Table 4. Baseline IN 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 | Resistance Subset Population Sequencing (n=59)b |
| Primary INSTI-Associatedc | 3.2% (10) | 4.9% (15) | 18.6% (11) |
| E92G/Q | 0 | 0.3% (1)e | 0 |
| T97A | 3.2% (10)d | 3.6% (11)d | 18.6% (11) |
| S147G | 0 | 0.6% (2)e | 0 |
| N155H/S | 0 | 0.3% (1)e | 0 |
|
| |||
| Secondary INSTI-Associatedf | 56.0% (173) | 62.8% (194) | 55.9% (33) |
| M50I | 16.8% (52) | 23.6% (73) | 23.7% (14) |
| H51Y | 0 | 0.3% (1) | 0 |
| L68I/V | 0.6% (2) | 2.3% (7) | 0 |
| V72A/N/T | 1.6% (5) | 2.3% (7) | 0 |
| L74M | 2.6% (8) | 2.9% (9) | 1.7% (1) |
| Q95K/R | 0.3% (1) | 0.6% (2) | 1.7% (1) |
| S119P/R/T | 40.1% (124) | 40.1% (124) | 33.9% (20) |
| F121C/Y | 0 | 0.3% (1) | 0 |
| A128T | 0 | 1.3% (4) | 0 |
| E138A/K | 0.3% (1) | 0.3% (1) | 0 |
| G140A/C/S | 0 | 0.3% (1) | 0 |
| Q146I/K/L/P/R | 0 | 1.3% (4) | 0 |
| S153A/F/Y | 0 | 1.3% (4) | 0 |
| E157K/Q | 3.2% (10) | 6.5% (20) | 0 |
| E170A | 0 | 0.3% (1) | 0 |
| R263K | 0 | 0.6% (2) | 0 |
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.
Baseline population sequencing was performed retrospectively on 69 samples, with 10 assay failures. These samples included those from subjects on both treatment arms in the resistance analysis population, and those that had primary IN resistance by deep sequencing at ≥15%.
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.
Eleven subjects had T97A by deep sequencing, at percentages ranging from 6.1% to 99.8%.
Four subjects had E92G, S147G, or N155H by deep sequencing, at percentages ranging from 2.1% to 3.7%. The mutational viral load of the E92G-containing sample was 920 copies/mL. The mutational viral loads of the S147G-containing samples were 430 copies/mL and 490 copies/mL. The mutational viral load of the N155H-containing sample was 770 copies/mL.
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.