Table 1. Summary of nirmatrelvir and ensitrelvir resistance phenotypes of SARS2 Mpro variants tested in the live-cell gain-of-signal assay.
Fold resistance for each mutant tested was calculated on the basis of relative IC50 in the live-cell gain-of-signal assay versus WT in assays ran in parallel to limit potential variability due to transfection efficiency. Frequency of variants based on sequences deposited in the GISAID database as of 10 December 2022 (7,391,988 “pre-Omicron” sequences and 6,830,473 “Omicron-present” sequences). CI, confidence interval.
| Mpro variant | Frequency in GISAID | Nirmatrelvir | Ensitrelvir | |||
|---|---|---|---|---|---|---|
| Pre-Omicron | Omicron-present | IC50 nM (95% CI) | Fold resistance (relative to WT) | IC50 nM (95% CI) | Fold resistance (relative to WT) | |
| WT | – | – | 31.6 | – | 23.0 | – |
| (26.1–37.7) | (20.4–25.9) | |||||
| T45I | 3.5 × 10−4 | 4.8 × 10−5 | 64.2 | ~2 | 111 | 4.1 |
| (46.2–85.7) | (92.4–132) | |||||
| S46F | 4.1 × 10−4 | 1.1 × 10−4 | 34.5 | <2 | 34.5 | <2 |
| (28.3–41.5) | (28.3–41.5) | |||||
| E47K | 1.2 × 10−4 | 7.6 × 10−6 | 27.3 | <2 | 17.4 | <2 |
| (10.0–44.3) | (12.8–21.8) | |||||
| D48Y | 1.4 × 10−5 | 1.6 × 10−6 | 62.7 | ~2 | 135 | 5.0 |
| (44.0–88.9) | (99.3–184) | |||||
| M49I | 2.5 × 10−4 | 2.3 × 10−5 | 33.5 | <2 | 335 | 12.4 |
| (20.6–46.7) | (197–664) | |||||
| M49L | 6 × 10−5 | 7.5 × 10−7 | 21.2 | <2 | 436 | 25.4 |
| (17.1–25.9) | (38–573) | |||||
| M49T | 1 × 10−5 | – | 11.1 | <2 | 69.0 | 4.0 |
| (10.2–12.1) | (63.3–75.2) | |||||
| M49V | 4.7 × 10−6 | 3.7 × 10−6 | 7.9 | <2 | 44.5 | 2.6 |
| (7.0–8.9) | (38.2–51.7) | |||||
| S144A | 1.3 × 10−6 | 6.5 × 10−7 | 267 | 12.2 | 395 | 16.9 |
| (215–334) | (304–523) | |||||
| M165I | 1.2 × 10−5 | 4.2 × 10−6 | 29.9 | <2 | 49.3 | ~2 |
| (22.4–39.5) | (33.3–67.2) | |||||
| P168S | 5.1 × 10−5 | 2 × 10−5 | 19.9 | <2 | 36.4 | <2 |
| (15.5–25.0) | (30.1–43.6) | |||||
| ∆P168 | 9.5 × 10−6 | 1.6 × 10−7 | 180 | 5.1 | 157 | 6.8 |
| (154–219) | (132–188) | |||||
| T169I | 5.1 × 10−5 | 9.2 × 10−6 | 34.0 | <2 | 30.9 | <2 |
| (23.7–45.0) | (24.1–38.7) | |||||
| V171I | 5.3 × 10−5 | 2.8 × 10−5 | 21.1 | <2 | 33.4 | <2 |
| (13.6–28.3) | (26.4–41.2) | |||||
| A173V | 1.8 × 10−5 | 1.0 × 10−5 | 328 | 11.6 | 29.6 | <2 |
| (186–796) | (24.2–35.4) | |||||
| A173T | 1.2 × 10−5 | 2.4 × 10−5 | 77.6 | 4.1 | 28.3 | <2 |
| (104–132) | (24.0–33.1) | |||||
| A173S | 1.1 × 10−5 | 1.3 × 10−6 | 18.6 | <2 | 26.2 | <2 |
| (15.9–21.2) | (22.3–30.5) | |||||
| ∆P168/A173V | – | – | 1510 | 51 | 90.5 | 2.8 |
| (1380–1660) | (80.9–102) | |||||
| T45I/M49L | – | – | 20.8 | <2 | 1030 | 54.5 |
| (16.4–25.6) | (814–1340) | |||||
| T45I/A173V | – | – | 414 | 20.6 | 79.2 | 4.2 |
| (351–494) | (66.4–94.7) | |||||
| D48Y/∆P168 | – | – | 921 | 45.9 | 754 | 39.9 |
| (732–1220) | (676–857) | |||||
| M49I/∆P168 | – | – | 151 | 7.5 | 990 | 52.5 |
| (11.9–210) | (772–1310) | |||||
| M49L/∆P168 | – | – | 144 | 7.2 | 2400 | 127 |
| (129–162) | (1890–3110) | |||||