TABLE 2.
Sensitivity and specificity of RT-qPCR analysis of patients’ samples from the day of admission to the third day, for various primers and probesa
| Primer sets | Sputum samples |
Nasopharynx samples |
||
|---|---|---|---|---|
| Ct-35 | Ct-40 | Ct-35 | Ct-40 | |
| NP-gene (iNP) Sensitivity/Specificity (AUC) |
94.8%/100% (0.97) |
100% /100% (1.0) |
69.6% /100% (0.82) |
73.9% /100% (0.87) |
| E-gene (Kogene kit) Sensitivity/Specificity (AUC) |
84.2% /100% (0.92) |
89.5% /100% (0.95) |
60.9% /100% (0.80) |
60.9% /100% (0.80) |
| RdRp-gene (Kogene kit) Sensitivity/Specificity (AUC) |
94.8%/100% (0.97) |
100% /100% (1.0) |
60.9% /100% (0.83) |
65.2% /100% (0.79) |
| WHO RdRp primers Sensitivity/Specificity (AUC) |
42.1%/100% (0.71) |
79.0%/100% (0.90) |
65.2% /100% (0.82) |
86.4% /96.4% (0.90) |
| CDC N1 primers Sensitivity/Specificity (AUC) |
57.9%/100% (0.79) |
89.5%/90.5% (0.86) |
69.6% /100% (0.85) |
82.6% /85.7% (0.84) |
| CDC N2 primers Sensitivity/Specificity (AUC) |
63.2%/90.5% (0.73) |
73.7%/100% (0.79) |
65.2% /96.4% (0.79) |
60.3% /96.4% (0.67) |
| CDC N3 primers Sensitivity/Specificity (AUC) |
57.9%/100% (0.79) |
89.5%/100% (0.95) |
69.6% /100% (0.85) |
73.9/100% (0.87) |
a
Number of SARS-CoV-2–positive sputum samples = 19; number of virus-negative sputum samples = 21; number of virus-positive nasopharyngeal samples = 23; number of virus-negative nasopharyngeal samples = 28; iNP, in-house–designed NP gene primer set; Ct-35, cutoff cycle threshold of 35; Ct-40, cutoff cycle threshold of 40.