SARS-CoV-2 molecular assay evaluation: results
Updated 3 July 2020
FIND conducted independent evaluations at the University Hospitals of Geneva (HUG) to verify the limit of detection (LOD) – as reported by the manufacturers – and the clinical performance of 21 manual molecular test kits in comparison to an in-house PCR protocol that was optimized based on the Tib Molbiol assay. Data for all the tests included in the first round of the evaluations are summarized in Table 1. Tests were selected for evaluation according to scoring criteria, but the order in which the evaluations were conducted does not reflect any endorsement or prioritization.
Additionally, a limited clinical performance evaluation of the Cepheid Xpert Xpress SARS-CoV-2 assay was also performed at the HUG. A second collaborating site, the Translational Health Science and Technology Institute (THSTI) conducted a similar limited clinical performance evaluation of the Molbio TrueNat SARS-CoV-2 assay. Results on the performance of these automated near-POC assays are shown in Table 2.
Table 1: Results for 21 manual (open) molecular tests included in the round 1 evaluation | ||||||||||
Company | Product name | Product number | Gene target | Verified LOD (copies / reaction) | Avg Ct (lowest dilution 10/10) | Clinical sensitivity (50 positives) | Clinical specificity* (100 negatives) |
Lot No. | PCR platform** | Supplier recommended Ct cut-off |
altona Diagnostics | RealStar® SARS-CoV-2 RT-PCR Kit 1.0 |
821003/ 821005 |
E | 1–10 | 35.45 | 92% (95%CI: 81, 97) |
100% (95%CI: 96, 100) |
023567 | BioRad CFX96 deep well | None; any signal can be considered positive |
S | 1–10 | 35.99 | 92% (95%CI: 81, 97) |
100% (95%CI: 96, 100) |
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Atila BioSystems Inc. | Atila iAMP COVID-19 Detection (isothermal detection) |
iAMP-COVID-100-RUO | ORF1ab | 50–100 | N/A | 100% (95%CI: 93, 100) |
99%* (95%CI: 95, 100) |
COVID20200320 | BioRad CFX96 deep well | Any signal is considered positive (isothermal) |
N | 1–10 | N/A | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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Beijing Wantai Biological Pharmacy Enterprise Co. Ltd | Wantai SARS-CoV-2 RT-PCR Kit |
WS-1248 | ORF1ab | 1–10 | 36.20 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
nCoVP20200305 | BioRad CFX96 deep well | ≤40 |
N | 1–10 | 37.12 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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BGI Health (HK) Co. Ltd | Real-time Fluorescent RT-PCR kit for detection 2019-nCOV (CE-IVD) |
MFG030010 | ORF1 | 1–10 | 32.43 | 100% (95%CI: 93, 100) |
99%* (95%CI: 95, 100) |
6220200305 | Roche LightCycler 480 | ≤38 |
bioMérieux SA |
ARGENE® SARS-COV-2 R-GENE®[b] |
423720 (CE-IVD) 423717 (RUO) |
N | 10–50 | 36.44 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
1007989610 1007947520 |
BioRad CFX96 deep well | Any signal considered as positive |
RdRP | 10–50 | 32.44 | 96%[a] (95%CI: 87, 99) |
100% (95%CI: 96, 100) |
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Bioneer Corporation |
AccuPower® SARS-CoV-2 Real-Time RT-PCR Kit |
SCV-2122 | E | 10–50 | 35.85 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
200931E | BioRad CFX96 deep well | <38 |
RdRP | 10–50 | 36.18 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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Boditech Med. Inc. | ExAmplar COVID-19 real-time PCR kit (L) |
UFPK-4 | E | 10–50 | 34.9 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
WLQCB02L | BioRad CFX96 deep well | ≤42 |
RdRP | 50–100 | 33.46 | 90% (95%CI: 79, 96) |
100% (95%CI: 96, 100) |
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CerTest Biotec S.L. |
VIASURE SARS-CoV-2 Real Time PCR Detection Kit | VS-NC0112L VS-NC0212L |
ORF1ab | 10–50 | 35.16 | 98% (95%CI: 90, 100) |
100% (95%CI: 96, 100) |
NCO212L-023 | BioRad CFX96 deep well | <40 |
N | 1–10 | 35.46 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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DAAN Gene Co. Ltd of Sun Yat-Sen University | Detection Kit for 2019 Novel Coronavirus (2019-nCoV) RNA (PCR-Fluorescence Probing) | DA0930-DA0932 | ORF1 | 1–10 | 38.76 | 100% (95%CI: 93, 100) |
96%* (95%CI: 90, 98) |
2020007 | Roche LightCycler 480 | ≤40 |
N | 1–10 | 36.97 | 100% (95%CI: 93, 100) |
98%* (95%CI: 93, 99) |
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EUROIMMUN AG | EURORealTime SARS-CoV-2[c] | MP 2606-0425 | ORF1ab/N | 1–10 | 37.88 | 100% (95%CI: 93, 100) |
98%* (95%CI: 93, 99) |
I200320AL | Light Cycler 480 II | Any signal considered positive |
GeneFirst Ltd | The Novel Coronavirus (2019-nCoV) Nucleic Acid Test Kit | MPA-COVID19 | ORF1 | 1–10 | 35.45 | 100% (95%CI: 93, 100) |
99%* (95%CI: 95, 100) |
00072 | BioRad CFX96 deep well | ≤37.0 positive; 37-40 indeterminate; >40 negative |
N | 1–10 | 36.72 | 98% (95%CI: 90, 100) |
100% (95%CI: 96, 100) |
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KH Medical Co. Ltd | RADI COVID-19 Detection Kit |
RV008 | S | 1–10 | 37.94 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
V008.200202 | BioRad CFX96 deep well | ≤40 |
RdRP | 10–50 | 36.74 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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PerkinElmer Inc. | PerkinElmer® SARS-CoV-2 Real-time RT-PCR Assay[c,d] |
SY580 | N | 1–10 | 39,43 | 100% (95%CI: 93, 100) |
99%* (95%CI: 95, 100) |
8220200303 | BioRad CFX96 deep well | ≤42 |
ORF1 | 1–10 | 38,99 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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Primerdesign Ltd |
Coronavirus COVID-19 genesig® Real-Time PCR assay[c] |
Z-Path-COVID-19-CE | RdRP | 1–10 | 36.7 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
JN-02780-0009 | LightCycler 480 | Any signal regarded as positive |
R-Biopharm AG | RIDA®GENE SARS-CoV-2 RUO | PG6815RUO | E | 1–10 | 37.99 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
21120N | BioRad CFX96 deep well | None; any signal can be considered positive |
Sansure Biotech Inc. | Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit (PCR-Fluorescence Probing)[e] | S3102E | ORF1 | 10–50 | 35.16 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
2020007ZC | Thermofisher Quantstudio 5 | ≤40 |
N | 10–50 | 34.96 | 100% (95%CI: 93, 100) |
95%* (95%CI: 89–98) |
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SD Biosensor Inc. | STANDARD M nCoV Real-Time Detection Kit |
M-NCOV-01 | E | 1–10 | 37.43 | 100% (95%CI: 93, 100) |
97%* (95%CI: 92, 99) |
MNC00120005 | Roche LightCycler 480 | ≤41 |
ORF1 | 1–10 | 36.99 | 100% (95%CI: 93, 100) |
99%* (95%CI: 95, 100) |
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Seegene Inc. | Allplex™ 2019-nCoV Assay |
RP10244Y RP10243X |
E | 1–10 | 33.3 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
RP4520C24 | BioRad CFX96 | ≤40 |
N | 1–10 | 36.74 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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RdRP | 1–10 | 34.73 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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Shanghai Kehua Bio-Engineering Co. Ltd |
KHB Diagnostic kit for SARS-CoV-2 Nucleic Acid (Real-time PCR) |
KH-G-M-574-48 | ORF1 | 1–10 | 30.39 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
20037410 | BioRad CFX96 deep well | More than two targets detected and curve is of S shape |
N | 1–10 | 32.95 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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E | 1–10 | 31.72 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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ThermoFisher Scientific | TaqPath™ COVID-19 CE-IVD RT-PCR Kit[f] |
A48067 | ORF1ab; S protein; N protein |
1–10 | NA | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
2225262 | Quantstudio 5 | Not Applicable (Automated software interpretation) |
Vela Diagnostics | ViroKey™ SARS-CoV-2 RT-PCR Test[c] | 300682 | RdRP | 10–50 | 30.95 | 94% (95%CI: 84, 98) |
100% (95%CI: 96, 100) |
1000000597 | BioRad CFX96 deep well | ≤40 |
ORF1 | 1–10 | 35.57 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
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Tib Molbiol/Roche Diagnostics | ModularDx Kit SARS-CoV (COVID19) E-gene (Tib Molbiol) + LightCycler Multiplex RNA Virus Master (Roche) | 53-0776-96 6754155001 |
E | 1–10 | 33.34 | 100% (95%CI: 93, 100) |
100% (95%CI: 96, 100) |
48202019 48274100 |
Roche LightCycler 480 | Define the cut-off 2–4 cycles higher than observed Cp value for 10 copies |
* Clinical specificity: Further investigation is needed to determine if apparent false positives are truly false positives or whether they are due to a false negative reference standard result ** PCR platform: All products were evaluated on a PCR platform recommended by the supplier, listed in this table. Each test can be performed on other PCR systems, detailed in the product’s instructions for use. [a] The two false negative samples tested positive with the second PCR (PCR 2) that targets E gene of SARS, SARS-COV-2 and/or SARS-like coronaviruses. [b] Samples for both analytical and clinical analyses were from already-extracted specimen, therefore the methods varied from those recommended by the supplier as the internal control was not included. [c] Samples for both analytical and clinical analyses were from already-extracted specimen, therefore the methods varied from those recommended by the supplier as the internal control was added to the master mix. [d] Evaluation procedure varied from recommended protocol. In order to achieve the recommended sample input volume, a 2.5 fold dilution of the samples was used. [e] Sansure claims a lower LOD of 6.4 cp/rxn, which has been independently verified. [f] Evaluation procedure varied from recommended protocol as source material was already-extracted RNA; extracted MS2 control was added directly to the master mix. |
Table 2: Results for 2 near-POC automated tests included in the round 1 evaluation | ||||||
Company | Product name | Product number | Gene target | Clinical sensitivity (50 positives) | Clinical specificity* (100 negatives) |
Comparator test |
Cepheid Inc. | Xpert® Xpress SARS-CoV-2 |
XPRSARS-COV2-10 | N2 | 100% (95%CI: 92,100) |
99% * (95%CI: 95, 100) |
Roche Cobas ® SARS-CoV-2
N = 44 positive |
E | 97.7% (95% CI: 88, 100) |
100% (95%CI: 96, 100) |
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Molbio Diagnostics Pvt Ltd | TrueNat SARS-CoV-2 [1] |
601410020 | E+RdRP[2] | 98% (95% CI: 90.98) |
96% * (95% CI:90,98) |
altona Diagnostics (n=86) /LabGun™ (n=64) and/or Seegene, Inc. (n=12)
N = 51 positive |
601420050 | ||||||
* Clinical specificity: Further investigation is needed to determine if apparent false positives are truly false positives or whether they are due to a false negative reference standard result [1] Note: evaluation performed at THSTI [2] RdRP is only used as a reflex test; the results are for combined E+RdRP positives |
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For questions relating to the evaluation of molecular tests, please contact our Emerging Threats team.
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