Table 6.
NNRTI Resistance Mutations and Estimated NNRTI Resistance Levels
| SID | Sanger and NGS | Sanger alone | NGS alone | Sanger score → NGS score |
||
|---|---|---|---|---|---|---|
| EFV | ETR | RPV | ||||
| Samples for which NGS reported higher levels of drug resistance for one or more NNRTIs | ||||||
| 23_PR,RT | V108VI,V179VD,Y188HL | K103KE (5.4%), G190GE (4.7%) | 5 | 3 → 5 | 5 | |
| 39_PR,RT | Y181YC | K103KN (20.8%) | 4 → 5 | 4 | 4 | |
| 92_PR,RT | K103KN (13.6%) | 1 → 5 | 1 | 1 | ||
| 166_PR,RT | V106IV (8.3%) | 1 | 1 → 2 | 1 → 2 | ||
| 227_PR,RT | V179VAD | K103KR (14.6%) | 2 → 4 | 2 | 2 → 3 | |
| 299_PR,RT | V179D,Y188L | V106VI (6.0%) | 5 | 3 → 4 | 5 | |
| Samples for which Sanger reported higher levels of drug resistance for one or more NNRTIs | ||||||
| 50_PR,RT | V106IV | 1 | 2 → 1 | 2 → 1 | ||
| 93_PR,RT | K101E | G190GA | 5 → 3 | 4 → 3 | 5 → 4 | |
| 269_PR,RT | V106IV | 1 | 2 → 1 | 2 → 1 | ||
| Samples for which Sanger or NGS detected different DRMs, but for which levels of NNRTI resistance were the same | ||||||
| 18_PR,RT | K103KE (5.2%) | 1 | 1 | 1 | ||
| 24_PR,RT | K103KE (6.3%) | 1 | 1 | 1 | ||
| 25_PR,RT | Y188L | K103KE (8.4%) | 5 | 2 | 5 | |
| 27_PR,RT | V179D | K103KE (5.8%) | 2 | 2 | 2 | |
| 30_PR,RT | K103KE (6.6%) | 1 | 1 | 1 | ||
| 46_PR,RT | K103KQ (5.1%) | 1 | 1 | 1 | ||
| 57_PR,RT | K103KE (5.1%) | 1 | 1 | 1 | ||
| 74_PR,RT | K103KE (4.7%) | 1 | 1 | 1 | ||
| 103_PR,RT | A98AG,K101KE,E138Q,Y181YC,H221HY | V106VI (20.3%) | 5 | 5 | 5 | |
| 157_PR,RT | K103N | E138AT | E138A (99.6%) | 5 | 4 | 5 |
| 161_PR,RT | K103KE (5.4%) | 1 | 1 | 1 | ||
| 163_PR,RT | K103KE (5.5%) | 1 | 1 | 1 | ||
| 190_PR,RT | K103KE (4.5%) | 1 | 1 | 1 | ||
| 191_PR,RT | K103KE (4.6%) | 1 | 1 | 1 | ||
| 192_PR,RT | V179E | K103KE (22.9%),V179DE (6.4%; 91.3%) | 2 | 2 | 2 | |
| 215_PR,RT | A98G | K238KT (5.8%) | 5 | 2 | 3 | |
| 221_PR,RT | K103KE (4.2%) | 1 | 1 | 1 | ||
| 222_PR,RT∗ | K103N | V108VI (10.0%),Y318YF (60.6%) | 5 | 1 | 1 | |
| 263_PR,RT∗ | K101E,G190A | V179IT (92.9%; 5.7%) | 5 | 4 | 5 | |
| 273_PR,RT | K103KN | Y318YF (72.3%) | 5 | 1 | 1 | |
Predicted levels of drug resistance according to the HIVdb genotypic resistance interpretation system: susceptible (1); potential low-level resistance (2); low-level resistance (3); intermediate resistance (4); high-level resistance (5). Percent mixtures are shown in parentheses.
DRM, drug resistance mutation; EFV, efavirenz; ETR, etravirine; NGS, next-generation sequencing; NNRTI, non-nucleoside reverse transcriptase inhibitor; PR, protease; RPV, rilpivirine; RT, reverse transcriptase; SID, sample ID.
∗
Sample 222 is subtype C, and sample 263 is subtype CRF01_AE. All other samples listed in this table are subtype B.