Native-like SARS-CoV-2 Spike Glycoprotein Expressed by ChAdOx1 nCoV-19/AZD1222 Vaccine

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1. Version published to 10.1021/acscentsci.1c00080

   Apr 2, 2021
2. 

   ScreenIT

   Jan 20, 2021

   SciScore for 10.1101/2021.01.15.426463: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Polyclonal rabbit anti-S1 antibody (Sinobiological, Cat: 40592-T62) and anti-S2 antibody (Abcam, Cat: ab272504) were used as primary antibodies.	anti-S1 suggested: None anti-S2 suggested: None
   Cells were washed 3 × with PBS-BSA-0.5% then incubated for 1h at RT with secondary antibodies conjugated with Alexafluor488 diluted at 1:1000 in PBS-BSA 0.5% (for ChAdOx1 nCov-19 serum staining Goat Anti mouse AlexaFluor 488 (Life Tech A11029)	Anti mouse suggested: (Thermo Fisher Scientific Cat# A-11029, RRID:AB_2534088)
   Isolation of human monoclonal antibodies from peripheral B cells by spike-specific single B cells …

   SciScore for 10.1101/2021.01.15.426463: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Polyclonal rabbit anti-S1 antibody (Sinobiological, Cat: 40592-T62) and anti-S2 antibody (Abcam, Cat: ab272504) were used as primary antibodies.	anti-S1 suggested: None anti-S2 suggested: None
   Cells were washed 3 × with PBS-BSA-0.5% then incubated for 1h at RT with secondary antibodies conjugated with Alexafluor488 diluted at 1:1000 in PBS-BSA 0.5% (for ChAdOx1 nCov-19 serum staining Goat Anti mouse AlexaFluor 488 (Life Tech A11029)	Anti mouse suggested: (Thermo Fisher Scientific Cat# A-11029, RRID:AB_2534088)
   Isolation of human monoclonal antibodies from peripheral B cells by spike-specific single B cells sorting: To isolate Spike-specific B cells, PBMCs were labelled with recombinant trimeric spike-twin-Strep and stained with antibody cocktail consisting of CD3-FITC, CD14-FITC, CD56-FITC, CD16-FITC, IgM-FITC, IgA-FITC, IgD-FITC, IgG-BV786, CD19-BUV395 and Strep-MAB-DY549 (iba) to probe the Strep tag of spike.	IgG-BV786 suggested: None CD19-BUV395 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Western blot analysis: Protein pellets from the HEK293F cell lysates were loaded onto an SDS-PAGE gel, then transferred to a PVDF membrane.	HEK293F suggested: RRID:CVCL_6642)
   FACS analysis for cell surface spike expression: Hela S3 cells at 4 ×105 cell/ml were infected with 10 MOI ChAdOx1 nCoV-19 and incubated at 37°C for 40-48h.	Hela S3 suggested: None
   Plasmids encoding heavy and light chains were then co-transfected into the 293T cell line by the polyethylenimine method (408727; Sigma), and antibody were harvested for further study.	293T suggested: None
   1.6×105 of U2OS or HeLa cells resuspended in 2 ml of DMEM 10% FBS, Pen/Strep were seeded on top of the grids in, in 6 well plate wells.	U2OS suggested: None HeLa suggested: None
   Software and Algorithms
   Sentences	Resources
   Data were analysed using FlowJo v9 (TreeStar).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Tilt series were acquired using SerialEM (44) at a pixel size of 2.13 Å.	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Movies were subsequently gain normalised during motion correction and Fourier cropped back to physical pixel size with MotionCor2 (46).	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   A representative glycoform presented at each site was modelled on to the N-linked carbohydrate attachment sites in Coot (50).	Coot suggested: (Coot, RRID:SCR_014222)
   Mass spectrometry raw files have been deposited in the MassIVE proteomics database (DOI: XXX).	MassIVE suggested: None

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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 did not find any issues relating to the usage of bar graphs.

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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 10.1101/2021.01.15.426463 on bioRxiv

   Jan 19, 2021