TABLE 4.

Clinical evaluation of molecular diagnostic tests for SARS-CoV

Diagnostic method and target geneClinical specimenDiagnostic gold standardCollection time after onset of symptoms (no. of samples)% Sensitivity (viral load [copies/ml])Reference
In-house RT-PCR
RNA polaNPALaboratory confirmedbDays 1-5c (72)59.7d 391
Days 1-5 (98)29.6 32
RNA polNPAWHO criteria, probable SARSDays 0-5 (501)41.1 56
Days 6-11 (211)58.8
Days 12-20 (62)37.1
Day >21 (15)13.3
RNA polThroat swabWHO criteria, probable SARSDays 1-13 (590)37.5 384
RNA polaNose and throat swabLaboratory confirmedbDays 1-5c (54)61.1d 391
Days 1-5 (53)28.3 32
RNA polUpper respiratoryeWHO criteria, probable SARSDays 0-5 (212)31.1 56
Days 6-11 (73)37
Days 12-20 (45)31.1
Day >21 (159)5.7
RNA polaRespiratoryfLaboratory confirmedb1 wk (243)26.3 39
2 wk (134)30.6
3-4 wk (94)18.1
RNA polStoolLaboratory confirmedbDays 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 polStoolWHO criteria, probable SARSDays 0-5 (77)23.4 56
Days 6-11 (86)57
Days 12-20 (72)52.8
Day >21 (297)15.2
RNA polUrineLaboratory confirmedbDays 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 polUrineWHO criteria, probable SARSDays 0-11 (16)12.5 56
Days 12-20 (21)4.8
Days >21-23 (161)1.9
    RNA polBlood (serum)WHO criteria, probable SARSDays 0-5 (64)17.2 56
Days 6-11 (14)35.7
Days 12-20 (9)11.1
    Nested RNA polBlood (plasma)Laboratory confirmedbDays 1-3 (24)79.2 108
In-house quantitative PCR
    ORF 1baNPALaboratory confirmedbDays 1-3 (32)50 263
Days 4-6 (35)31.4
Days 7-10 (31)51.6
    ORF 1bgNPALaboratory confirmedbDay 1 (8)62.5d 264
Day 2 (16)87.5d
Day 3 (26)80.1d
    ORF 1bNPAWHO criteria, probable SARS or laboratory confirmedbDays 10-15 (142)42.3 (2.4 log [mean]) 156
    1-step ORF 1bgNPALaboratory confirmedbDays 1-3 (29)96.6d 266
Days 4-9 (57)80.7d
    1-step ORF 1bThroat washWHO criteria, laboratory-confirmed SARSDays 2-9 (17)9.58 × 102 (min)-5.93 × 106 (max) 349
SalivaDays 2-9 (17)7.08 × 102 (min)-6.38 × 108 (max)
    NRespiratoryhWHO criteria, laboratory-confirmed SARSDays 2-54 (31)74.2 88
    NNPA and stoolWHO criteria, probable SARSDays 1-4 (32)18.8 155
Days 5-10 (37)35.1
    RNA polStoolLaboratory confirmedbDays 1-10 (8)75 189
Days 11-20 (27)81.5
Days 21-30 (5)80
    ORF 1bStoolWHO criteria, probable SARS or laboratory confirmedbDays 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
    NStoolWHO criteria, probable SARSDays 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
    NStoolWHO criteria, laboratory-confirmed SARSDays 2-54 (23)87 (5.5 × 104 [median]) 88
    RNA polUrineLaboratory confirmedbDays 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 1bUrineWHO criteria, probable SARS or laboratory confirmedbDays 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 1biBlood (plasma)WHO criteria, laboratory-confirmed SARSDays 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
    NBlood (plasma)WHO criteria, laboratory-confirmed SARSDays 2-54 (7)42.9 88
    NBlood (whole blood)WHO criteria, probable SARSDays 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 1bgNPALaboratory confirmedbDays 1-3 (15)60d 267
Days 4-7 (37)70.3d
Day >7 (7)100d
    1-step replicaseRespiratory specimenskWHO criteria, probable SARSDay 3 (49)26.5d 146
Commercial quantitative PCR
    Roche kitlRespiratoryhWHO criteria, laboratory-confirmed SARSDays 2-54 (30)m73.3 88
    Roche kitNPA and throat swabLaboratory confirmedbDays 1-5c (47)85d 390
    Roche kitStoolWHO criteria, laboratory-confirmed SARSDays 2-54 (23)78.3 (4.3 × 104 [median]) 88
    Roche kitStoolLaboratory confirmedbDays 1-5c (32)88d 390
    Commercial kitnStoolWHO criteria, probable SARSDay ≤7 (13)46-62d 230
Days 8-21 (12)58-75d
Day >21 (31)13-19d
    Roche kitUrineLaboratory confirmedbDays 1-5c (22)82d 390
    Roche kitBlood (plasma)WHO criteria, laboratory-confirmed SARSDays 2-54 (7)28.6 88
    Artus kitoRespiratoryhWHO criteria, laboratory-confirmed SARSDays 2-54 (31)74.2 88
    Artus kitNPA and throat swabLaboratory confirmedbDays 1-5c (47)87d 390
    Artus kitStoolWHO criteria, laboratory-confirmed SARSDays 2-54 (22)g81.8 88
    Artus kitStoolLaboratory confirmedbDays 1-5c (32)91d 390
    Artus kitUrineLaboratory confirmedbDays 1-5c (22)82d 390
    Artus kitBlood (plasma)WHO criteria, laboratory-confirmed SARSDays 2-54 (7)14.3 88
    Artus kitLung tissueWHO criteria, probable SARSDays 5-51 (19)100 (2 × 104 [min]-1 × 1010 [max]) 96
    Artus kitSmall bowel tissueWHO criteria, probable SARSDays 10-29 (15)73 (2.7 × 103 [min]-2.7 × 109 [max]) 96
    Artus kitLarge bowel tissueWHO criteria, probable SARSDays 10-43 (15)73 (5.3 × 103 [min]-3.7 × 108 [max]) 96
    Artus kitLymph node tissueWHO criteria, probable SARSDays 14-34 (13)69 (1.5 × 104 [min]-8.9 × 108 [max]) 96
    Artus kitLiver tissueWHO criteria, probable SARSDays 10-24 (17)41 (6 × 103 [min]-5 × 104 [max]) 96
    Artus kitCardiac tissueWHO criteria, probable SARSDays 5-23 (18)40 (1 × 104 [min]-2.8 × 107 [max]) 96
    Artus kitKidney tissueWHO criteria, probable SARSDays 11-27 (16)38 (4.3 × 103 [min]-7.4 × 105 [max]) 96
  • a For the RNA extraction protocol, 140 μl of nasopharyngeal aspirate (NPA) was used.

  • b A rise of fourfold or more in antibody titer against SARS-CoV.

  • c Day after admission.

  • d Specificity of the test was 100%.

  • e Upper respiratory specimens consisted of throat and nasal swabs (n = 216), throat swabs (n = 164), nasopharyngeal swabs (n = 47), and nasal swabs (n = 62).

  • f Respiratory 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).

  • g For the modified RNA extraction protocol, 560 μl of NPA was used.

  • h Respiratory specimens consisted of saliva (n = 3), nasopharyngeal swabs (n = 16), sputum (n = 8), endotracheal aspirate (n = 2), and bronchoalveolar lavage fluid (n = 2).

  • i The test adopted the SARS1S_AS TaqMan assay design (Applied Biosystems, Foster City, CA), and 280 μl of plasma was used for RNA extraction.

  • j LAMP, real-time loop-mediated amplification.

  • k Respiratory specimens consisted of throat wash (n = 15), throat swabs (n = 13), and throat and nasal swabs (n = 21).

  • l Roche kit indicates a LightCycler SARS-CoV quantification kit (b-Test_Lot) (Roche Diagnostics, Germany).

  • m There was no result for one sample due to failed internal control. The sample was omitted from the sensitivity evaluation of this assay.

  • n Commercial 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).

  • o Artus kit indicates a RealArt HPA-Coronavirus LC RT-PCR kit (Artus GmbH, Hamburg, Germany).