Broad-spectrum antiviral activity of 3D8, a nucleic acid-hydrolyzing single chain variable fragment (scFv), targeting SARS-CoV-2 and multiple coronaviruses in vitro

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1. 

   Version published to 10.1101/2020.11.25.398909v2 on bioRxiv

   Feb 15, 2021
2. 

   ScreenIT

   Nov 26, 2020

   SciScore for 10.1101/2020.11.25.398909: (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	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After transmembrane transfer, it was incubated with primary antibodies; anti-SARS-CoV-2 (PA1-41098, Invitrogen, Thermo Fisher Scientific, Massachusetts, USA)	anti-SARS-CoV-2 ( PA1-41098 suggested: None
   , anti-PEDV (9191, Median Diagnostics, Chuncheon-si, ROK), anti-HCoV-OC43(LS-C79764, LS-bio, Seattle, WA, USA) and anti-human GAPDH antibody (ab9485, Abcam, Cambridge, UK) overnight at 4°C and then incubated with anti-mouse or rabbit IgG-HRP conjugate …

   SciScore for 10.1101/2020.11.25.398909: (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	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After transmembrane transfer, it was incubated with primary antibodies; anti-SARS-CoV-2 (PA1-41098, Invitrogen, Thermo Fisher Scientific, Massachusetts, USA)	anti-SARS-CoV-2 ( PA1-41098 suggested: None
   , anti-PEDV (9191, Median Diagnostics, Chuncheon-si, ROK), anti-HCoV-OC43(LS-C79764, LS-bio, Seattle, WA, USA) and anti-human GAPDH antibody (ab9485, Abcam, Cambridge, UK) overnight at 4°C and then incubated with anti-mouse or rabbit IgG-HRP conjugate (209-035-082 or 309-035-003, Jackson ImmunoResearch, West Grove, PA, USA) for 1 h at 37 °C.	anti-PEDV suggested: None anti-human GAPDH suggested: None anti-mouse suggested: None rabbit IgG-HRP suggested: None
   After blocking with 1% BSA and 0.3 M (22.52 mg/ml) glycine in PBST buffer for 1 h at room temperature, primary antibodies for detecting PEDV (mouse anti-PEDV monoclonal Ab, MBS313516, Mybio), HCoV-OC43 (mouse anti-OC43 monoclonal Ab, LS-C79764, LS-bio) and 3D8 (polyclonal rabbit IgG serum Ab) were incubated overnight at 4 °C.	HCoV-OC43 suggested: None anti-OC43 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells and viruses: African green monkey kidney epithelial Vero cells (ATCC® CCL-81) and Vero E6 cells (ATCC® CRL-1586) were maintained in Dulbecco’s modified Eagle’s medium (12-604F, Lonza, BioWhittaker®, Walkersville, MD, USA) supplemented with 10% Fetal bovine serum (FBS, Gibco, Life Technologies, Grand Island, NY, USA), 1% 10 mM HEPES in 0.85% NaCl (17-737E, Lonza, BioWhittaker®, Walkersville, MD, USA) and 100 U/ml Penicillin-100 µg/ml Streptomycin (15140-122, Gibco, Life Technologies, Grand Island, NY, USA)	Vero suggested: ATCC Cat# CRL-1586, RRID:CVCL_0574)
   In case of prophylactic treatment, Vero E6 cells were treated with 3D8 and incubated overnight before the virus challenge.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Viral RNA was quantified using Power SYBR® Green PCR Master Mix (4367659, Applied Biosystems™, Life Technologies Ltd., Woolston	Applied Biosystems™ suggested: (Applied Biosystems, RRID:SCR_005039)

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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: We detected the following sentences addressing limitations in the study:

   However, the absence of in vivo studies in animal models is a major limitation. To address this issue, further studies are needed to illustrate the in vivo inhibitory effect of 3D8 scFv in transgenic mice, Syrian hamsters and non-human primate models. In conclusion, 3D8 scFv confers broad-spectrum antiviral activity against SARS-CoV-2 and multiple coronaviruses. This study provides insights into the effective antiviral countermeasure of scFv against emerging viral outbreaks.

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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:

   • 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.

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3. 

   Version published to 10.1101/2020.11.25.398909v1 on bioRxiv

   Nov 25, 2020