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. 2020 Nov 11;27(3):341–351. doi: 10.1016/j.cmi.2020.11.002

Table 1.

Characteristics of included studiesa

First author, year Coronavirus b Study design Infection n patients/samples Index test type Index test name Type of specimen Reference standard
Nolte FS, 2007 [40] OC43, NL63 Retrospective ILI 27 Multiplex RT-PCR EraGen Bioscience2 Nasopharyngeal, nose, throat, and lung tissue, BAL, sputum Real-time RT-PCR
Gadsby NJ, 2010 [20] OC43, 229E, NL63, HKU1 Retrospective ILI 286 Multiplex real-time RT-PCR Luminex Molecular Diagnostics NPS, BAL Real-time RT-PCR
Gharabaghi F, 2011 [21] OC43/HKU1, 229E/NL63 Retrospective ILI 750 Multiplex RT-PCR Seegene NPS Multiplex RT-PCR
Pabbaraju K, 2011 [42] 229E, HKU1, NL63, OC43 Prospective NR 334 Multiplex RT-PCR Luminex NxTAG Respiratory NPS, NPA, nasal swab, throat swab, BAL, sputum, unkown respiratory origin Multiplex RT-PCR
Bierbaum S, 2012 [12] HKU1, NL63, OC43, 229E Prospective Upper and lower tract infection symptoms 300 Multiplex RT-PCR Qiagen Pharyngeal swabs/nasopharyngeal spirates Monoplex real-time RT-PCR
Li J, 2012 [31] OC43, NL63, 229E, HKU1 Prospective Pneumonitis, broncho-pneumonia 126 Multiplex RT-PCR GeXP multiplex RT-PCR assay Nasopharyngeal aspirate Multiplex RT-PCR
Puppe W, 2012 [44] OC43, 229E Retrospective NR 178 Multiplex RT-PCR BioRad iCycler, Perkin-Elmer GeneAmp Nasopharyngeal aspirate, NPS, BAL Culture, RT-PCR
Sakthivel SK, 2012 [48] OC43, 229E, NL63 Prospective ILI 308 Multiplex real-time RT-PCR Applied Biosystems Nasopharyngeal aspirates Real-time RT-PCR
Choudhary ML, 2013 [16] OC43 Retrospective ILI/severe acute respiratory illness 843 Multiplex RT-PCR GeneAmp PCR System 9700 Nasal, nasopharyngeal, throat swab Real-time RT-PCR
Kim HK, 2013 [28] OC43/HKU1 Mixed ILI 482 Multiplex real-time RT-PCR Seegene Nasopharyngeal aspirate, NPS, BAL Multiplex RT-PCR
Li J, 2013 [32] OC43, NL63, 229E, HKU1 Prospective ILI, Pneumonia 247 Multiplex RT-PCR Qiagen Nasopharyngeal aspirate Multiplex RT-PCR
Bierbaum S, 2014 [11] OC43, NL63, 229E Prospective ILI 369 Multiplex real-time RT-PCR Inhouse 214 pharyngeal swab, 152 nasopharyngeal aspirates, 3 BAL Monoplex real-time RT-PCR
Salez N, 2015 [49] Any COV, 229E, NL63, OC43, HKU1 Prospective ILI 166 Multiplex RT-PCR RespiFinder SMART 22 NPS Duplex PCR or RT-PCR
Beckmann C, 2016 [10] OC43, 229E, HKU1, NL63 Mixed ILI 282 Multiplex RT-PCR Luminex NxTAG Respiratory NPS, BAL, throat swabs, tracheal secretion, sputum Multiplex RT-PCR (MLPA)
Chen H, 2017 [15] OC43, 229E, HKU1, NL63 Prospective CAP 74 Multiplex RT-PCR BioFire FilmArray Respiratory Nasal swab Multiplex real-time RT-PCR
Ko DH, 2017 [29] OC43/HKU1, NL63, 229E Retrospective NR 254 Multiplex RT-PCR Luminex NxTAG Respiratory Sputum, NPS Multiplex real-time RT-PCR
Mohamed DH, 2017 [37] MERS-CoV Retrospective ILI 234 Real-time RT-PCR NR NPS/oropharyngeal swab Real-time RT-PCR
Babady NE, 2018 [8] NR Mixed ILI 2908 Multiplex RT-PCR GenMark ePlex Respiratory NPS Multiplex RT-PCR
Leber AL, 2018 [30] HKU1, 229E, NL63, OC43 Prospective ILI 1612 Multiplex RT-PCR BioFire FilmArray RP2 NPS Multiplex RT-PCR
Vos LM, 2018 [52] NR Prospective ILI 62 Multiplex RT-PCR BioFire FilmArray Respiratory NPS Real-time RT-PCR
Hecht LS, 2019 [24] MERS-CoV Retrospective ILI 29 Real-time RT-PCR RealStar MERS-CoV Nasal swab, nasopharyngeal aspirates Real-time RT-PCR
Li X, 2019 [33] NR Prospective CAP 289 Multiplex RT-PCR Ningbo HEALTH Gene Sputum, BAL, pharyngeal swab Multiplex RT-PCR
Assennato SM, preprint [7] SARS-CoV-2 Retrospective Symptoms of COVID-19 172 RT-LAMP SAMBA-II NPS Real-time RT-PCR
Basu A, 2020 [9] SARS-CoV-2 Prospective Symptoms of COVID-19 101 Isothermal amplification Abbott ID NOW Nasal swab Real-time RT-PCR
Bisoffi Z, preprint [13] SARS-CoV-2 Prospective Symptoms of COVID-19 345 Real-time RT-PCR CDC 2019-Novel Coronavirus NPS Real-time RT-PCR, serology + clinical
Brandsma E, preprint [14] SARS-CoV-2 Retrospective Symptoms of COVID-19 378 RT-LAMP + Cas12 DETECTR NPS, BAL, sputum qRT-PCR
Collier D, preprint [17] SARS-CoV-2 Prospective Symptoms of COVID-19 149 RT-LAMP SAMBA-II NPS RT-PCR
Cradic K, 2020 [18] SARS-CoV-2 Prospective Symptoms of COVID-19 184 Isothermal amplification Abbott ID NOW NPS Real-time RT-PCR
Dao Thi VL, preprint [19] SARS-CoV-2 Retrospective NR 775 RT-LAMP Inhouse Pharyngeal swabs RT-PCR
Ghofrani M, preprint [22] SARS-CoV-2 Prospective Symptoms of COVID-19, proven COVID-19 113 Isothermal amplification Abbott ID NOW NPS, nasal, other clinical PCR
Harrington A, 2020 [23] SARS-CoV-2 Prospective Symptoms of COVID-19 524 Isothermal amplification Abbott ID NOW Nasal swab Real-time RT-PCR
Hogan CA, 2020 [25] SARS-CoV-2 Retrospective NR 100 RT-PCR + lateral flow Accula SARS-CoV-2 POCT NPS Real-time RT-PCR
Hou T, 2020 [26] SARS-CoV-2 Retrospective NR 114 CRIPSR CRIPSR-COVID NPS, BAL Metagenomic NGS
Jiang M, 2020 [27] SARS-CoV-2 Prospective Symptoms of COVID-19 260 RT-LAMP Inhouse NPS, sputum, tears qRT-PCR
Loeffelholz MJ, 2020 [34] SARS-CoV-2 Prospective Symptoms of COVID-19 481 Real-time RT-PCR Cepheid Xpert/GeneXpert NPS, pharyngeal swab, tracheal aspirate Real-time RT-PCR
Matzkies, LM 2020 [35] SARS-CoV-2 Retrospective Symptoms of COVID-19, asymptomatic 95 RT-PCR VIASURE SARSCoV-2 NPS/oropharyngeal swab qRT-PCR
Mitchell SL, 2020 [36] SARS-CoV-2 Retrospective NR 61 Isothermal amplification Abbott ID NOW NPS Real-time RT-PCR
Moore NM, preprint [38] SARS-CoV-2 Retrospective Symptoms of COVID-19 198 Isothermal amplification Abbott ID NOW NPS Real-time RT-PCR + clinical
Moran A, 2020 [39] SARS-CoV-2 Retrospective NR 103 Real-time RT-PCR Cepheid Xpert/GeneXpert NPS and nasal swa qRT-PCR
Österdahl MF, preprint [41] SARS-CoV-2 Prospective COVID-19 contacts in nursing home 21 RT-LAMP with magnetic bead capture RT-LAMP with magnetic bead capture NPS RT-PCR
Poljak M, 2020 [43] SARS-CoV-2 Prospective Symptoms of COVID-19 501 qRT-PCR Cobas 6800, Roche Nasopharyngeal/oropharyngeal swab Real-time RT-PCR
Poljak M, 2020 [43] SARS-CoV-2 Retrospective Symptoms of COVID-19 215 qRT-PCR Cobas 6800, Roche Nasopharyngeal/oropharyngeal swab Real-time RT-PCR
Ridgday JP, 2020 [45] SARS-CoV-2 Prospective Symptoms of COVID-19 2442 Real-time RT-PCR Cepheid Xpert/GeneXpert and Roche cobas SARS-CoV-2 NPS Real-time RT-PCR
Rodriguez-Manzano J, preprint [46] SARS-CoV-2 Retrospective Symptoms of COVID-19 181 RT-qLAMP Inhouse NPS, pharyngeal, nasal swabs Real-time RT-PCR
Rohaim MA, preprint [47] SARS-CoV-2 Retrospective NR 199 RT-LAMP RT-LAMP with automatic AI based color interpretation NPS Real-time RT-PCR
Smithgall MC, 2020 [50] SARS-CoV-2 Retrospective NR 113 Real-time RT-PCR Cepheid Xpert/GeneXpert NPS RT-PCR
Suo T, preprint [51] SARS-CoV-2 Prospective Symptoms of COVID-19 58 Droplet Digital PCR Inhouse Pharyngeal swabs RT-PCR + clinical
Wei S, preprint [53] SARS-CoV-2 Retrospective Symptoms of COVID-19, close contact 20 RT-LAMP Inhouse NPS qRT-PCR
Williams E, preprint [54] SARS-CoV-2 Retrospective Symptoms of COVID-19, close contact 675 Heminested, multiplex, tandem real-time RT-PCR Inhouse NPS 98% RT-PCR
Wolters F, 2020 [55] SARS-CoV-2 Retrospective NR 60 Real-time RT-PCR Cepheid Xpert/GeneXpert NPS RT-PCR
Zhen W, 2020 [56] SARS-CoV-2 Mixed Symptoms of COVID-19 104 Real-time RT-PCR Applied Biosystems ThermoFisher Scientific NPS RT-PCR

NR, not reported; ILI, influenza-like illness; CAP, community-acquired pneumonia; NPS, nasopharyngeal swab; BAL, bronchoalveolar lavage; MLPA, multiplex ligation-dependent probe amplification technology; NGS, next-generation sequencing; RT-LAMP, reverse transcriptase loop-mediated isothermal amplification.

a

Studies are sorted by year of publication and author.

b

In bold: the species selected for the main analysis.