Table 4.
Association between the major drug resistance mutations emerging in treatment failures from the ALIVE cohort, the drug regimens reported at the time of failure, and expected resistance profile based on genotype results
| Sample # visit # | Drug resistance mutation | Gene product | Frequency of DR mutation (coverage)* | Mutational load (copies/ml) | Treatment at time point of failure | Stanford resistance profile for major mutations |
|---|---|---|---|---|---|---|
| 2v15 | M41L | RT | 13.3%(5316) | 6913 | ZDV, 3TC | H: 3TC, FTC |
| M184V | RT | 99.9%(7721) | 51926 | L: ABC, DDI | ||
| 5v20 | K103N | RT | 100%(5807) | 513564 | ZDV, 3TC, | H: 3TC, FTC, |
| M184V | RT | 82.8%(5266) | 425231 | ABC, EFV | EFV, NVP | |
| L: ABC | ||||||
| PL: DDI | ||||||
| 6v20 | L90M | PI | 16.2%(3602) | 179820 | TDF, FTC, DRVr, RAL | H: NFV |
| I: IDV, SQV | ||||||
| L: ATV, LPV, FPV, | ||||||
| 9v33 | M184V | RT | 99.8%(7493) | 420158 | ZDV, 3TC, ABC, RTV, FTC | H: 3TC, FTC |
| L: ABC | ||||||
| PL: DDI | ||||||
| 10v10 | K103N | RT | 100%(5979) | 40200 | EFV, TDF, FTC | H: 3TC, FTC, EFV, NVP |
| M184V | RT | 100%(5399) | 40200 | L: ABC | ||
| PL: DDI | ||||||
| 16v11 | E138K | RT | 7.6%(8955) | 27149 | 3TC, RTV, LPV | H: 3TC, FTC |
| M184V | RT | 56.6%(8222) | 202190 | I: RPV | ||
| S147G | IN | 7.0%(3123) | 25006 | L: ABC | ||
| PL: DDI, EFV, ETR, NVP | ||||||
| 23v17 | K103N | RT | 99.8%(6110) | 16168 | EFV, TDF, FTC | H: 3TC, FTC, EFV, NVP |
| M184V | RT | 67.1%(6182) | 10870 | |||
| L: ABC | ||||||
| PL: DDI | ||||||
| 27v05 | M46I** | PI | 7.3%(3591) | 1262 | d4T, 3TC, ABC, IDVr | L: NFV |
| PL: ATV, FPV, IDVr, LPV (non-emerging DR related to treatment: H: 3TC, L: ABC) |
Boldface: correlation between mutation, treatment and drug resistance profile in each patient sample at the time point of treatment failure. H = high level drug resistance, I = intermediate drug resistance, L = low level drug resistance, PL: potential low level drug resistance. Drug resistance mutations in italics are not associated with any reported drug taken by the patients throughout the course of this study. *Coverage refers to the number of sequencing reads representing a given nucleotide. **Patient 27 virus also harbored I54V, L90M, K103N and M184V at both time points. These mutations did not emerge between treatment success and failure, but likely contributed to overall failure.