Table 3.
Overall Diagnostic Performance of 12 Molecular Assays
| Assay | Sensitivity (95% CI) | Specificity (95% CI) | Kappa (95% CI) |
|---|---|---|---|
| CDC N1 kit∗ | 98.5% (92.1%–100%) | 100% (95.8%–100%) | 0.99 (0.96–1) |
| CDC N2 kit∗ | 100% (94.7%–100%) | 100% (95.8%–100%) | 1† |
| NIID N2 | 100% (94.7%–100%) | 100% (95.8%–100%) | 1† |
| NIID N2 with EAV‡ | 95.6% (87.6%–99.1%) | 100% (95.8%–100%) | 0.96 (0.91–1) |
| Corman E | 98.5% (92.1%–100%) | 100% (95.8%–100%) | 0.99 (0.96–1) |
| Corman N | 69.1%§ (56.7%–79.8%) | 100% (95.8%–100%) | 0.72 (0.60–0.83) |
| Roche E kit‡¶ | 86.8%§ (76.3%–93.8%) | 100% (95.8%–100%) | 0.88 (0.80–0.96) |
| Roche RdRP kit‡¶ | 42.6%§ (30.7%–55.3%) | 100% (95.8%–100%) | 0.46 (0.33–0.58) |
| Roche N kit‡¶ | 67.6%§ (55.2%–78.5%) | 100% (95.8%–100%) | 0.70 (0.59–0.82) |
| Thermo Combo kit‡ǁ | 85.3%§ (74.6%–92.8%) | 100% (95.8%–100%) | 0.87 (0.78–0.95) |
| BGI kit‡∗∗ | 88.2%§ (78.1%–94.8%) | 100% (95.8%–100%) | 0.89 (0.82–0.97) |
| LAMP kit | 80.9%§ (69.5%–89.5%) | 100% (95.8%–100%) | 0.83 (0.73–0.92) |
All samples yielded positive signals in separate CDC RNaseP reactions. The CDC N1 assay was negative, but the CDC N2 assay was positive for two true-positive samples. Repeat testing showed that one sputum sample was positive for both assays, whereas results of the other nasopharyngeal sample were unchanged. Thus, the former was considered positive, and the latter was considered inconclusive as the results of the CDC assay.
95% CI could not be calculated.
All reactions yielded positive signals for control targets.
P < 0.05 in comparison with the defined reference standard.
Cutoff was defined by two cycles higher than the observed CT value for 10 copies according to the manufacturer's instructions (E, 36.7; RdRP, 40; N, 39.3). When the fixed cutoff shown in the instructions was used (E, 36; RdRP, 39; N, 37), the sensitivity was changed as follows: E, 83.8%; RdRP, 36.8%; N, 50.0%, and the specificity was unchanged.
Seven samples were positive for only the N gene that warranted repeat testing. Repeat testing showed that four samples (two true-positive sputum samples, one true-positive pharyngeal sample, and one true-negative sputum sample) were negative for all genes, and these were considered negative. The other three true-positive sputum samples were positive again for only the N gene and were considered positive.
Four samples were positive, but the CT values were >38, which warranted repeat testing. Repeat testing showed that two true-negative pharyngeal samples and one true-negative nasopharyngeal sample were negative, and they were considered negative. The other true-positive sputum sample was positive again with a CT value of 39.12 and was considered positive.