Table 5.
Different direct RT-qPCR methods for diagnosing SARS-CoV-2 RNA
| Sample type | No. of sample | Inactivation method | Sensitivity | Specificity | Overall agreement | Detection limit | Detection time | Ref. |
|---|---|---|---|---|---|---|---|---|
| NPS | 597 | Adding Lysis Buffer + Heating at 65 ˚C for 30 min | 96.0% | 99.8% | 98.8% | ORF1: 0.009 TCID50/mL E: 0.003 TCID50/mL |
- | (10) |
| NPS | Pooled patient sample | Heating at 70 °C for 5 min | 95% on samples with a clinical Ct at or below 32 |
- | - | 1.7×104copies RNA/mL | - | (11) |
| Saliva | - | Buffer Dilution+ heating at 95 °C for 30 min+ Tween-20 | 88.9% | 98.9% | - | 1,000 copies of SARS-CoV-2 virus per mL of saliva spiked with γ-irradiated SARS-CoV-2 | - | (34) |
| NPS | 80 | Heating at 95 ºC for 5 min | Over 90% | - | 95% | - | Saving time: 2 h compare to standard RT-qPCR |
(42) |
| Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium |
132 | 4- fold specimen dilution+ incubation at 65 ˚C | 95% | 99% | 98.5% | 6,600 copies per mL of a viral suspension spiked with synthetic SARS-CoV-2 RNA | - | (43) |
| Nasal and pharyngeal swab | 78 | PK (3 μg/μL, 56 ˚C for 10 min) and thermal shock (98 ˚C for 5 min followed by 4 ˚C for 2 min) | - | - | 100% | - | Saving time: 30 min compare to standard RT-qPCR | (44) |
| NPS | 90 | Incubation at 70 ˚C + additives in formamide-EDTA (FAE) buffer and RNAsnapTM buffer | 87.8% | 100% | 99.9% | - | Saving time: 1-1.2 h compare to standard RT-qPCR | (45) |
| NPS nasalSwab | - | Heating at 75 ˚C for 10 min | - | - | 98% | 550 virus copies/mL of swab | Less than one hour | (46) |
| Saliva | - | Incubation in an alkaline-glycol solution samples (pH 12.2 to 12.8) | 32-foldincrease in detectionsensitivity by AG processing | - | - | 300 copies per mL of saliva | - | (47) |
| Sputum and nasal exudate | - | Dithiothreitol (Sputasol) + ribonuclease inhibitor | - | - | - | 12 copies per PCR reaction volume | 36 min | (48) |
| Throat swabsand other materials from the respiratory tract |
- | PK treatment + repetitive heating steps (56 ˚C for 3 min and then at 95 ˚C for 3 min) | 94.6% | - | - | 5–10genome per mL | 90 min | (49) |
Ct: cycle threshold; NPS: nasopharyngeal swabs; PK: Proteinase K; RT: room temperature; RT-qPCR: quantitative reverse transcription polymerase chain reaction; UVT: universal viral transport.