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  1. SciScore for 10.1101/2022.05.06.490907: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethical approval for this project (IB 4165/20 PI, 6 April 2020) was obtained from the ethics committee of the Balearic Islands and waived the requirement for informed consent, due to the emergency situation.
    Consent: Ethical approval for this project (IB 4165/20 PI, 6 April 2020) was obtained from the ethics committee of the Balearic Islands and waived the requirement for informed consent, due to the emergency situation.
    Sex as a biological variablenot detected.
    RandomizationThe reaction mixture contained 250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2, 2.5 µM random hexamers, 500 µM of each dNTP, 20 U RNase inhibitor, 10 mM DTT, and 200 U M-Mlv reverse transcriptase.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    To generate SARS-Cov-2 pseudovirus, Human embryonic kidney 293 (HEK 293, ATCC® CRL-1573™) cells were seeded in a 10 cm2-plate at 4.5×106 cells/plate, in DMEM (ThermoFisher Scientific, #11995073
    HEK 293
    suggested: ATCC Cat# CRL-1573, RRID:CVCL_0045)
    Pseudovirus entry assay: A549 cells (ATCC® CCL-185) seeded in 6-multiwell plates at 0.23 × 106 cells/well in DMEM (10% FBS and 1x Normocin), and grown overnight at 37 °C, 85%
    suggested: None
    Recombinant DNA
    psPAX2 was a gift from Dr Didier Trono
    suggested: RRID:Addgene_12260)
    Addgene plasmid # 12260); pLV-mCherry was a gift from Dr Pantelis Tsoulfas
    suggested: RRID:Addgene_36084)
    Addgene plasmid # 36084); pcDNA3 mCherry was a gift from Dr Scott Gradia
    suggested: RRID:Addgene_15475)
    (Addgene plasmid # 30125); pcDNA3.1(+)eGFP was a gift from Dr Jeremy Wilusz
    suggested: RRID:Addgene_79663)
    Addgene plasmid # 129020); pcDNA3.1-SARS2-Spike was a gift from Dr Fang Li
    suggested: RRID:Addgene_145032)
    (Addgene plasmid # 145032); pcDNA3.1-ACE2-GFP was a gift from Dr Utpal Pajvani
    suggested: RRID:Addgene_154962)
    Next day, HEK 293 cells were then cotransfected with 15 μg of psPAX2 : pcDNA3.1SpikeVOCs : pLV-mCherry at ratio 1:1:1 (i.e. 5:5:5 μg) using Lipofectamin™ 3000 transfection reagent (Thermo-Fisher Scientific, #L3000015)
    suggested: None
    Next day, cells were transfected with either pcDNA3.1(+)eGFP (control) or pcDNA3.1-GFP-ACE2 expressing the ACE2 SNPs.
    suggested: None
    Software and Algorithms
    100k Genomes Project (100KGP) as the main sources of aggregated data for ACE2 protein altering variations in populations groups across the world.
    100k Genomes Project
    suggested: (MedBlast, RRID:SCR_008202)
    PCR product was purified by clean-up (FAGCK001, Favorgen) and further sequenced by Macrogen.
    suggested: (Macrogen, RRID:SCR_014454)
    Statistical analyses were performed using R Studio version 3.5.2 of the R programming language (R Project for Statistical Computing; R Foundation, Vienna, Austria). and Stata v17.0 program.
    R Project for Statistical
    suggested: (R Project for Statistical Computing, RRID:SCR_001905)

    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 limitations. First the study population is small, including patients from Hospital Son Llatzer and Hospital Son Espases, two of the main hospitals in the Balearic Health System. There might be a selection bias when identifying factors that differ between patients with COVID-19, although COVID-19 patients were matched for age and sex as well with the control group. Second, it is a retrospective study conducted in an emergency situation, and in which not all the clinical characteristics of the patients were recorded. Third, some patients had elevated biomarker data in some laboratory measurements, as well as in GDF15 and ACE2 levels, and we did not exclude them from the analysis due to small sample size and because those numbers were physiological and not due to technical errors. Finally, the study is cross-sectional and no causal inferences can be made. Despite the limitations, our study provides convincing evidence that in patients with COVID-19, the levels of GDF15 and ACE2 could be associated with increased inflammation and disease severity while ACE2 missense SNPs might be linked to infection susceptibility. In conclusion, critically ill patients with COVID-19 present higher levels of GDF15 and ACE2, as well as acute inflammation. These two proteins might be of importance because of its association with disease severity in patients infected with SARS-CoV-2. Our results suggest that certain genetic variations in ACE2 might modulate susceptibility to SARS-CoV-2...

    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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