Table 2.
Factors underlying heterogeneity of the diagnostic accuracy of nucleic acid amplification tests (NAATs) for the diagnosis of coronavirus infection
| Variable | Sensitivity (%) with 95%CR | Specificity (%) with 95%CR | Significance a |
|---|---|---|---|
| All coronavirus species | |||
| SARS-CoV-2 versus others | 90.4 (83.7–94.5) versus 86.2 (77.1–92.1) | 98.1 (95.9–99.2) versus 99.4 (99.1–99.6) | SP p 0.002 |
| Real-time RT-PCR versus other PCR | 95.2 (90.5–97.6) versus 82.8 (75.8–88.1) | 98.9 (97.3–99.6) versus 98.8 (97.7–99.4) | SE p < 0.001 |
| Reference standard risk of bias (high versus low versus unclear) | 86.9 (78.5–92.3) versus 89.6 (61.4–97.9) versus 91.6 (83.6–95.9) | 99.3 (98.8–99.6) versus 94.3 (50.9–99.6) versus 98.2 (95.4–99.3) | SP p 0.009 |
| SARS-CoV-2 | |||
| Nasopharyngeal sample versus others b | 88.0 (79.5–93.3) versus 95.8 (88.1–98.6) | 98.0 (94.9–99.3) versus 98.3 94.1–99.5) | SE p 0.04 |
| Index test type (GeneXpert versus RT-LAMP/ isothermal versus others) | 98.9 (96.2–99.7) versus 84.2 (75.0–90.5) versus 93.8 (78.1–98.5) | 95.5 (91.8–97.5) versus 97.7 (92.8–99.3) versus 98.6 (94.4–99.7) | SE p 0.017 |
| Real-time RT-PCR versus other PCR | 96.2 (91.0–98.4) versus 82.7 (73.1–89.4) | 98.5 (95.2–99.6) versus 97.8 (93.7–99.3) | SE p < 0.001 |
| Single gene target versus more than one gene | 82.3 (72.4–89.2) versus 95.6 (89.6–98.2) | 97.6 (91.9–99.3) versus 98.5 (96.4–99.4) | SE p 0.001 |
| E gene included in test versus not included | 97.8 (95.6–98.9) versus 85.3 (77.3–90.9) | 98.6 (93.9–99.7) versus 98.0 (94.8–99.2) | SE p < 0.001 |
| N gene included in test versus not included | 93.9 (86.5–97.3) versus 84.6 (72.6–91.9) | 98.2 (95.8–99.3) versus 98.0 (92.4–99.5) | SE p 0.045 |
| RdRp gene alone versus other one or more genesc | 77.0 (65.7–85.4) versus 93.2 (86.8–96.6) | 97.5 (84.6–99.6) versus 98.3 (96.1–99.3) | SE 0.014 |
a
P values for sensitivity (SE) or specificity (SP). Only statistically significant differences are shown.
b
Studies in which samples taken from the upper respiratory tract (nasal, pharyngeal or nasopharyngeal) compared to studies reporting a mix of upper and lower respiratory tract samples.
c
All the studies using the RNA-dependent RNA polymerase (RdRp) gene targeted it as a single gene and all assessed different reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) or isothermal tests as index test.