No association between the SARS-CoV-2 variants and mortality rates in the Eastern Mediterranean Region

  1. Saad Omais
  2. Samer Kharroubi
  3. Hassan Zaraket

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Abstract

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  1. Version published to 10.1016/j.gene.2021.145843
  2. Version published to 10.1101/2021.01.06.21249332v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.01.06.21249332: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableAn independent t-test was used to chart the comparison of variants via gender (male vs female), while one-way ANOVA was carried out for age distribution (0-9, 10-18, 19-49, 50-59, and >60).

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    These were then analyzed by CoVsurver enabled by GISAID (https://www.gisaid.org/epiflu-applications/covsurver-mutations-app/) and compared with reference strain hCoV-19/Wuhan/WIV04/2019 (accession number: EPI_ISL_402124)
    CoVsurver
    suggested: None
    Statistical Analysis: The data were checked for completeness, and responses were coded and entered into the Statistical Package for the Social Sciences (SPSS) software version 20 for Windows, which was later used for statistical analyses [IBM: Statistical Package for the Social Sciences.
    SPSS
    suggested: (SPSS, RRID:SCR_002865)
    Statistical Package for the Social Sciences
    suggested: (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: We detected the following sentences addressing limitations in the study:
    Considering the limitations due to the discrepant number of sequences available (as mentioned above) or to country-specific variations in managing the COVID-19 pandemic (such as testing capacity, age stratification, enforcing/relaxing lockdown policies, etc.), we assessed the association of ‘D614G & P323L’ incidence with CFR within each of the top four represented countries over time. Interestingly, we found a positive, albeit non-significant, correlation between ‘D614G & P323L’ incidence and COVID-19 CFR in Saudi Arabia, Oman, and Egypt, but a statistically significant negative correlation in UAE (Figure 7B). This suggests that the reported correlation between these variants and increased CFR might be a mere coincidence rather than true causation. Noteworthy, our method of calculating daily/monthly CFR is credited for accounting for a 13-day lag between cumulative cases and deaths [18]. Yet, it overestimates the case fatality risk early on in the pandemic [37], a limitation that would apply to our final analysis. Then again, considering the overwhelming discrepancy in fatality correlations between countries (especially in UAE versus Oman with similar sequence counts (Figure 7B)), it is unlikely that early bias in CFR estimation would have altered our conclusion. Additionally, a more accurate method to estimate COVID-19 mortality would be the infection fatality rate (IFR), inferred from seroprevalence studies. However, such data is only available for Iran, Pakistan, and Qatar...

    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.

    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.

  4. Version published to 10.1101/2021.01.06.21249332v1 on medRxiv