1. SciScore for 10.1101/2021.11.24.21266735: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    RandomizationSARS-CoV-2 molecular surveillance program sequences whole virus genomes of randomly selected SARS-CoV-2 positive specimens from both community testing (via PHS) and hospitals, using a proper nationwide geographical distribution.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    GridION data was analyzed to get consensus genomes, with the SARS2seq pipeline and additional manual curation24.
    suggested: None

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Some limitations of our study need to be addressed. Asymptomatic or mild cases with low viral load are less likely to be identified and only detectable infections can be sequenced and included. In addition, sequencing is more successful in samples with low to medium Ct values (high to medium viral load). If infection with Beta, Gamma or Delta leads to lower Ct values than Alpha and Ct values are higher for infections after vaccination30–32, this could have led to an overestimation of the studied association. Another limitation is that prior infections could go undetected, especially if occurred during the first wave when there was no mass scale testing capacity. This could lead to an underestimation of cases with a previous infection, as we do not directly measure pre-existing infection-induced immunity. In conclusion, our results confirm a lower vaccine effectiveness against infection for the Delta variant, and similarly the Beta and Gamma variant, compared to Alpha. This effect was largest early after complete vaccination. These findings are informative for considerations on vaccine updates, future vaccination and pandemic control strategies.

    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.

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