What is the probability that this patient, who presents to a UK hospital, will be diagnosed with Covid-19? Prospective validation of the open-source CovidCalculatorUK resource
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Abstract
Introduction
The novel coronavirus SARS-CoV2 and the associated disease, Covid-19, continue to pose a global health threat. The CovidCalculatorUK is an open-source online tool (covidcalculatoruk.org) that estimates the probability that an individual patient, who presents to a UK hospital, will later test positive for SARS-CoV2. The objective is to aid cohorting decisions and minimise nosocomial transmission of SARS-CoV2.
Methods
This n = 500 prospective, observational, multicentre, validation study compared the CovidCalculatorUK’s estimated probability of Covid-19 with the first SARS-CoV2 oropharyngeal/nasopharyngeal swab result for individual patients admitted to hospital during the study period (01.04.20 − 18.05.20). A comparison with senior clinicians’ estimates of the probability of Covid-19 was also made.
Results
Patients who were prospectively grouped, by the CovidCalculatorUK, into 0-30% estimated probability, 30-60% and 60-100% estimated probability went on to have first swab SARS-CoV2 positive results in: 15.7%, 30.5% and 61.9% of cases, respectively. CovidCalculatorUK performance demonstrated an area under the curve of 0.76 (95% CI 0.71 – 0.81) (p < 0.001). Senior clinician stratification of the estimated probability of Covid-19 performed similarly to the CovidCalculatorUK.
Conclusion
The CovidCalculatorUK provides a reasonably accurate estimate of the probability of an individual testing positive on their first SARS-CoV2 nasopharyngeal/oropharyngeal swab. The CovidCalculatorUK output performs similarly to a senior clinician’s estimate. Further evolution of the calculator may improve performance.
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SciScore for 10.1101/2020.12.06.20243691: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Statistical analysis (SPSS V26, Excel 2016) was performed by grouping the CovidCalculatorUK output into estimated probability groups of 0-30%, 30-60% and 60-100% (group thresholds were determined post hoc). SPSSsuggested: (SPSS, RRID:SCR_002865)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 …SciScore for 10.1101/2020.12.06.20243691: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Statistical analysis (SPSS V26, Excel 2016) was performed by grouping the CovidCalculatorUK output into estimated probability groups of 0-30%, 30-60% and 60-100% (group thresholds were determined post hoc). SPSSsuggested: (SPSS, RRID:SCR_002865)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.
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