Evaluation and Modelling of the Performance of an Automated SARS-CoV-2 Antigen Assay According to Sample Type, Target Population and Epidemic Trends
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Abstract
The Lumipulse® G SARS-CoV-2 Ag assay performance was evaluated on prospectively collected saliva and nasopharyngeal swabs (NPS) of recently ill in- and outpatients and according to the estimated viral load. Performances were calculated using RT-PCR positive NPS from patients with symptoms ≤ 7 days and RT-PCR negative NPS as gold standard. In addition, non-selected positive NPS were analyzed to assess the performances on various viral loads. This assay yielded a sensitivity of 93.1% on NPS and 71.4% on saliva for recently ill patients. For NPS with a viral load > 103 RNA copies/mL, sensitivity was 96.4%. A model established on our daily routine showed fluctuations of the performances depending on the epidemic trends but an overall good negative predictive value. Lumipulse® G SARS-CoV-2 assay yielded good performance for an automated antigen detection assay on NPS. Using it for the detection of recently ill patients or to screen high-risk patients could be an interesting alternative to the more expensive RT-PCR.
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SciScore for 10.1101/2022.01.14.22269064: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization SARS-CoV-2 variant determination: Samples with a minimal SARS-CoV-2 viral load of 105 RNA copies/mL were randomly sequenced for surveillance purpose. 2.5. Model: Positive RT-PCR results performed routinely in our laboratory are semi-quantified according to their Ct values regardless of their indication (symptoms, screening…). Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Statistical analyses: Statistical analyses and receiver operating characteristic (ROC) curves were performed using Analyse-it® for Microsoft Excel v5.30.4. 2.7. Microsoft Excelsuggested: (Microsoft …SciScore for 10.1101/2022.01.14.22269064: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization SARS-CoV-2 variant determination: Samples with a minimal SARS-CoV-2 viral load of 105 RNA copies/mL were randomly sequenced for surveillance purpose. 2.5. Model: Positive RT-PCR results performed routinely in our laboratory are semi-quantified according to their Ct values regardless of their indication (symptoms, screening…). Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Statistical analyses: Statistical analyses and receiver operating characteristic (ROC) curves were performed using Analyse-it® for Microsoft Excel v5.30.4. 2.7. Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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