Table 5. Baseline PR, RT, and IN Genotypic Substitutions and Virologic Outcome Through Week 48, n=575.
| Resistance Substitutions at Baseline | Subjects with Substitutions by Population or Deep Sequencing, ≥2%, n (%)a | Week 48 Snapshot Outcome | Week 48 Resistance Analysis (Resistance Developed/Analyzed) | |||
|---|---|---|---|---|---|---|
|
| ||||||
| HIV-1 RNA <50 copies/mL | HIV-1 RNA ≥50 copies/mL | No virologic data in window | EVG/COBI/FTC/TDF | ATV+RTV+ FTC/TDF | ||
|
| ||||||
| NRTI-Associatedb | 95 (16.5%) | 75 (78.9%) | 12 (12.6%) | 8 (8.4%) | 0/5 | 0/3 |
| M41L | 5 (0.9%) | 3 (60.0%) | 1 (20.0%) | 1 (20.0%) | 0/0 | 0/0 |
| A62V | 80 (13.9%) | 63 (78.8%) | 11 (13.8%) | 6 (7.5%) | 0/4 | 0/3 |
| D67N | 2 (0.3%) | 2 (100%) | 0 | 0 | 0/0 | 0/0 |
| F77L | 1 (0.2%) | 1 (100%) | 0 | 0 | 0/1 | 0/0 |
| M184V/I | 4 (0.7%) | 3 (75.0%) | 0 | 1 (25.0%) | 0/0 | 0/0 |
| L210W | 2 (0.3%) | 2 (100%) | 0 | 0 | 0/0 | 0/0 |
| K219E/N/Q/R | 3 (0.5%) | 3 (100%) | 0 | 0 | 0/0 | 0/0 |
|
| ||||||
| NNRTI-Associatedc | 148 (25.7%) | 111 (75.0%) | 25 (16.9%) | 12 (8.1%) | 0/8 | 3/10 |
| V90I | 50 (8.7%) | 34 (68.0%) | 12 (24.0%) | 4 (8.0%) | 0/5 | 0/3 |
| A98G | 3 (0.5%) | 3 (100%) | 0 | 0 | 0/0 | 0/0 |
| K101E/H/P | 7 (1.2%) | 7 (100%) | 0 | 0 | 0/0 | 0/1 |
| K103N | 18 (3.1%) | 14 (77.8%) | 3 (16.7%) | 1 (5.6%) | 0/2 | 1/3 |
| K103S | 3 (0.5%) | 1 (33.3%) | 1 (33.3%) | 1 (33.3%) | 0/1 | 0/0 |
| V106A/M/I | 17 (3.0%) | 14 (82.4%) | 1 (5.9%) | 2 (11.8%) | 0/0 | 1/1 |
| V108I | 4 (0.7%) | 2 (50.0%) | 1 (25.0%) | 1 (25.0%) | 0/0 | 0/0 |
| E138A/G/K/Q/R | 44 (7.7%) | 36 (81.8%) | 6 (13.6%) | 2 (4.5%) | 0/0 | 1/3 |
| V179D/F/L/T | 10 (1.7%) | 6 (60.0%) | 3 (30.0%) | 1 (10.0%) | 0/0 | 0/0 |
| G190A/E/Q/S | 5 (0.9%) | 4 (80.0%) | 1 (20.0%) | 0 | 0/0 | 0/0 |
| P225H | 1 (0.2%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
| M230I/L | 11 (1.9%) | 9 (81.8%) | 1 (9.1%) | 1 (9.1%) | 0/1 | 0/0 |
|
| ||||||
| Primary PI-Associatedd | 30 (5.2%) | 23 (76.7%) | 5 (16.7%) | 2 (6.7%) | 0/2 | 0/0 |
| D30N | 1 (0.2%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
| V32I | 2 (0.3%) | 1 (50.0%) | 0 | 1 (50.0%) | 0/0 | 0/0 |
| L33F | 4 (0.7%) | 3 (75.0%) | 1 (25.0%) | 0 | 0/0 | 0/0 |
| M46I/L | 10 (1.7%) | 8 (80.0%) | 1 (10.0%) | 1 (10.0%) | 0/1 | 0/0 |
| G48V | 12 (2.1%) | 10 (83.3%) | 1 (8.3%) | 1 (8.3%) | 0/1 | 0/0 |
| I50L/V | 1 (0.2%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
| Q58E | 2 (0.3%) | 1 (50.0%) | 1 (50.0%) | 0 | 0/0 | 0/0 |
| L90M | 1 (0.2%) | 0 | 1 (100%) | 0 | 0/0 | 0/0 |
|
| ||||||
| Primary INSTI-Associatede | 16 (4.8%) | 15 (93.8%) | 1 (6.3%) | 0 | 0/0 | 1/1 |
| E92G/Q | 1 (0.3%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
| T97A | 12 (3.6%) | 11 (91.7%) | 1 (8.3%) | 0 | 0/0 | 1/1 |
| S147G | 2 (0.6%) | 2 (100%) | 0 | 0 | 0/0 | 0/0 |
| N155H/S | 1 (0.3%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
|
| ||||||
| Secondary INSTI-Associatedf | 212 (63.3%) | 176 (83.0%) | 28 (13.2%) | 8 (3.8%) | 0/12 | 3/15 |
| M50I | 83 (24.8%) | 68 (81.9%) | 12 (14.5%) | 3 (3.6%) | 0/3 | 0/7 |
| H51Y | 1 (0.3%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
| L68I/V | 7 (2.1%) | 7 (100%) | 0 | 0 | 0/0 | 0/0 |
| V72A/N/T | 7 (2.1%) | 7 (100%) | 0 | 0 | 0/0 | 0/0 |
| L74M | 10 (3.0%) | 8 (80.0%) | 1 (10.0%) | 1 (10.0%) | 0/1 | 0/0 |
| Q95K/R | 2 (0.6%) | 1 (50.0%) | 1 (50.0%) | 0 | 0/1 | 0/0 |
| S119P/R/T | 135 (40.3%) | 111 (82.2%) | 20 (14.8%) | 4 (3.0%) | 0/8 | 2/9 |
| F121C/Y | 1 (0.3%) | 0 | 1 (100%) | 0 | 0/0 | 0/0 |
| A128T | 4 (1.2%) | 3 (75.0%) | 1 (25.0%) | 0 | 0/0 | 0/0 |
| E138A/K | 1 (0.3%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
| G140A/C/S | 1 (0.3%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
| Q146I/K/L/P/R | 4 (1.2%) | 4 (100%) | 0 | 0 | 0/0 | 0/0 |
| S153A/F/Y | 4 (1.2%) | 2 (50.0%) | 1 (25.0%) | 1 (25.0%) | 0/1 | 0/0 |
| E157K/Q | 20 (6.0%) | 17 (85.0%) | 2 (10.0%) | 1 (5.0%) | 0/0 | 1/1 |
| E170A | 1 (0.3%) | 1 (100%) | 0 | 0 | 0/0 | 0/0 |
| R263K | 2 (0.6%) | 2 (100%) | 0 | 0 | 0/0 | 0/0 |
This analysis includes any subject with resistance detected by either population or deep sequencing. PR and RT data was available for 575 subjects total, 575 with population sequencing data and 309 with deep sequencing data. IN data was available for 335 subjects total, 59 with population sequencing data and 309 with deep sequencing data.
NRTI resistance substitutions (NRTI-R) are M41L, A62V, K65R, D67N, T69 insertions, K70E/R, L74I/V, V75I, F77L, Y115F, F116Y, Q151M, M184V/I, L210W, T215F/Y, K219E/N/Q/R in RT.
NNRTI resistance substitutions (NNRTI-R) are V90I, A98G, L100I, K101E/H/P, K103N/S, V106A/I/M, V108I, E138A/G/K/Q/R, V179D/F/L/T, Y181C/I/V, Y188C/H/L, G190A/E/Q/S, H221Y, P225H, F227C, M230I/L in RT.
Primary protease inhibitor resistance substitutions (PI-R) are D30N, V32I, L33F, M46I/L, I47A/V, G48V, I50L/V, I54L/M, Q58E, T74P, L76V, V82A/F/L/S/T, I84V, N88S, L90M in protease.
Primary integrase strand transfer inhibitor resistance substitutions (INSTI-R) are T66A/I/K, E92G/Q, T97A, Y143C/H/R, S147G, Q148H/K/R, N155H/S in IN.
Secondary INSTI-R are M50I, H51Y, L68I/V, V72A/N/T, L74M, Q95K/R, G118R, S119P/R/T, F121C/Y, A128T, E138A/K, G140A/C/S, P145S, Q146I/K/L/P/R, V151A/L, S153A/F/Y, E157K/Q, G163K/R, E170A, R263K in IN.