The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines

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   ScreenIT

   Aug 25, 2021

   SciScore for 10.1101/2021.08.22.457114: (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
   Anti-spike monoclonal antibodies from COVID-19 patients: The variable regions of anti-SARS-CoV-2 spike antibodies from COVID-19 patients were synthesized according to the published sequence (IDT) (Brouwer et al., 2020; Chi et al., 2020; Li et al., 2021; Robbiani et al., 2020; Suryadevara et al., 2021; Zost et al., 2020).	Anti-spike suggested: (GeneTex Cat# GTX632604, RRID:AB_2864418) anti-SARS-CoV-2 spike suggested: None
   donkey anti-mouse IgG Fc fragment antibody and APC-conjugated anti-human IgG Fc fragment specific antibody (Jackson ImmunoResearch, USA) were used.	anti-mouse IgG suggested: None anti-human IgG

   SciScore for 10.1101/2021.08.22.457114: (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
   Anti-spike monoclonal antibodies from COVID-19 patients: The variable regions of anti-SARS-CoV-2 spike antibodies from COVID-19 patients were synthesized according to the published sequence (IDT) (Brouwer et al., 2020; Chi et al., 2020; Li et al., 2021; Robbiani et al., 2020; Suryadevara et al., 2021; Zost et al., 2020).	Anti-spike suggested: (GeneTex Cat# GTX632604, RRID:AB_2864418) anti-SARS-CoV-2 spike suggested: None
   donkey anti-mouse IgG Fc fragment antibody and APC-conjugated anti-human IgG Fc fragment specific antibody (Jackson ImmunoResearch, USA) were used.	anti-mouse IgG suggested: None anti-human IgG suggested: None
   Flow cytometric analysis of antibodies: Plasmids expressing the full-length SARS-CoV-2 spike protein, Flag-NTD-PILR-TM and Flag-RBD-PILR-TM were co-transfected with the GFP vector into HEK293T cells.	SARS-CoV-2 spike protein , Flag-NTD-PILR-TM suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   ACE2-stably transfected HEK293 cells (HEK293T-ACE2-transfectants) were reported previously (Liu et al., 2021b).	HEK293 suggested: None
   The pcDNA3.4 expression vector containing the sequence that encodes the His-tagged extracellular domain of the spike protein was transfected into Expi293 cells and the His-tagged spike protein produced in the culture supernatants was then purified with a Talon resin (Clontech).	Expi293 suggested: RRID:CVCL_D615)
   48 hours later, B16F10 cells were washed twice with PBS,and then the cells were collected and frozen and thawed.	B16F10 suggested: NCI-DTP Cat# B16F10, RRID:CVCL_0159)
   Flow cytometric analysis of antibodies: Plasmids expressing the full-length SARS-CoV-2 spike protein, Flag-NTD-PILR-TM and Flag-RBD-PILR-TM were co-transfected with the GFP vector into HEK293T cells.	HEK293T suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Balb/c female mice (7-weeks-old females) were purchased from SLC.	Balb/c suggested: None
   Recombinant DNA
   Sentences	Resources
   For Cryo-EM analysis, the sequence encoding the spike protein’s extracellular domain with a foldon and His-tag at the C-terminus (Cai et al., 2020) was cloned into a pcDNA3.4 expression vector containing the SLAM signal sequence.	pcDNA3.4 suggested: RRID:Addgene_131198)
   Transfection: A pME18S expression plasmid containing the full-length or subunit spike protein was transiently transfected into HEK293T cells using PEI max (Polysciences); the pMx-GFP expression plasmid was used as the marker of transfected cells.	pME18S suggested: RRID:Addgene_52384) pMx-GFP suggested: None
   The cDNA of the variable regions of the heavy chain and light chain were cloned into a pCAGGS vector containing sequences that encode the human IgG1 or kappa constant region.	pCAGGS suggested: RRID:Addgene_18926)
   Software and Algorithms
   Sentences	Resources
   The primers for mutagenesis were designed on Agilent’s website (https://www.agilent.com/store/primerDesignProgram.jsp).	Agilent’s suggested: None
   Transfection: A pME18S expression plasmid containing the full-length or subunit spike protein was transiently transfected into HEK293T cells using PEI max (Polysciences); the pMx-GFP expression plasmid was used as the marker of transfected cells.	Polysciences) suggested: None
   Antibodies binding to the GFP-positive cells were shown in the figures using FlowJo software (BD bioscience).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   The PRNT50 neutralization titers for vaccinated sera were determined using 3-parameter nonlinear regression curve (GraphPad Prism).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   For automated data acquisition, SerialEM software was used to collect cryo-EM image data.	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Image processing and 3D reconstruction: All of image processes were carried out on cryoSPARC software (Punjani et al., 2017).	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   The corrected model was refined by the phenix.real_space_refine program (Liebschner et al., 2019) with secondary structure and Ramachandran restraints, then the resulting model was manually checked by COOT.	COOT suggested: (Coot, RRID:SCR_014222)
   This iterative process was performed for several rounds to correct remaining errors until the model was in good agreement with geometry, as reflected by the MolProbity score of 2.07 (Williams et al., 2018).	MolProbity suggested: (MolProbity, RRID:SCR_014226)
   Data and statistical analysis: FlowJo version 10.7 (BD Biosciences, USA) was used to analyze the flow cytometry data, and Graphpad Prism version 7.0e was used for graph generation and statistical analysis.	Graphpad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results from OddPub: Thank you for sharing your data.

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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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   Results from scite Reference Check: We found no unreliable references.

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   Version published to 10.1101/2021.08.22.457114 on bioRxiv

   Aug 23, 2021