Clinical prediction rule for SARS-CoV-2 infection from 116 U.S. emergency departments 2-22-2021
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Abstract
Accurate and reliable criteria to rapidly estimate the probability of infection with the novel coronavirus-2 that causes the severe acute respiratory syndrome (SARS-CoV-2) and associated disease (COVID-19) remain an urgent unmet need, especially in emergency care. The objective was to derive and validate a clinical prediction score for SARS-CoV-2 infection that uses simple criteria widely available at the point of care.
Methods
Data came from the registry data from the national REgistry of suspected COVID-19 in EmeRgency care (RECOVER network) comprising 116 hospitals from 25 states in the US. Clinical variables and 30-day outcomes were abstracted from medical records of 19,850 emergency department (ED) patients tested for SARS-CoV-2. The criterion standard for diagnosis of SARS-CoV-2 required a positive molecular test from a swabbed sample or positive antibody testing within 30 days. The prediction score was derived from a 50% random sample (n = 9,925) using unadjusted analysis of 107 candidate variables as a screening step, followed by stepwise forward logistic regression on 72 variables.
Results
Multivariable regression yielded a 13-variable score, which was simplified to a 13-point score: +1 point each for age>50 years, measured temperature>37.5°C, oxygen saturation<95%, Black race, Hispanic or Latino ethnicity, household contact with known or suspected COVID-19, patient reported history of dry cough, anosmia/dysgeusia, myalgias or fever; and -1 point each for White race, no direct contact with infected person, or smoking. In the validation sample (n = 9,975), the probability from logistic regression score produced an area under the receiver operating characteristic curve of 0.80 (95% CI: 0.79–0.81), and this level of accuracy was retained across patients enrolled from the early spring to summer of 2020. In the simplified score, a score of zero produced a sensitivity of 95.6% (94.8–96.3%), specificity of 20.0% (19.0–21.0%), negative likelihood ratio of 0.22 (0.19–0.26). Increasing points on the simplified score predicted higher probability of infection (e.g., >75% probability with +5 or more points).
Conclusion
Criteria that are available at the point of care can accurately predict the probability of SARS-CoV-2 infection. These criteria could assist with decisions about isolation and testing at high throughput checkpoints.
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SciScore for 10.1101/2021.01.20.21249656: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The design, collection, recording and analysis of data for this report were conducted in accordance with the transparency in reporting of a multivariable prediction model for individual diagnosis and prognosis (TRIPOD) criteria.12 The RECOVER registry protocol was reviewed by the institutional review boards (IRBs) at all sites; 42 IRBs provided an exemption from human subjects designation, whereas three IRBs provided approval with waiver of informed consent.
Consent: The design, collection, recording and analysis of data for this report were conducted in accordance with the transparency in reporting of a multivariable prediction model for individual …SciScore for 10.1101/2021.01.20.21249656: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The design, collection, recording and analysis of data for this report were conducted in accordance with the transparency in reporting of a multivariable prediction model for individual diagnosis and prognosis (TRIPOD) criteria.12 The RECOVER registry protocol was reviewed by the institutional review boards (IRBs) at all sites; 42 IRBs provided an exemption from human subjects designation, whereas three IRBs provided approval with waiver of informed consent.
Consent: The design, collection, recording and analysis of data for this report were conducted in accordance with the transparency in reporting of a multivariable prediction model for individual diagnosis and prognosis (TRIPOD) criteria.12 The RECOVER registry protocol was reviewed by the institutional review boards (IRBs) at all sites; 42 IRBs provided an exemption from human subjects designation, whereas three IRBs provided approval with waiver of informed consent.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources The criterion standard for disease positive was evidence of SARs-CoV-2 infection, from either a positive molecular diagnostic test from a swab sample (usually from the nasopharynx), or a positive serological IgM or IgG antibody, documented within 30 days of enrollment. IgGsuggested: (Rockland Cat# 00-8800-25, RRID:AB_2610703)Software and Algorithms Sentences Resources IBM SPSS Statistics for Windows, Version 27.0. SPSSsuggested: (SPSS, RRID:SCR_002865)Data were analyzed with SPSS® software with the Complex Sampling and Testing module. SPSS®suggested: (SPSS, RRID:SCR_002865)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The retrospective collection of data introduces the primary limitation of this work inasmuch as the CORC score and rule performance, including metrics of inter-rater reliability and operational characteristics, have not been used yet in real practice. For example, in terms of generalizability for high throughput screening, it remains unknown whether the temperature component, measured by an infrared thermometer, and the oxygen saturation, measured by a portable pulse oximeter, would provide similar diagnostic accuracy. Based upon the estimated likelihood ratio negative of 0.22, a CORC rule of zero or less would allow a very low posterior probability (e.g., <2.0%) in populations with a relatively low prevalence of infection (<9%).27 Symptoms not recorded were assumed to be absent, which could affect rule precision and accuracy. Another limitation is the relative lack of data from most recent cases. The most recent patient was evaluated in October and most cases came from early spring of 2020. The genotype of the virus, as well as the phenotype of infected patients, may have changed with time, and the effect on accuracy and imprecision are unknown. Additionally, it remains possible that machine-based learning methods may offer a superior role, although one study using ED-based data that directly compared three derivation techniques, including backward stepwise logistic regression, decision-tree based approaches random forest, and a gradient boosted decision tree method found lo...
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.
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- No protocol registration statement was detected.
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