PMC full text:
TABLE 4.
Clinical evaluation of molecular diagnostic tests for SARS-CoV
| Diagnostic method and target gene | Clinical specimen | Diagnostic gold standard | Collection time after onset of symptoms (no. of samples) | % Sensitivity (viral load [copies/ml]) | Reference |
|---|---|---|---|---|---|
| In-house RT-PCR | |||||
| RNA pola | NPA | Laboratory confirmedb | Days 1-5c (72) | 59.7d | 391 |
| Days 1-5 (98) | 29.6 | 32 | |||
| RNA pol | NPA | WHO criteria, probable SARS | Days 0-5 (501) | 41.1 | 56 |
| Days 6-11 (211) | 58.8 | ||||
| Days 12-20 (62) | 37.1 | ||||
| Day >21 (15) | 13.3 | ||||
| RNA pol | Throat swab | WHO criteria, probable SARS | Days 1-13 (590) | 37.5 | 384 |
| RNA pola | Nose and throat swab | Laboratory confirmedb | Days 1-5c (54) | 61.1d | 391 |
| Days 1-5 (53) | 28.3 | 32 | |||
| RNA pol | Upper respiratorye | WHO criteria, probable SARS | Days 0-5 (212) | 31.1 | 56 |
| Days 6-11 (73) | 37 | ||||
| Days 12-20 (45) | 31.1 | ||||
| Day >21 (159) | 5.7 | ||||
| RNA pola | Respiratoryf | Laboratory confirmedb | 1 wk (243) | 26.3 | 39 |
| 2 wk (134) | 30.6 | ||||
| 3-4 wk (94) | 18.1 | ||||
| RNA pol | Stool | Laboratory confirmedb | Days 5-10c (19) | 57.9d | 391 |
| Days 1-5 (25) | 20 | 32 | |||
| 1 wk (21) | 42.9 | 39 | |||
| 2 wk (25) | 68 | ||||
| 3-4 wk (80) | 42.5 | ||||
| RNA pol | Stool | WHO criteria, probable SARS | Days 0-5 (77) | 23.4 | 56 |
| Days 6-11 (86) | 57 | ||||
| Days 12-20 (72) | 52.8 | ||||
| Day >21 (297) | 15.2 | ||||
| RNA pol | Urine | Laboratory confirmedb | Days 5-10c (78) | 50d | 391 |
| Days 1-5 (15) | 0 | 32 | |||
| 1 wk (75) | 2.7 | 39 | |||
| 2 wk (82) | 6.1 | ||||
| 3-4 wk (54) | 11.1 | ||||
| RNA pol | Urine | WHO criteria, probable SARS | Days 0-11 (16) | 12.5 | 56 |
| Days 12-20 (21) | 4.8 | ||||
| Days >21-23 (161) | 1.9 | ||||
| RNA pol | Blood (serum) | WHO criteria, probable SARS | Days 0-5 (64) | 17.2 | 56 |
| Days 6-11 (14) | 35.7 | ||||
| Days 12-20 (9) | 11.1 | ||||
| Nested RNA pol | Blood (plasma) | Laboratory confirmedb | Days 1-3 (24) | 79.2 | 108 |
| In-house quantitative PCR | |||||
| ORF 1ba | NPA | Laboratory confirmedb | Days 1-3 (32) | 50 | 263 |
| Days 4-6 (35) | 31.4 | ||||
| Days 7-10 (31) | 51.6 | ||||
| ORF 1bg | NPA | Laboratory confirmedb | Day 1 (8) | 62.5d | 264 |
| Day 2 (16) | 87.5d | ||||
| Day 3 (26) | 80.1d | ||||
| ORF 1b | NPA | WHO criteria, probable SARS or laboratory confirmedb | Days 10-15 (142) | 42.3 (2.4 log [mean]) | 156 |
| 1-step ORF 1bg | NPA | Laboratory confirmedb | Days 1-3 (29) | 96.6d | 266 |
| Days 4-9 (57) | 80.7d | ||||
| 1-step ORF 1b | Throat wash | WHO criteria, laboratory-confirmed SARS | Days 2-9 (17) | 9.58 × 102 (min)-5.93 × 106 (max) | 349 |
| Saliva | Days 2-9 (17) | 7.08 × 102 (min)-6.38 × 108 (max) | |||
| N | Respiratoryh | WHO criteria, laboratory-confirmed SARS | Days 2-54 (31) | 74.2 | 88 |
| N | NPA and stool | WHO criteria, probable SARS | Days 1-4 (32) | 18.8 | 155 |
| Days 5-10 (37) | 35.1 | ||||
| RNA pol | Stool | Laboratory confirmedb | Days 1-10 (8) | 75 | 189 |
| Days 11-20 (27) | 81.5 | ||||
| Days 21-30 (5) | 80 | ||||
| ORF 1b | Stool | WHO criteria, probable SARS or laboratory confirmedb | Days 1-3 (6) | 66.7 | 263 |
| Days 4-6 (15) | 80 | ||||
| Days 7-10 (16) | 62.5 | ||||
| Days 10-15 (94) | 87.2 (6.1 log [median]) | 156 | |||
| N | Stool | WHO criteria, probable SARS | Days 1-10 (37) | 27 | 413 |
| Days 11-20 (71) | 26.8 | ||||
| Days 21-30 (77) | 15.6 | ||||
| Days 31-40 (67) | 17.9 | ||||
| Day >40 (74) | 9.5 | ||||
| N | Stool | WHO criteria, laboratory-confirmed SARS | Days 2-54 (23) | 87 (5.5 × 104 [median]) | 88 |
| RNA pol | Urine | Laboratory confirmedb | Days 1-10 (14) | 7.1 | 189 |
| Days 11-20 (86) | 31.4 | ||||
| Days 21-30 (21) | 14.3 | ||||
| Days 31-60 (12) | 16.7 | ||||
| ORF 1b | Urine | WHO criteria, probable SARS or laboratory confirmedb | Days 10-15 (111) | 28.8 (1.3 log [mean]) | 156 |
| Blood (serum) | Days 10-15 (53) | 41.5 (1.1 log [mean]) | |||
| 1-step ORF 1bi | Blood (plasma) | WHO criteria, laboratory-confirmed SARS | Days 2-4 (20) | 50 (2.36 × 103 [median])d | 349 |
| Days 5-7 (12) | 75 (6.91 × 103 [median])d | ||||
| Days 8-11 (11) | 63.6 (1.74 × 104 [median])d | ||||
| Days 12-16 (8) | 37.5 (3.83 × 103 [median])d | ||||
| N | Blood (plasma) | WHO criteria, laboratory-confirmed SARS | Days 2-54 (7) | 42.9 | 88 |
| N | Blood (whole blood) | WHO criteria, probable SARS | Days 1-10 (62) | 45.2 | 413 |
| Days 11-20 (41) | 48.8 | ||||
| Days 21-30 (165) | 13.3 | ||||
| Days 31-40 (158) | 16.5 | ||||
| In-house LAMPj | |||||
| ORF 1bg | NPA | Laboratory confirmedb | Days 1-3 (15) | 60d | 267 |
| Days 4-7 (37) | 70.3d | ||||
| Day >7 (7) | 100d | ||||
| 1-step replicase | Respiratory specimensk | WHO criteria, probable SARS | Day 3 (49) | 26.5d | 146 |
| Commercial quantitative PCR | |||||
| Roche kitl | Respiratoryh | WHO criteria, laboratory-confirmed SARS | Days 2-54 (30)m | 73.3 | 88 |
| Roche kit | NPA and throat swab | Laboratory confirmedb | Days 1-5c (47) | 85d | 390 |
| Roche kit | Stool | WHO criteria, laboratory-confirmed SARS | Days 2-54 (23) | 78.3 (4.3 × 104 [median]) | 88 |
| Roche kit | Stool | Laboratory confirmedb | Days 1-5c (32) | 88d | 390 |
| Commercial kitn | Stool | WHO criteria, probable SARS | Day ≤7 (13) | 46-62d | 230 |
| Days 8-21 (12) | 58-75d | ||||
| Day >21 (31) | 13-19d | ||||
| Roche kit | Urine | Laboratory confirmedb | Days 1-5c (22) | 82d | 390 |
| Roche kit | Blood (plasma) | WHO criteria, laboratory-confirmed SARS | Days 2-54 (7) | 28.6 | 88 |
| Artus kito | Respiratoryh | WHO criteria, laboratory-confirmed SARS | Days 2-54 (31) | 74.2 | 88 |
| Artus kit | NPA and throat swab | Laboratory confirmedb | Days 1-5c (47) | 87d | 390 |
| Artus kit | Stool | WHO criteria, laboratory-confirmed SARS | Days 2-54 (22)g | 81.8 | 88 |
| Artus kit | Stool | Laboratory confirmedb | Days 1-5c (32) | 91d | 390 |
| Artus kit | Urine | Laboratory confirmedb | Days 1-5c (22) | 82d | 390 |
| Artus kit | Blood (plasma) | WHO criteria, laboratory-confirmed SARS | Days 2-54 (7) | 14.3 | 88 |
| Artus kit | Lung tissue | WHO criteria, probable SARS | Days 5-51 (19) | 100 (2 × 104 [min]-1 × 1010 [max]) | 96 |
| Artus kit | Small bowel tissue | WHO criteria, probable SARS | Days 10-29 (15) | 73 (2.7 × 103 [min]-2.7 × 109 [max]) | 96 |
| Artus kit | Large bowel tissue | WHO criteria, probable SARS | Days 10-43 (15) | 73 (5.3 × 103 [min]-3.7 × 108 [max]) | 96 |
| Artus kit | Lymph node tissue | WHO criteria, probable SARS | Days 14-34 (13) | 69 (1.5 × 104 [min]-8.9 × 108 [max]) | 96 |
| Artus kit | Liver tissue | WHO criteria, probable SARS | Days 10-24 (17) | 41 (6 × 103 [min]-5 × 104 [max]) | 96 |
| Artus kit | Cardiac tissue | WHO criteria, probable SARS | Days 5-23 (18) | 40 (1 × 104 [min]-2.8 × 107 [max]) | 96 |
| Artus kit | Kidney tissue | WHO criteria, probable SARS | Days 11-27 (16) | 38 (4.3 × 103 [min]-7.4 × 105 [max]) | 96 |
aFor the RNA extraction protocol, 140 μl of nasopharyngeal aspirate (NPA) was used.
bA rise of fourfold or more in antibody titer against SARS-CoV.
cDay after admission.
dSpecificity of the test was 100%.
eUpper respiratory specimens consisted of throat and nasal swabs (n = 216), throat swabs (n = 164), nasopharyngeal swabs (n = 47), and nasal swabs (n = 62).
fRespiratory specimens consisted of tracheal aspirate (n = 7), pooled throat and nasal swabs (n = 25), nasal swabs (n = 58), NPA (n = 192), throat swabs (n = 43), and throat washing (n = 146).
gFor the modified RNA extraction protocol, 560 μl of NPA was used.
hRespiratory specimens consisted of saliva (n = 3), nasopharyngeal swabs (n = 16), sputum (n = 8), endotracheal aspirate (n = 2), and bronchoalveolar lavage fluid (n = 2).
iThe test adopted the SARS1S_AS TaqMan assay design (Applied Biosystems, Foster City, CA), and 280 μl of plasma was used for RNA extraction.
jLAMP, real-time loop-mediated amplification.
kRespiratory specimens consisted of throat wash (n = 15), throat swabs (n = 13), and throat and nasal swabs (n = 21).
lRoche kit indicates a LightCycler SARS-CoV quantification kit (b-Test_Lot) (Roche Diagnostics, Germany).
mThere was no result for one sample due to failed internal control. The sample was omitted from the sensitivity evaluation of this assay.
nCommercial kit indicates a RealArt HPA-Coronavirus LC RT PCR kit (Artus GmbH, Hamburg, Germany) and a SARS-CoV POL assay (EraGen Biosciences, Madison, WI) with different extraction methods (QIAGEN viral RNA Minikit, bioMerieux miniMg, and Cortex MagaZorb).
oArtus kit indicates a RealArt HPA-Coronavirus LC RT-PCR kit (Artus GmbH, Hamburg, Germany).