Table 1.
Overview of the SDRMs identified in the Portuguese cohort, at each position for each drug class with prevalence and transmission ratios.
| Protease inhibitor | ||||
| Protease inhibitor-SDRM | Prevalence (%) in drug-naive patients (N = 1685) (95% CI) | Prevalence (%) in protease inhibitor-treatment-failing patients (N = 1352) (95% CI) | Normalized prevalence (%) in treatment-failing patients (N = 1921) (95% CI) | Transmission ratio |
| 83D | 0.1 (0.0–0.3) (N = l) | 0.4 (0.1–0.9) (N = 5) | 0.3 (0.1–0.6) (N = 5) | 0.2 |
| 88D/S | 0.7 (0.4–1.2) (N = 12) | 5.3 (4.2-S.7) (N = 72) | 3.7 (2.9–4.7) (N = 72) | 0.1 |
| 30N | 0.7 (0.4–1.2) (N = 12) | 5.5 (4.3-S.8) (N = 74) | 3.9 (3.0–4.8) (N = 74) | 0.1 |
| 32I | 0.3 (0.1–0.7) (N = 5) | 3.0 (2.2–4.1) (N = 41) | 2.1 (1.5–2.9) (N = 41) | 0.1 |
| 24I | 0.2 (0.1–0.6) (N = 4) | 2.7 (1.9–3.8) (N = 37) | 1.9 (1.4–2.6) (N = 37) | 0.1 |
| 85V | 0.2 (0.0–0.5) (N = 3) | 2.5 (1.7–3.5) (N = 34) | 1.7 (1.2–2.5) (N = 34) | 0.1 |
| 90M | 1.4 (0.9–2.0) (N = 23) | 19.7 (17.6–21.9) (N = 266) | 13.8 (12.3–15.5) (N = 266) | 0.1 |
| 46I/L | 0.9 (0.5–1.5) (N = 16) | 17.5 (15.5–19.7) (N = 237) | 12.3 (10.9–13.9) (N = 237) | 0.1 |
| 53L/Y | 0.1 (0.0–0.4] (N = 2) | 2.4 (1.6–3.3) (N = 32) | 1.7 (1.1–2.3) (N = 32) | 0.1 |
| 82A/C/F/L/M/S/T | 0.8 (0.4–1.3) (N = 13) | 15.5 (13.5–17.5) (N = 209) | 10.8 (9.5–12.4) (N = 209) | 0.1 |
| 54A/L/M/S/T/V | 0.5 (0.2–1.0) (N = 9) | 16.0 (14.1–18.0) (N = 216) | 11.2 (9.9–12.7) (N = 216) | 0.0 |
| 48M/V | 0.1 (0.0–0.3) (N = l) | 2.0 (1.3–2.9) (N = 27) | 1.4 (0.9–2.0) (N = 27) | 0.0 |
| 84V | 0.1 (0.0–0.4) (N = 2) | 6.2 (5.0–7.6) (N = 84) | 4.4 (3.5–5.4J (N = 84) | 0.0 |
| 73A/C/S/T | 0.1 (0.0–0.3) (N = 1) | 7.0 (5.7–8.5) (N = 95) | 4.9 (4.0–6.0) (N = 95) | 0.0 |
| 23I | 0.0 (0.0–0.2) (N = 0) | 0.7 (0.3–1.3) (N = 9) | 0.5 (0.2–0.9) (N = 9) | 0.0 |
| 47A/V | 0.0 (0.0–0.2) (N = 0) | 2.2 (1.5–3.2) (N = 30) | 1.6 (1.1–2.2) (N = 30) | 0.0 |
| 50L/V | 0.0 (0.0–0.2) (N = 0) | 1.2 (0.7–1.9) (N = 16) | 0.8 (0.5–1.3) (N = 16) | 0.0 |
| 76V | 0.0 (0.0–0.2) (N = 0) | 1.5 (0.9–2.3) (N = 20) | 1.0 (0.6–1.6) (N = 20) | 0.0 |
| Any protease inhibitor-SDRM | 3.5 (2.7–4.5) (N = 59) | 38.3 (35.7–41.0) (N = 518) | 27.0 (25.0–29.0) (N = 518) | |
| NRTI | ||||
| NRTI-SDRM | Prevalence (%) in drug-naive patients (N = 1685) (95% CI) | Prevalence (%) in NRTI-treatment-failing patients (N = 1920) (95% CI) | Normalized prevalence (%) in treatment-failing patients (N = 1921) (95% CI) | Transmission ratio |
| 215rev | 1.8 (1.2–2.5) (N = 30) | 2.4 (1.8–3.2) (N = 47) | 2.4 (1.8–3.2) (N = 47) | 0.7 |
| 75A/M/S/T | 0.2 (0.1–0.6) (N = 4) | 2.0 (1.4–2.7) (N = 38) | 2.0 [1.4–2.7) (N = 38) | 0.1 |
| 219E/N/Q/R | 1.2 (0.8–1.9) (N = 21) | 13.8 (12.2–15.4) (N = 264) | 13.7 (12.2–15.4) (N = 264) | 0.1 |
| 41L | 2.1 (1.5–2.9) (N = 35) | 23.3 (21.4–25.2) (N = 447) | 23.3 (21.4–25.2) (N = 447) | 0.1 |
| 69D | 0.2 (0.1–0.6) (N = 4) | 2.7 (2.0–3.5) (N = 52) | 2.7 (2.0–3.5) (N = 52) | 0.1 |
| 215Y/F + rev | 2.6 (1.9–3.5) (N = 44) | 31.3 (29.2–33.4) (N = 600) | 31.2 (29.2–33.4) (N = 600) | 0.1 |
| 67E/G/N | 1.4 (0.9–2.1) (N = 24) | 20.7 (18.9–22.6) (N = 398) | 20.7 (18.9–22.6) (N = 398) | 0.1 |
| 210W | 0.8 (0.4–1.3) (N = 13) | 15.6 (14.0–17.3) (N = 300) | 15.6 (14.0–17.3) (N = 300) | 0.0 |
| 151M | 0.1 (0.0–0.3) (N = 1) | 1.7 (1.1–2.3) (N = 32) | 1.7 (1.1–2.3) (N = 32) | 0.0 |
| 215Y/F | 0.8 (0.5–1.4) (N = 14) | 28.8 (26.8–30.9) (N = 553) | 28.8 (26.8–30.9) (N = 553) | 0.0 |
| 184I/V | 1.2 (0.8–1.9) (N = 21) | 44.0 ((41.7–46.2) (N = 844) | 43.9 (41.7–46.2) (N = 844) | 0.0 |
| 70E/R | 0.2 (0.1–0.6) (N = 4) | 12.4 (11.0–14.0) (N = 238) | 12.4 (10.9–13.9) (N = 238) | 0.0 |
| 74I/V | 0.1 (0.0–0.3) (N = l) | 7.4 (6.3–8.7) (N = 142) | 7.4 (6.3–8.7) (N = 142) | 0.0 |
| 65R | 0.0 (0.0–0.2) (N = 0) | 2.7 (2.0–3.5) (N = 52) | 2.7 (2.0–3.5) (N = 52) | 0.0 |
| 77L | 0.0 (0.0–0.2) (N = 0) | 0.9 (0.5–1.4) (N = 17) | 0.9 (0.5–1.4) (N = 17) | 0.0 |
| 115F | 0.0 (0.0–0.2) (N = 0) | 1.6 (1.1–2.3) (N = 31) | 1.6 (1.1–2.3) (N = 31) | 0.0 |
| 116Y | 0.0 (0.0–0.2) (N = 0) | 1.4 (0.9–2.0) (N = 26) | 1.4 (0.9–2.0) (N = 26) | 0.0 |
| Any NRTI-SDRM | 5.0 (4.0–6.2) (N = 85) | 61.1 (58.9–63.3) (N = 1174) | 61.1 (58.9–63.3) (N = 1174) | |
| NNRTI | ||||
| NNRTI-SDRM | Prevalence in drug-naive patients (N = 1685) (95% CI) | Prevalence (%) in NNRTI-treatment-failing patients (N = 1237) (95% CI) | Normalized prevalence (%) in treatment-failing patients (N = 1921) (95% CI) | Transmission ratio |
| 101E/P | 0.6 (0.3–1.1) (N = 10) | 6.5 (5.2–8.0) (N = 80) | 4.2 (3.3–5.2) (N = 80) | 0.1 |
| 190A/E/S | 1.4 (0.9–2.1) (N = 24) | 15.6 (13.6–17.7) (N = 193) | 10.0 (8.7–11.5) (N = 193) | 0.1 |
| 103N/S | 2.3 (1.6–3.1) (N = 38) | 32.3 (29.7–34.9) (N = 399) | 20.8 (19.0–22.7) (N = 399) | 0.1 |
| 225H | 0.2 [0.0–0.5) (N = 3) | 3.2 (2.3–4.3) (N = 39) | 2.0 (1.4–2.8) (N = 39) | 0.1 |
| 181C/I/V | 0.6 (0.3–1.1) (N = 10) | 12.4 (10.7–14.4) (N = 154) | 8.0 (6.8–9.3) (N = 154) | 0.0 |
| 188C/H/L | 0.2 (0.0–0.5) (N = 3) | 5.2 (4.0–6.6) (N = 64) | 3.3 (2.6–4.2) (N = 64) | 0.0 |
| 100I | 0.0 (0.0–0.2) (N = 0) | 4.1 (3.1–5.4) (N = 51) | 2.7 (1.9–3.5) (N = 51) | 0.0 |
| 106A/M | 0.0 (0.0–0.2) (N = 0) | 2.7 (1.8–3.7) (N = 33) | 1.7 (1.2–2.4) (N = 33) | 0.0 |
| 230L | 0.0 (0.0–0.2) (N = 0) | 1.1 (0.6–1.8) (N = 13) | 0.7 (0.4–1.2) (N = 13) | 0.0 |
| Any NNRTI-SDRM | 4.3 (3.4–5.4) (N = 73) | 57.8 (55.0–60.6) (N = 715) | 37.2 (35.1–39.4) (N = 715) | |
Bold entries indicate an SDRM located above or below the 95% CI in the robust linear regression (Fig. 1). Variants at a single position are pooled (e.g. 46I/L). CI, confidence interval; NNRTI, nonnucleoside reverse transcriptase inhibitors; NRTI, nucleoside reverse transcriptase inhibitors; SDRM, surveillance drug resistance mutations.