Table 2.
Diagnostic assay performance tables for RT-qPCR versus LamPORE assay for whole cohort, asymptomatic cohort (swabs), asymptomatic cohort (saliva) and retrospective symptomatic cohort
| Whole cohort | ||||
| RT-qPCR |
||||
| Positive | Negative | |||
| LamPORE | Positive | 477 | 124 | 601 |
| Negative | 2 | 22 824 | 22 826 | |
| 479 | 22 948 | |||
| Sensitivity | Specificity | PPV | NPV | |
| 99.58% (95% CI 98.46%–99.95%) | 99.46% (95% CI 99.36%–99.55%) | 79.37% (95% CI 76.34%–82.10%) | 99.99% (95% CI 99.9%–100%) | |
| Asymptomatic cohort—swabs | ||||
| Positive | Negative | |||
| LamPORE | Positive | 23 | 11 | 34 |
| Negative | 0 | 3932 | 3932 | |
| 23 | 3943 | |||
| Sensitivity | Specificity | PPV | NPV | |
| 100% (95% CI 85.2%–100%) | 99.72% (95% CI 99.5%–99.7%) | 67.65% (95% CI 53.7%–79.1%) | 100% | |
| Asymptomatic cohort—saliva | ||||
| Positive | Negative | |||
| LamPORE | Positive | 187 | 112 | 299 |
| Negative | 2 | 18 134 | 18 136 | |
| 189 | 18 246 | |||
| Sensitivity | Specificity | PPV | NPV | |
| 98.9% (95% CI 96.2%–99.9%) | 99.4% (95% CI 99.3%–99.5%) | 62.5% (95% CI 58.1%–66.8%) | 99.9% (95% CI 99.9%–100%) | |
| Symptomatic cohort | ||||
| Positive | Negative | |||
| LamPORE | Positive | 116 | 0 | 116 |
| Negative | 0 | 752 | 752 | |
| 116 | 752 | 868 | ||
| Sensitivity | Specificity | PPV | NPV | |
| 100% (95% CI 96.9%–100%) | 100% (95% CI 99.51%–100%) | 100% | 100% | |
Abbreviations: LamPORE, loop-mediated isothermal amplification (LAMP) coupled to nanopore sequencing technology; RT-qPCR, quantitative RT-PCR.
Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for each cohort are shown at the bottom of each sub-table.