Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparation of SARS-CoV-2 Control Material
2.2. Distribution of SARS-CoV-2 Control Material and Setup of Standard Curves
2.3. Data Processing: Data Requirements
2.4. Data Processing: Approach for Each PCR Assay
3. Results
3.1. Preparation of the SARS-CoV-2 Control Material
3.2. Distribution of the SARS-CoV-2 Control Material to the Testing Laboratories in Belgium
3.3. The SARS-CoV-2 Nucleocapsid Gene Is Most Often Targeted in PCR Assays Used in Routine Diagnostics in Belgium
3.4. The Difference in Cycle Threshold Values between the Wide Arsenal of SARS-CoV-2 Assays
4. Discussion
4.1. Harmonized Semi-Quantitative Reporting of 85% of the PCR Tests in Belgium
4.2. Limitations When Reporting Test Results Based on Ct Values
4.3. Impact of the Target Composition of PCR Assays on SARS-CoV-2 Genomic Surveillance
4.4. Interpretation of SARS-CoV-2 PCR Test Results
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Category of SARS-CoV-2 Positivity | SARS-CoV-2 Viral Load (RNA Copies/mL) | Interpretation with Respect to Infectivity |
---|---|---|
Very strongly positive | ≥107 | patient is contagious |
Strongly positive | ≥105–<107 | patient is probably contagious |
Moderate positive | ≥103–<105 | patient is potentially contagious, unless there is clinical and/or serological evidence of an old, cleared infection |
Weakly positive | <103 | patient is probably not or no longer contagious if there is also clinical and/or serological evidence of an old, cleared infection |
SARS-CoV-2 PCR Assay | Number of Laboratories | Targeted SARS-CoV-2 Genes |
---|---|---|
Abbott Realtime SARS-CoV-2 assay (m2000) * | 3 | RdRp and N |
Alinity m SARS-CoV-2 assay * | 6 | RdRp and N |
Allplex SARS-CoV-2 assay * | 21 | E, RdRp, S and N |
Allplex SARS-CoV-2/FluA/FluB/RSV assay * | 8 | S, RdRp and N |
Aries SARS-CoV-2 LDT | 4 | E |
Aries SARS-CoV-2 RUO * | 10 | ORF1ab and N |
BD SARS-CoV-2 for BD Max * | 3 | N1 and N2 |
CE-IVD Perkin Elmer SARS-CoV-2 RT-qPCR * | 2 | ORF1ab and N |
Cobas SARS-CoV-2 * | 4 | ORF1ab and E |
GeneFinderTM COVID-19 Plus RealAmp kit * | 12 | RdRp, E and N |
Ingenius | 2 | RdRp, E and N |
Liat Cobas SARS-CoV-2 and influenza A/B 1 | 4 | RdRp and N |
LightMix Modular SARS and Wuhan CoV E-gene kit 2 | 5 | E |
N1 CDC PCR | 2 | N1 |
NeuMoDx SARS-CoV-2 * | 2 | N and Nsp2 |
Powerchek SARS-CoV-2 Real-time PCR kit 1 | 2 | ORF1ab and E |
R-DiaSARS-CoV-2 * | 3 | E |
RealStar SARS-CoV-2 RT-PCR kit 1.0 * | 5 | E and S |
SARS-CoV-2 ELITe MGB kit * | 2 | RdRp and ORF8 |
SARS-CoV-2 plus ELITe MGB * | 2 | RdRp, ORF8 |
SARS-CoV-2 N1 + N2 Qiagen 2 | 3 | N1 and N2 |
TaqPath COVID-19 CE-IVD RT-PCR kit * | 22 | N, S and ORF1ab |
Viasure SARS-CoV-2 RT PCR 1 | 2 | ORF1ab and N |
Xpert Xpress SARS-CoV-2 * | 14 | N2 and E |
Xpert Xpress SARS-CoV-2/Flu/RSV * | 11 | N2 and E |
PCR Assay | Included (Contributed) Laboratories | SARS-CoV-2 Gene | Mean Ct Value or Equivalent Metric (SD) | ||
---|---|---|---|---|---|
107 RNA Copies/mL * | 105 RNA Copies/mL * | 103 RNA Copies/mL * | |||
Abbott RealTime SARS-CoV-2 | 3 (3) | RdRp/N | 6.2 (0.34) | 12.7 (0.37) | 19.1 (0.50) |
Alinity m SARS-CoV-2 | 6 (6) | RdRp/N | 15.0 (0.65) | 21.9 (0.68) | 28.9 (0.75) |
Allplex SARS-CoV-2 | 15 (19) | E | 17.0 (0.49) | 24.3 (0.72) | 31.5 (1.02) |
RdRp/S | 17.9 (0.76) | 25.1 (0.96) | 32.2 (1.28) | ||
N | 17.9 (0.67) | 24.9 (0.80) | 31.9 (1.04) | ||
Allplex SARS-CoV-2/FluA/FluB/RSV | 7 (8) | S | 15.7 (0.44) | 22.6 (0.55) | 29.6 (0.82) |
RdRp | 15.3 (0.47) | 22.5 (0.63) | 29.7 (0.89) | ||
N | 15.4 (0.54) | 22.1 (0.71) | 28.8 (0.99) | ||
Aries SARS-CoV-2 RUO | 7 (9) | N | 20.3 (0.68) | 27.4 (0.78) | 34.4 (0.96) |
ORF1ab | 18.3 (0.54) | 25.3 (0.73) | 32.4 (1.06) | ||
BioGX SARS-CoV-2 BD MAX | 3 (3) | N1 | 16.4 (0.71) | 23.4 (0.56) | 30.4 (0.42) |
N2 | 16.8 (0.97) | 23.8 (0.99) | 30.9 (1.03) | ||
Cobas SARS-CoV-2 | 4 (4) | ORF1ab | 17.3 (0.50) | 23.6 (0.52) | 29.8 (0.56) |
E | 17.6 (0.50) | 24.0 (0.51) | 30.4 (0.55) | ||
GeneFinder COVID-19 Plus RealAmp | 6 (13) | E | 18.9 (0.37) | 26.1 (0.61) | 33.3 (0.85) |
RdRp | 18.6 (0.65) | 25.3 (0.74) | 32.1 (0.88) | ||
N | 19.4 (0.99) | 26.2 (1.00) | 33.0 (1.06) | ||
NeuMoDx SARS-CoV-2 | 2 (2) | N | 15.7 (0.09) | 22.6 (0.10) | 29.4 (0.29) |
Nsp2 | 16.4 (0.01) | 23.3 (0.31) | 30.2 (0.62) | ||
PerkinElmer SARS-CoV-2 RT-PCR | 2 (2) | N | 18.8 (2.34) | 25.1 (1.89) | 31.5 (1.45) |
ORF1ab | 16.4 (1.82) | 22.7 (1.63) | 28.9 (1.44) | ||
R-DiaSARS-CoV-2 | 3 (3) | E | 17.6 (0.39) | 23.9 (0.44) | 30.3 (0.68) |
RealStar SARS-CoV-2 RT-PCR kit 1.0 | 2 (4) | S | 16.3 (1.38) | 23.1 (1.69) | 30.0 (2.00) |
E | 19.1 (1.10) | 25.6 (1.49) | 32.2 (1.87) | ||
SARS-CoV-2 ELITe MGB | 2 (2) | RdRp | 18.8 (0.84) | 25.4 (0.84) | 32.0 (0.83) |
ORF8 | 17.8 (0.86) | 24.6 (0.94) | 31.3 (1.02) | ||
SARS-CoV-2 plus ELITe MGB | 2 (2) | RdRp/ORF8 | 16.8 (0.66) | 23.8 (0.71) | 30.9 (0.76) |
TaqPath COVID-19 CE-IVD RT-PCR | 17 (21) | N | 14.5 (0.69) | 21.3 (0.78) | 28.1 (0.95) |
ORF1ab | 14.1 (0.71) | 20.9 (0.75) | 27.8 (0.95) | ||
S | 14.1 (0.70) | 20.9 (0.74) | 27.8 (0.92) | ||
Xpert Xpress SARS-CoV-2 | 7 (13) | N2 | 19.1 (0.48) | 26.2 (0.69) | 33.2 (1.04) |
E | 16.7 (0.49) | 23.4 (0.51) | 30.1 (0.54) | ||
Xpert Xpress SARS-CoV-2/Flu/RSV | 9 (11) | N2/E | 16.5 (0.57) | 23.2 (0.92) | 29.9 (1.35) |
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Cuypers, L.; Bode, J.; Beuselinck, K.; Laenen, L.; Dewaele, K.; Janssen, R.; Capron, A.; Lafort, Y.; Paridaens, H.; Bearzatto, B.; et al. Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium. Viruses 2022, 14, 1294. https://doi.org/10.3390/v14061294
Cuypers L, Bode J, Beuselinck K, Laenen L, Dewaele K, Janssen R, Capron A, Lafort Y, Paridaens H, Bearzatto B, et al. Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium. Viruses. 2022; 14(6):1294. https://doi.org/10.3390/v14061294
Chicago/Turabian StyleCuypers, Lize, Jannes Bode, Kurt Beuselinck, Lies Laenen, Klaas Dewaele, Reile Janssen, Arnaud Capron, Yves Lafort, Henry Paridaens, Bertrand Bearzatto, and et al. 2022. "Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium" Viruses 14, no. 6: 1294. https://doi.org/10.3390/v14061294