Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability

SciScore for 10.1101/2022.01.25.477770: (What is this?)

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

Table 1: Rigor

Ethics	IACUC: DETAILS: Mouse Studies: Animal experiments were carried out in compliance with all pertinent US National Institutes of Health regulations and approval from the Animal Care and Use Committee (ACUC) of the Vaccine Research Center.
Sex as a biological variable	not detected.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
Anti-mouse whole IgG horseradish peroxidase conjugates (Jackson Laboratory) were used as secondary antibodies, and 3,5,3′5′-tetramethylbenzidine (TMB) (KPL, Gaithersburg, MD) was used as the substrate.	Anti-mouse whole IgG horseradish peroxidase conjugates suggested: …

SciScore for 10.1101/2022.01.25.477770: (What is this?)

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

Table 1: Rigor

Ethics	IACUC: DETAILS: Mouse Studies: Animal experiments were carried out in compliance with all pertinent US National Institutes of Health regulations and approval from the Animal Care and Use Committee (ACUC) of the Vaccine Research Center.
Sex as a biological variable	not detected.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
Anti-mouse whole IgG horseradish peroxidase conjugates (Jackson Laboratory) were used as secondary antibodies, and 3,5,3′5′-tetramethylbenzidine (TMB) (KPL, Gaithersburg, MD) was used as the substrate.	Anti-mouse whole IgG horseradish peroxidase conjugates suggested: None Anti-mouse whole IgG suggested: None
After wash three times with PBS-T buffer, the membrane was incubated half hour with anti-mouse IgG horseradish peroxidase conjugates (Jackson Laboratory) as secondary antibody.	anti-mouse IgG suggested: None
The frequency of cc40.8 class antibody was calculated by masking IGHV3-23 with 94ITMA, 101V and 102V on 8 amino acids CDR H3 and IGLV3-10 with T91, 94SGN, and A96 on 11 amino acids CDR L3.	94SGN suggested: None
Experimental Models: Cell Lines
Sentences	Resources
Cell Lines: FreeStyle 293-F (cat# R79007) and Expi293F cells (cat# A14528; RRID: CVCL_D615) were purchased from ThermoFisher Scientific Inc	Expi293F detected: ( RRID:CVCL_D615)
FreeStyle 293-F cells were maintained in FreeStyle 293 Expression Medium, while Expi293F cells were maintained in Expi Expression Medium.	Expi293F suggested: RRID:CVCL_D615)
Analysis of WS6 binding to cell surface expressed spike protein: Expi-293 cells were transiently transfected with plasmids encoding full-length spike proteins of coronaviruses using Turbo293 transfection reagent (Speed BioSystems) following manufacturer’ s protocol.	Expi-293 suggested: None
transducing plasmid pHR’ CMV-Luc, a TMPRSS2 plasmid and S plasmids from human and animal coronaviruses (SARS-CoV-2 variants, SARS-CoV, MERS-CoV and SARS-CoV-2, SARS-CoV related coronaviruses) into 293T cells using Lipofectamine 3000 transfection reagent (L3000-001, ThermoFisher Scientific, Asheville, NC) (Naldini et al., 1996).	293T suggested: None
293T-ACE2 cells (provided by Dr. Michael Farzan) or 293 flpin-TMPRSS2-ACE2 cells (made at the VRC) were plated into 96-well white/black Isoplates (PerkinElmer, Waltham, MA) at 75,00 cells per well the day before infection of pseudovirus.	293T-ACE2 suggested: None
Experimental Models: Organisms/Strains
Sentences	Resources
BALB/cJ mice (Jackson Laboratory), 6- to 8-week-old female, were used.	BALB/cJ suggested: None
Recombinant DNA
Sentences	Resources
DNA sequences encoding diverse beta-coronavirus S2P proteins were cloned into mammalian expression vector pVRC8400 and the proteins expressed by transient transfection of FreeStyle 293-F cells as previously described (Zhou et al., 2020b).	pVRC8400 suggested: RRID:Addgene_63163)
Spike-containing lentiviral pseudovirions were produced by co-transfection of packaging plasmid pCMVdR8.2,	pCMVdR8.2 suggested: RRID:Addgene_8455)
transducing plasmid pHR’ CMV-Luc, a TMPRSS2 plasmid and S plasmids from human and animal coronaviruses (SARS-CoV-2 variants, SARS-CoV, MERS-CoV and SARS-CoV-2, SARS-CoV related coronaviruses) into 293T cells using Lipofectamine 3000 transfection reagent (L3000-001, ThermoFisher Scientific, Asheville, NC) (Naldini et al., 1996).	pHR’ suggested: None TMPRSS2 suggested: RRID:Addgene_53887)
Software and Algorithms
Sentences	Resources
Production of antibodies: Antibody heavy and light variable region gene sequences were synthesized (Gene Universal Inc, Newark DE) and subcloned into corresponding pVRC8400 vectors (https://www.addgene.org).	https://www.addgene.org suggested: (Addgene, RRID:SCR_002037)
Flow cytometry data were acquired in a BD LSRFortessa X-50 flow cytometer (BD biosciences) and analyzed using Flowjo (BD biosciences)	Flowjo suggested: (FlowJo, RRID:SCR_008520)
Percent neutralization and neutralization IC50s, IC80s were calculated using GraphPad Prism 8.0.2.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
The structures were determined by molecular replacement with Phaser (McCoy et al., 2007) in the CCP4 Program Suite (Collaborative Computational Project, 1994)	CCP4 suggested: (CCP4, RRID:SCR_007255)
Further refinement was carried out with PHENIX (Adams et al., 2010), starting with torsion-angle simulated annealing with slow cooling.	PHENIX suggested: (Phenix, RRID:SCR_014224)
Iterative manual model building was carried out with COOT (Emsley and Cowtan, 2004) with maps generated from combinations of standard positional, individual B-factor and TLS refinement algorithms.	COOT suggested: (Coot, RRID:SCR_014222)
Antibody germline assignment: Germline gene of heavy and light chain were assigned by querying nucleotide sequences on IGBLAST server.	Germline suggested: (GERMLINE, RRID:SCR_001720) IGBLAST suggested: (IgBLAST, RRID:SCR_002873)
Beta-coronavirus spike sequences were downloaded from NCBI server using accession codes listed in Full-length spike constructs.	NCBI suggested: (NCBI, RRID:SCR_006472)
ClustalW was used to calculate neighbor joining (NJ) tree (Larkin et al., 2007), and Dendroscope was used to plot the Neighbor Joining tree (Albrecht et al., 2012)	ClustalW suggested: (ClustalW, RRID:SCR_017277)
Crystal diffraction data and structural refinement statistics were analyzed with HKL2000, Phenix, and Molprobity.	Molprobity suggested: (MolProbity, RRID:SCR_014226)

Results from OddPub: Thank you for sharing your data.

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.

Read the original source

Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability

This article has been Reviewed by the following groups

Listed in

Abstract

Article activity feed