Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1/BA.1.1 or BA.2 subvariant infection in Southern California

  1. Joseph A. Lewnard
  2. Vennis X. Hong
  3. Manish M. Patel
  4. Rebecca Kahn
  5. Marc Lipsitch
  6. Sara Y. Tartof

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Abstract

No abstract available

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  1. Version published to 10.1038/s41591-022-01887-z
  2. ScreenIT

    SciScore for 10.1101/2022.01.11.22269045: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: The study protocol was reviewed and approved by the KPSC institutional review board, which waived requirement for informed consent.
    Consent: The study protocol was reviewed and approved by the KPSC institutional review board, which waived requirement for informed consent.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Samples collected in hospitals are processed by either these regional laboratories or by in-house hospital laboratories, which use the ThermoFisher TaqPath COVID-19 Comboo Kit as well as the Roche cobas 8800 system for diagnostic testing.
    ThermoFisher TaqPath
    suggested: None

    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: We detected the following sentences addressing limitations in the study:
    Our study has certain limitations. While limited follow-up time was available for identifying hospitalizations of long duration, discharge dispositions were known for 84% of cases hospitalized with Omicron variant infections and 78% of those with Delta variant infections, providing a robust basis for time-to-event analyses. Incidental detections of SARS-CoV-2 among hospitalized patients might also have been more commonly associated with Omicron variant than Delta variant infections, leading to underestimates of attenuated disease severity in analyses of all hospitalizations. This consideration supports our use of EHR data on symptoms (assessed for all patients tested at KSPC) to define an endpoint of hospitalizations associated with acute respiratory symptoms, and our use of a prospective cohort design monitoring for new inpatient admissions among cases first ascertained by outpatient testing. This analytic framework also helped to mitigate bias that could result from exclusion of cases who were first tested using assays that would not identify SGTF, as such tests were used more often for patients tested in hospital settings. Follow-up was shorter for Omicron variant infections because these became most common near the end of the study period; use of a Cox proportional hazards model accounted for the resulting censoring. As access to testing may differ among KPSC members versus the general population, case-to-hospitalization ratios for Omicron and non-Omicron variant infectio...

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2022.01.11.22269045 on medRxiv