutant was tested in duplicate in at least two independent experiments.
- FIG 3
Phenotypic resistance to ETR, RPV, EFV, and NVP of viruses with double resistance-associated amino acid substitutions. Positively associated double mutations (n = 14) were introduced into the p8.MJ4 subtype C HIV-1 expression plasmid. Phenotypic susceptibilities to ETR (A), RPV (B), EFV (C), and NVP (D) were determined with a single-cycle nonreplicative phenotypic assay. The lower cutoff values determined for this assay are indicated for each drug. Columns indicate mean values, while error bars indicate the standard errors of the means (SEMs). Each mutant was tested in duplicate in at least two independent experiments.
- FIG 4
Impact of E138K and M184IV on phenotypic susceptibility to ETR, RPV, EFV, and NVP. The phenotypic susceptibility to ETR, RPV, EFV, and NVP of site-directed mutants containing amino acid substitutions M184I, M184V, E138K, and their combinations were determined. The lower cutoff values determined for this assay are indicated for each drug. Columns indicate mean values, while error bars indicate the standard errors of the mean (SEMs). Each mutant was tested in duplicate in at least two independent experiments. n.s., not significant; **, P < 0.01 (2-way analysis of variance); ***, P < 0.001 (2-way analysis of variance).
- FIG 5
Phenotypic susceptibility of mutants with single and double NNRTI resistance-associated mutations. The in vitro phenotypic responses of mutants with site-directed single and double NNRTI resistance-associated mutations, ranked according to the prevalence of the mutation among the 1,433 sequences with NNRTI resistance-associated mutations used in this analysis, are summarized. Some mutations (*) were not observed among the sequences but were included, as they are implicated in ETR and RPV resistance. Light gray shading, FCs of >3.6 (ETR), >2.6 (RPV), >3.8 (EFV), and >2.8 (NVP); dark gray shading, FC of >10.
- FIG 6
Genotypic and phenotypic analysis of samples from EFV/NVP-experienced patients. Patient samples with NNRTI resistance-associated NNRTI resistance-associated amino acid substitutions were screened for NNRTI susceptibility in an in vitro phenotypic assay. The Stanford HIV Drug Resistance Database genotypic resistance scores are included for reference purposes. Light gray shading, FCs of >3.6 (ETR), >2.6 (RPV), >3.8 (EFV), and >2.8 (NVP); dark gray shading, FC of >10. Pt. patient number; STD, standard deviation.
- FIG 7
Contribution of T369I to NNRTI resistance. Site-directed mutants containing the T369I amino acid substitution, an amino acid substitution found in the connection domain of patient 12 (Fig. 6), in combination with Y181C were tested for susceptibility to ETR, RPV, EFV, and NVP. The lower cutoff values are indicated for each drug. Columns indicate mean values, while error bars indicate the standard errors of the means (SEMs). Each mutant was tested in duplicate in at least two independent experiments. ***, P < 0.001 (2-way analysis of variance).
- FIG 8
Contribution of N348I to NNRTI resistance. Site-directed mutants containing the N348I amino acid substitution, an amino acid substitution in the connection domain of some patients (Fig. 6), in combination with K103N or Y181C were tested for susceptibility to ETR, RPV, EFV, and NVP. The lower cutoff values are indicated for each drug. Columns indicate mean values, while error bars indicate the standard errors of the mean (SEMs). Each mutant was tested in duplicate in at least two independent experiments. n.s., not significant; *, P < 0.05 (2-way analysis of variance); ***, P < 0.001 (2-way analysis of variance).
Tables
- TABLE 1
HIV-1 subtype C sequences with NNRTI resistance-associated mutations used in this study
NNRTI treatment(s) No. (%) of patients SATuRN database Stanford database Total EFV 630 (82.2) 278 (41.6) 908 (63.3) NVP 124 (16.1) 316 (47.4) 440 (30.7) NVP, EFV 12 (1.6) 31 (4.6) 43 (3.0) Unknown 39 (5.8) 39 (2.7) Othera 3 (0.4) 3 (0.2) Total 766 667 1,433 ↵a The patients received delavirdine (DLV) or MKC422.
- TABLE 2
Pairs of positively correlated NNRTI resistance-associated amino acid substitutions
Combination P value for association Prevalence (%) Subtype C data seta K101E-G190A <0.0001 5.6 K103N-P225H <0.0001 7.7 V106M-V179D <0.0001 4.4 V106M-F227L <0.0001 4.0 Y181C-H221Y <0.0001 3.5 Subtype B data setb Y181C-G190A <0.0001 6.5 K101E-G190A <0.0001 3.4 K101E-Y181C <0.0001 2.7 K101E-G190S <0.0001 1.0 H101H-G190A <0.0001 0.9 A98G-Y181C <0.0001 2.4 K101H-Y181C <0.0001 0.7 A98G-G190A <0.0001 1.6 Y181C-G190S <0.0001 0.9 V179F-Y181C <0.0001 0.2
