TABLE 2.
Diagnostic performance comparison of RT-LAMP and RT-qPCR for SARS-CoV-2 in different cohorts
| Subjects | No. of samples |
% (95% CI)a
|
PLR (95% CI) | NLR (95% CI) | Agreement | ||||
|---|---|---|---|---|---|---|---|---|---|
| Clinically positive | Clinically negative | Sensitivity | Specificity | PPV | NPV | ||||
| Cohort Ib | (n = 35) | (n = 294) | Kappa, 0.89 (0.79–1.00); positive predictive agreement, 100%; negative predictive agreement, 98.01% | ||||||
| RT-LAMP | 88.57 (74.05–95.46) | 98.98 (97.04–99.65) | 91.18 (77.04–96.95) | 98.64 (96.57–99.47) | 86.80 (44.8–168.2) | 0.12 (0.07–0.19) | |||
| Positive | 31 | 3 | |||||||
| Negative | 4 | 291 | |||||||
| RT-qPCR | 80.00 (64.11–89.96) | 100.00 (98.71–100.00) | 100.00 (87.94–100.00) | 97.67 (95.28–98.87) | 0.20 (0.15–0.26) | ||||
| Positive | 28 | 0 | |||||||
| Negative | 7 | 294 | |||||||
| Cohort IIc | (n = 46) | (n = 106) | Kappa, 0.93 (0.77–1.00); positive predictive agreement, 100%; negative predictive agreement, 96.49% | ||||||
| RT-LAMP | 89.13 (76.96–95.27) | 99.06 (94.85–99.83) | 97.62 (87.68–99.58) | 95.45 (89.8–98.04) | 94.48 (13.23–674.7) | 0.11 (0.07–0.16) | |||
| Positive | 41 | 1 | |||||||
| Negative | 5 | 105 | |||||||
| RT-qPCR | 82.61 (69.28–90.91) | 100.00 (96.50–100.00) | 100.00 (90.82–100.00) | 92.98 (86.76–96.40) | 0.17 (0.14–0.22) | ||||
| Positive | 38 | 0 | |||||||
| Negative | 8 | 106 | |||||||
a
PPV, positive predictive value; NPV, negative predictive value; PLR, positive likelihood ratio; NLR, negative likelihood ratio.
b
In Cohort I, 35 of 37 nasopharyngeal swabs from 24 COVID-19 patients were confirmed to be SARS-CoV-2 positive according to the criteria of RT-qPCR (28 samples) and NGS confirmation (7 samples) (see Table S3 in the supplemental material).
c
In Cohort II, 46 of 56 samples (paired nasopharyngeal swabs and sputum samples) from 28 COVID-19 patients were determined to be SARS-CoV-2 positive accordingly (38 were RT-qPCR-positive, and 8 were NGS-positive) (Table S3).