SARS-CoV-2 and SARS-CoV differ in their cell tropism and drug sensitivity profiles

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   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.04.03.024257: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	Authentication: Cells were regularly authenticated by short tandem repeat (STR) analysis and tested for mycoplasma contamination. Contamination: Cells were regularly authenticated by short tandem repeat (STR) analysis and tested for mycoplasma contamination.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Detection occurred by using specific antibodies against β-actin (1:2500 dilution, Sigma-Aldrich, Munich, Germany), ACE2, and TMPRSS2 (both 1:1000 dilution, abcam, Cambridge, UK)	β-actin suggested: None TMPRSS2 suggested:…

   SciScore for 10.1101/2020.04.03.024257: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	Authentication: Cells were regularly authenticated by short tandem repeat (STR) analysis and tested for mycoplasma contamination. Contamination: Cells were regularly authenticated by short tandem repeat (STR) analysis and tested for mycoplasma contamination.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Detection occurred by using specific antibodies against β-actin (1:2500 dilution, Sigma-Aldrich, Munich, Germany), ACE2, and TMPRSS2 (both 1:1000 dilution, abcam, Cambridge, UK)	β-actin suggested: None TMPRSS2 suggested: None
   Receptor blocking experiments: To investigate whether ACE2 or DPP4 receptors are involved in SARS-CoV-2 internalisation and replication, Caco2 cells were pre-treated for 30 min at 37°C with goat antibody directed against the human ACE2 or DDP4 ectodomain (R&D Systems, Wiesbaden-Nordenstadt, Germany).	DPP4 suggested: None ACE2 suggested: None
   Immunostaining for double-stranded RNA: Immunostaining was performed as previously described [Cinatl et al., 1995], using a monoclonal antibody directed against double-stranded RNA (1:150 dilution, SCICONS J2, mouse, IgG2a, kappa chain, English & Scientific Consulting Kft.,	mouse, IgG2a suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   293 cells (PD-02-01; Microbix Bisosystems Inc.) and 293/ACE2 cells [Kamitani et al., 2006] (kindly provided by Shinji Makino, UTMB, Galveston, Texas) were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% FBS), 50 IU/ mL penicillin, and 50µg/ mL streptomycin.	293 suggested: None 293/ACE2 suggested: RRID:CVCL_DR94)
   Receptor blocking experiments: To investigate whether ACE2 or DPP4 receptors are involved in SARS-CoV-2 internalisation and replication, Caco2 cells were pre-treated for 30 min at 37°C with goat antibody directed against the human ACE2 or DDP4 ectodomain (R&D Systems, Wiesbaden-Nordenstadt, Germany).	Caco2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Fifty-three SARS-CoV genome sequences were downloaded from VIPR [Pickett et al., 2012; Pickett et al., 2012A] restricted to sequences with a collection year between 2003-2004 and a human or unknown host.	VIPR suggested: (vipR, RRID:SCR_010685)
   Frames (ORFs) were extracted using EMBOSS getorf	EMBOSS suggested: (EMBOSS, RRID:SCR_008493)
   These ORFs were matched to known proteins using BLAST, and fragments and mismatches were discarded.	BLAST suggested: (BLASTX, RRID:SCR_001653)
   Where structures were not available they were modelled using Phyre2 [Kelley et al., 2015]	Phyre2 suggested: None
   SDPs were mapped onto protein structures using PyMOL from structures obtained from the Protein Databank (PDB).	PyMOL suggested: (PyMOL, RRID:SCR_000305)

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   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).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from rtransparent:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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2. 

   Version published to 10.1101/2020.04.03.024257v1 on bioRxiv

   Apr 5, 2020