Table 2.
Clinical sensitivity, specificity, PPV, and NPV of LAMP, RT-PCR, microscopy, and RDT; and agreement (Cohen’s kappa) of these techniques vs. multiplex nPCR taken as reference method
| Methods | Positive | Negative | Sensitivity (%) (95% CI) | Specificity (%) (95% CI) | PPV (%) (95% CI) | NPV (%) (95% CI) | Cohen’s kappa (κ) of agreement |
|---|---|---|---|---|---|---|---|
| nPCR | |||||||
| LAMP | – | – | 100 | 100 | 100 | 100 | 1.000* |
| Positive | 148 | 0 | – | – | – | – | – |
| Negative | 0 | 17 | – | – | – | – | – |
| RT-PCR | – | – | 100 | 100 | 100 | 100 | 1.000* |
| Positive | 148 | 0 | – | – | – | – | – |
| Negative | 0 | 17 | – | – | – | – | – |
| Microscopy | – | – | 97.97 | 100 | 100 | 85 | 0.909* |
| Positive | 145 | 3 | – | – | – | – | – |
| Negative | 0 | 17 | – | – | – | – | – |
| RDT | – | – | 96.6 | 100 | 100 | 77.3 | 0.855* |
| Positive | 143 | 0 | – | – | – | – | – |
| Negative | 5 | 17 | – | – | – | – | – |
CI = confidence interval; LAMP = loop-mediated isothermal amplification; nPCR = nested PCR; NPV = negative predictive value; PCR = polymerase chain reaction; PPV = positive predictive value; RDT = rapid diagnostic test; RT-PCR = real-time PCR.
*
P value < 0.0001.