1. SciScore for 10.1101/2021.11.09.467693: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: Sample collection and studies were performed in accordance with the UK Policy Framework for Health and Social Care Research and with specific Research Ethics Committee approval (REC 20/SC/0310).
    IRB: Sample collection and studies were performed in accordance with the UK Policy Framework for Health and Social Care Research and with specific Research Ethics Committee approval (REC 20/SC/0310).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Membranes were blocked in milk prior to detection with specific antibodies: 1:1000 ACE2 rabbit (Abcam, Ab108209),1:5000
    ACE2
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Cells and plasmids: HEK293T-17 (ATCC, CRL-11268™), Calu-3 (ATCC, HTB-55™), A549-ACE2, Vero-E6, Vero-E6-TMPRSS2 and A549-ACE2 expressing the individual IFITM proteins were cultured in DMEM (Gibco) with 10% FBS (Invitrogen) and 200μg/ml Gentamicin (Sigma), and incubated at 37°C, 5% CO2.
    Calu-3
    suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)
    A549 stable cell lines expressing ACE2 (pMIGR1-puro), and IFITMs (pLHCX) were generated and selected as described previously (Winstone et al., 2021)
    A549
    suggested: None
    Passage and titration of SARS-CoV-2: PHE England strain 02/2020 was propagated in Vero-E6-TMPRSS2 cells and titre was determined by plaque assay (Winstone et al., 2021).
    Vero-E6-TMPRSS2
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Approximately 2.5 μg of the in vitro synthesized RNA was used to transfect ∼6 ×105 BHK-hACE2-N cells stably expressing the SARS-CoV-2 N and the human ACE2 genes(Rihn et al., 2021) using the MessengerMax lipofection kit (Thermo Scientific) as per the manufacturer’s instructions.
    BHK-hACE2-N
    suggested: None
    Cells were then incubated until signs of viral replication (syncytia formation) became visible (usually after 2-3 days), at which time the medium was collected (P0 stock) and used further as a source of rescued virus to infect VERO E6 cells to generate P1 and P2 stocks.
    VERO E6
    suggested: RRID:CVCL_XD71)
    Generation of Clinical Viral Isolates: Viruses were isolated on Vero.E6 cells (ATCC CRL 1586™) from combined naso-oropharyngeal swabs submitted for routine diagnostic testing by real-time RT-PCR and shown to be from the B.1.1.7 (alpha) variant by on-site whole-genome sequencing (Oxford Nanopore Technologies, Oxford, UK) (Pickering et al., 2021)
    Vero.E6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Viral RNA levels in cells or supernatants were measured 48 hours after infection by RT-qPCR. siRNA knockdown of IFITM2: A549-ACE2 cells were reverse transfected using 20pmol of Non-targeting siRNA (D-001206-13-20) or IFITM2 siRNA (M-020103-02-0010) and 1μL of RNAi max (Invitrogen).
    A549-ACE2
    suggested: None
    Recombinant DNA
    SentencesResources
    A549 stable cell lines expressing ACE2 (pMIGR1-puro), and IFITMs (pLHCX) were generated and selected as described previously (Winstone et al., 2021)
    pMIGR1-puro
    suggested: None
    Briefly, a set of overlapping cDNA fragments representing the entire genomes of SARS-CoV-2 Wuhan isolate (GenBank: MN908947.3) and the B.1.1.7 alpha variant were chemically synthesized and cloned into pUC57-Kan (Bio Basic Canada Inc and Genewiz, respectively).
    pUC57-Kan
    suggested: RRID:Addgene_123653)
    To generate Wuhan virus carrying the alpha variant spike, a mixture of the relevant synthetic cDNA fragments of the Wuhan and alpha variants was co-transformed with XhoI-BamHI-cut pEB2 into the Saccharomyces cerevisiae strain TYC1 (MATa, ura3-52, leu2Δ1, cyh2r, containing a knockout of DNA Ligase 4) (Gaida et al., 2011) that had been made competent for DNA uptake using the LiCl2-based Yeast transformation kit (YEAST1-1KT, Merck).
    pEB2
    suggested: RRID:Addgene_104001)
    Software and Algorithms
    SentencesResources
    Viruses were sequenced using Oxford Nanopore as previously described(da Silva Filipe et al., 2021).
    Oxford Nanopore
    suggested: (Oxford Nanopore Technologies, RRID:SCR_003756)

    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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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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