TABLE 2.
Comparison between SAVED CRISPR-Cas12a detection and CT valuea
| Mutation(s) | Detection | All samples |
Samples within specific CT range (positive) | |
|---|---|---|---|---|
| Positive | Negative | |||
| N501Y | No. positive | 16 | 0 | 12 |
| No. negative | 4 | 59 | 0 | |
| Total no. | 20 | 59 | 12 | |
| Sensitivity (%) (95% CI) | 80.00 (56.34–94.27) | NA | 100.00 (73.54–100.00) | |
| Specificity (%) (95% CI) | NA | 100.00 (93.94–100.00) | NA | |
| CT range | 20.3–35.9 | 16.3–34.9 | 20.3–30.3 | |
| T478K | No. positive | 15 | 0 | 13 |
| No. negative | 5 | 59 | 0 | |
| Total no. | 20 | 59 | 13 | |
| Sensitivity (%) (95% CI) | 75.00 (50.90–91.34) | NA | 100.00 (75.30–100.00) | |
| Specificity (%) (95% CI) | NA | 100.00 (93.94–100.00) | NA | |
| CT range | 17.1–34.6 | 16.3–35.9 | 17.1–30.8 | |
| E484A | No. positive | 24 | 0 | 24 |
| No. negative | 0 | 55 | 0 | |
| Total no. | 24 | 55 | 24 | |
| Sensitivity (%) (95% CI) | 100.00 (85.75–100.00) | NA | 100.00 (85.75–100.00) | |
| Specificity (%) (95% CI) | NA | 100.00 (93.51–100.00) | NA | |
| CT range | 25.5–34.9 | 16.3–35.9 | 25.5–34.9 | |
| Δ144 | No. positive | 10 | 0 | 10 |
| No. negative | 0 | 10 | 0 | |
| Total no. | 10 | 10 | 10 | |
| Sensitivity (%) (95% CI) | 100.00 (69.15–100.00) | NA | 100.00 (69.15–100.00) | |
| Specificity (%) (95% CI) | NA | 100.00 (69.15–100.00) | NA | |
| CT range | 20.3–30.3 | 20.9–35.9 | 20.3–30.3 | |
| Δ242–244 | No. positive | 10 | 0 | 10 |
| No. negative | 0 | 10 | 0 | |
| Total no. | 10 | 10 | 10 | |
| Sensitivity (%) (95% CI) | 100.00 (69.15–100.00) | NA | 100.00 (69.15–100.00) | |
| Specificity (%) (95% CI) | NA | 100.00 (69.15–100.00) | NA | |
| CT range | 20.9–35.9 | 20.3–30.3 | 20.9–35.9 | |
| L452R | No. positive | 15 | NA | 13 |
| No. negative | 5 | NA | 0 | |
| Total no. | 20 | NA | 13 | |
| Sensitivity (%) (95% CI) | 75.00 (50.90–91.34) | NA | 100.00 (75.30–100.00) | |
| Specificity (%) (95% CI) | NA | NA | NA | |
| CT range | 17.1–34.6 | NA | 17.1–30.8 | |
| G142D+Δ143−145 | No. positive | 5 | 0 | 5 |
| No. negative | 0 | 19 | 0 | |
| Total no. | 5 | 19 | 5 | |
| Sensitivity (%) (95% CI) | 100.00 (47.82–100.00) | NA | 100.00 (47.82–100.00) | |
| Specificity (%) (95% CI) | NA | 100.00 (82.35–100.00) | NA | |
| CT range | 25.5–30.3 | 25.9–34.9 | 25.5–30.3 | |
| G142D | No. positive | 18 | 0 | 16 |
| No. negative | 1 | 5 | 0 | |
| Total no. | 19 | 5 | 16 | |
| Sensitivity (%) (95% CI) | 94.74 (73.97–99.87) | NA | 100.00 (79.41–100.00) | |
| Specificity (%) (95% CI) | NA | 100.00 (47.82–100.00) | NA | |
| CT range | 25.9–34.9 | 25.5–30.3 | 25.9–32.1 | |
| N2 | No. positive | 48 | 0 | 38 |
| No. negative | 21 | 10 | 0 | |
| Total no. | 69 | 10 | 38 | |
| Sensitivity (%) (95% CI) | 69.57 (57.31–80.08) | NA | 100.00 (90.75–100.00) | |
| Specificity (%) (95% CI) | NA | 100.00 (69.15–100.00) | NA | |
| CT range | 16.3–35.9 | NA | 16.3–30.2 | |
aIn total, 79 blinded samples (10 Alpha, 10 Beta, 20 Delta, 5 Omicron BA.1, 19 Omicron BA.2, 5 wild-type strains, and 10 NTC) were detected by a fluorescence reader in a 384-well plate and visualized under UV light in 0.2-mL 8-strip tubes. As fluorescence detection and UV visualization results are the same for incubation from 30 min to 1.5 h, this table only shows the results after 30 min incubation without mentioning which detection method was used. NA, not applicable; CI, confidence interval (26).