Table 3. Baseline PR and RT Genotypic Analysis by Deep Sequencing.
| Percent of Subjects (n) | |||
|---|---|---|---|
| Resistance Mutations at Baseline | Deep Sequencing, 15% Cutoff (n=309)a | Deep Sequencing, 2% Cutoff (n=309)a | Population Sequencing (n=575) |
| NRTI-Associatedb | 15.2% (47) | 16.5% (51) | 15.3% (88) |
| M41L | 0 | 0 | 0.9% (5) |
| A62V | 14.9% (46) | 14.9% (46) | 13.6% (78) |
| K65R | 0 | 0 | 0 |
| D67N | 0 | 0.3% (1) | 0.2% (1) |
| F77L | 0 | 0 | 0.2% (1) |
| M184V/I | 0 | 1.3% (4)c | 0 |
| L210W | 0.3% (1) | 0.3% (1) | 0.2% (1) |
| K219E/N/Q/R | 0.3% (1) | 0.3% (1) | 0.3% (2) |
|
| |||
| NNRTI-Associatedd | 17.8% (55) | 27.8% (86) | 20.0% (115) |
| V90I | 5.8% (18) | 9.1% (28) | 7.1% (41) |
| A98G | 0.3% (1) | 0.6% (2) | 0.3% (2) |
| K101E/H/P | 1.0% (3) | 1.3% (4) | 0.7% (4) |
| K103N | 2.9% (9) | 3.2% (10) | 3.0% (17) |
| K103S | 0.3% (1) | 0.3% (1) | 0.5% (3) |
| V106A/M/I | 1.9% (6) | 3.9% (12) | 1.9% (11) |
| V108I | 0.6% (2) | 1.0% (3) | 0.5% (3) |
| E138A/G/K/Q/R | 6.1% (19) | 7.4% (23) | 6.6% (38) |
| V179D/F/L/T | 1.3% (4) | 1.9% (6) | 1.4% (8) |
| G190A/E/Q/S | 0.3% (1) | 1.0% (3) | 0.5% (3) |
| P225H | 0 | 0.3% (1) | 0 |
| M230I/L | 0 | 3.6% (11) | 0 |
|
| |||
| Primary PI-Associatede | 1.3% (4) | 8.1% (25) | 1.7% (10) |
| D30N | 0 | 0.3% (1) | 0 |
| V32I | 0.3% (1) | 0.6% (2) | 0 |
| L33F | 0.3% (1) | 0.6% (2) | 0.5% (3) |
| M46I/L | 0 | 2.3% (7) | 0.7% (4) |
| G48V | 0 | 3.9% (12) | 0 |
| I50L/V | 0 | 0 | 0.2% (1) |
| Q58E | 0.6% (2) | 0.6% (2) | 0.3% (2) |
| L90M | 0.3% (1) | 0.3% (1) | 0.2% (1) |
Baseline deep sequencing data was available for 288/289 subjects in the EVG/COBI/FTC/TDF group and for 21/286 subjects in the ATV+RTV+FTC/TDF group.
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.
Four subjects had M184I by deep sequencing, at percentages ranging from 2.0% to 9.7%. The mutational viral loads of the samples were 44 copies/mL, 620 copies/mL, 2020 copies/mL, and 10590 copies/mL.
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.