mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

Article activity feed

1. 

   Rapid Reviews Infectious Diseases

   Apr 14, 2022

   Rino Rappuoli

   Review 1: "mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants"

   Reviewer: Rino Rappuoli (GSK) | 📘📘📘📘📘

   Read the original source
2. 

   Rapid Reviews Infectious Diseases

   Apr 14, 2022

   Rino Rappuoli

   Review of "mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants'

   Reviewer: Rino Rappuoli (GSK) | 📘📘📘📘📘

   Read the original source
3. Version published to 10.1038/s41586-021-03324-6

   Feb 10, 2021
4. 

   Version published to 10.1101/2021.01.15.426911v2 on bioRxiv

   Jan 30, 2021
5. 

   ScreenIT

   Jan 28, 2021

   SciScore for 10.1101/2021.01.15.426911: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   Consent: Informed consent was obtained from all participants and the study was conducted in accordance with Good Clinical Practice. IRB: The study visits and blood draws were reviewed and approved under the National Institutes of Health’s Federalwide Assurance (FWA00005897), in accordance with Federal regulations 45 CFR 46 and 21 CFR 5 by the NIH Intramural Research Program IRB committee (IRB# 99CC0168, Collection and Distribution of Blood Components from Healthy Donors for In Vitro Research Use) and by the Institutional Review Board of the Rockefeller University (IRB# DRO-1006, Peripheral Blood of Coronavirus Survivors to Identify Virus-Neutralizing Antibodies).

   R…

   SciScore for 10.1101/2021.01.15.426911: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Informed consent was obtained from all participants and the study was conducted in accordance with Good Clinical Practice. IRB: The study visits and blood draws were reviewed and approved under the National Institutes of Health’s Federalwide Assurance (FWA00005897), in accordance with Federal regulations 45 CFR 46 and 21 CFR 5 by the NIH Intramural Research Program IRB committee (IRB# 99CC0168, Collection and Distribution of Blood Components from Healthy Donors for In Vitro Research Use) and by the Institutional Review Board of the Rockefeller University (IRB# DRO-1006, Peripheral Blood of Coronavirus Survivors to Identify Virus-Neutralizing Antibodies).
   Randomization	The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.
   Blinding	The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	Contamination: Cells were periodically tested for contamination with mycoplasma or retroviruses. rVSV/SARS-CoV-2/GFP chimeric virus stocks were generated by infecting 293T/ACE2.cl22 cells.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Study participants: To isolate and characterize anti-SARS-CoV-2 RBD antibodies from vaccinees, a cohort of 20 individuals that participated in either the Moderna or Pfizer-BioNTech phase 3 vaccine clinical trials and did not report prior history of SARS-CoV-2 infection was recruited at the NIH Blood Center and the Rockefeller University Hospital for blood donation.	anti-SARS-CoV-2 RBD suggested: None Pfizer-BioNTech phase 3 suggested: None
   Plates were washed 6 times with washing buffer and then incubated with anti-human IgG, IgM or IgA secondary antibody conjugated to horseradish peroxidase (HRP) (Jackson Immuno Research	anti-human IgG suggested: None IgA suggested: None
   The half-maximal neutralization titers for plasma (NT50) or half-maximal and 90% inhibitory concentrations for monoclonal antibodies (IC50 and IC90, respectively) were determined using four-parameter nonlinear regression (least squares regression method without weighting; constraints: top=1, bottom=0) (GraphPad Prism).	IC90 suggested: None
   The enriched B cells were incubated in FACS buffer (1× PBS, 2% FCS, 1 mM EDTA) with the following anti-human antibodies (all at 1:200 dilution): anti-CD20-PECy7 (BD Biosciences, 335793), anti-CD3-APC-eFluro 780 (Invitrogen, 47-0037-41)	anti-human suggested: (GenWay Biotech Inc. Cat# 18-202-335793-0.1 mg, RRID:AB_1981874) anti-CD20-PECy7 suggested: None anti-CD3-APC-eFluro 780 suggested: None
   The frequency distributions of human V genes in anti-SARS-CoV-2 antibodies from this study was compared to 131,284,220 IgH and IgL sequences generated by 50 and downloaded from cAb-Rep 51, a database of human shared BCR clonotypes available at https://cab-rep.c2b2.columbia.edu/.	anti-SARS-CoV-2 suggested: (Thermo Fisher Scientific Cat# 51-6490-82, RRID:AB_2884044)
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells were periodically tested for contamination with mycoplasma or retroviruses. rVSV/SARS-CoV-2/GFP chimeric virus stocks were generated by infecting 293T/ACE2.cl22 cells.	293T/ACE2.cl22 suggested: None
   Then, the virus-antibody mixtures were incubated with 5× 105 293T/ACE2cl.22 cells in 6-well plates.	293T/ACE2cl.22 suggested: None
   Briefly, 293T cells were transfected with pNL4-3DEnv-nanoluc and pSARS-CoV-2-SΔ19 and pseudotyped virus stocks were harvested 48 hours after transfection, filtered and stored at −80°C.	293T suggested: None
   Software and Algorithms
   Sentences	Resources
   The study visits and blood draws were reviewed and approved under the National Institutes of Health’s Federalwide Assurance (FWA00005897), in accordance with Federal regulations 45 CFR 46 and 21 CFR 5 by the NIH Intramural Research Program IRB committee (IRB# 99CC0168, Collection and Distribution of Blood Components from Healthy Donors for In Vitro Research Use) and by the Institutional Review Board of the Rockefeller University (IRB# DRO-1006, Peripheral Blood of Coronavirus Survivors to Identify Virus-Neutralizing Antibodies).	NIH Intramural Research Program suggested: None
   The average of its signal was used for normalization of all of the other values on the same plate with Excel software before calculating the area under the curve using Prism V8.4 (GraphPad).	Excel suggested: None Prism suggested: (PRISM, RRID:SCR_005375)
   For monoclonal antibodies, the EC50 was determined using four-parameter nonlinear regression (GraphPad Prism V8.4).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   For analysis of the sequencing data, the raw paired-end reads were pre-processed to remove trim adapter sequences and to remove low-quality reads (Phred quality score < 20) using BBDuk.	Phred suggested: (Phred, RRID:SCR_001017)
   SARS-CoV-2 pseudotype neutralization assays: Plasma or monoclonal antibodies from vaccine recipients were four-fold or five-fold serially diluted and then incubated with SARS-CoV-2 pseudotyped HIV-1 reporter virus for 1 h at 37 °C.	Plasma suggested: None
   Single CD3-CD8-CD14-CD16-CD20+Ova-RBD-PE+RBD-AF647+ B cells were sorted into individual wells of 96-well plates containing 4 μl of lysis buffer (0.5× PBS, 10 mM DTT, 3,000 units/ml RNasin Ribonuclease Inhibitors (Promega, N2615) per well using a FACS Aria III and FACSDiva software (Becton Dickinson) for acquisition and FlowJo for analysis.	FACSDiva suggested: (BD FACSDiva Software, RRID:SCR_001456) FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Sequence analysis was performed using MacVector.	MacVector suggested: (MacVector, RRID:SCR_015700)
   Data were collected using SerialEM automated data collection software44 and movies were recorded with a K3 camera (Gatan).	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   The non-dose-weighted images were used to estimate CTF parameters using cryoSPARC implementation of the Patch CTF job.	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   Models were then refined into cryo-EM maps by rigid body and real space refinement in Phenix47 If the resolution allowed, partial CDR3 loops were built manually in Coot48 and then refined using real-space refinement in Phenix.	Phenix suggested: (Phenix, RRID:SCR_014224)

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   Results from OddPub: Thank you for sharing your code and 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.

   ---

   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.

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

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

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   About SciScore

   SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

   Read the original source
6. 

   ScreenIT

   Jan 20, 2021

   SciScore for 10.1101/2021.01.15.426911: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   Informed consent was obtained from all participants and the study was conducted in accordance with Good Clinical Practice.

   Randomization

   The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.

   Blinding

   The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.

   Power Analysis

   not detected.

   Sex as a biological variable

   Ages of the analyzed volunteers ranged from 29-69 years (median 43); ( 60%) were male and 8 (40%) female. 16 participants identified as Caucasian, 2 as Hispanic, and as African American or Asian, respectively.

   Cel…

   SciScore for 10.1101/2021.01.15.426911: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   Informed consent was obtained from all participants and the study was conducted in accordance with Good Clinical Practice.

   Randomization

   The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.

   Blinding

   The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.

   Power Analysis

   not detected.

   Sex as a biological variable

   Ages of the analyzed volunteers ranged from 29-69 years (median 43); ( 60%) were male and 8 (40%) female. 16 participants identified as Caucasian, 2 as Hispanic, and as African American or Asian, respectively.

   Cell Line Authentication

   Cells were periodically tested for contamination with mycoplasma or retroviruses. rVSV/SARS-CoV-2/GFP chimeric virus stocks were generated by infecting 293T/ACE2.cl22 cells.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   To isolate and characterize anti-SARS-CoV-2 RBD antibodies from vaccinees, a cohort of 20 individuals that participated in either the Moderna or Pfizer-BioNTech phase 3 vaccine clinical trials and did not report prior history of SARS-CoV-2 infection was recruited at the NIH Blood Center and the Rockefeller University Hospital for blood donation.	anti-SARS-CoV-2 RBD suggested: None Pfizer-BioNTech phase 3 suggested: None
   Plates were washed 6 times with washing buffer and then incubated with anti-human IgG, IgM or IgA secondary antibody conjugated to horseradish peroxidase (HRP) (Jackson Immuno Research 109-036-088	anti-human IgG suggested: None IgA suggested: None
   The half-maximal neutralization titers for plasma (NT50) or half-maximal and 90% inhibitory concentrations for monoclonal antibodies (IC50 and IC90, respectively) were determined using four-parameter nonlinear regression (least squares regression method without weighting; constraints: top=1, bottom=0) (GraphPad Prism).	IC90 suggested: None
   The enriched B cells were incubated in FACS buffer (1× PBS, 2% FCS, 1 mM EDTA) with the following anti-human antibodies (all at 1:200 dilution): anti-CD20-PECy7 (BD Biosciences, 335793), anti-CD3-APC-eFluro 780 (Invitrogen, 47-0037-41), anti-CD8-APC-eFluor (Invitrogen, 47-0086-42)	anti-human suggested: (GenWay Biotech Inc. Cat# 18-202-335793-0.1 mg, RRID:AB_1981874) anti-CD20-PECy7 suggested: None anti-CD3-APC-eFluro 780 suggested: None anti-CD8-APC-eFluor suggested: None
   The frequency distributions of human V genes in anti-SARS-CoV-2 antibodies from this study was compared to 131,284,220 IgH and IgL sequences generated by 50 and downloaded from cAb-Rep 51, a database of human shared BCR clonotypes available at https://cab- rep.c2b2.columbia.edu/.	anti-SARS-CoV-2 suggested: (Thermo Fisher Scientific Cat# 51-6490-82, RRID:AB_2884044)
   Average of two or more experiments. g-i, Correlations of plasma antibodies measurements. g, Normalized AUC for IgG anti-S plotted against normalized AUC for IgG anti-RBD. h, Normalized AUC for IgM anti-S plotted against normalized AUC for IgM anti-RBD. i, Normalized AUC for IgA anti-S plotted against normalized AUC for IgA anti-RBD.	Normalized AUC for IgG suggested: None plotted against normalized AUC for IgG anti-RBD . h , Normalized AUC for IgM suggested: None plotted against normalized AUC for IgM anti-RBD . i , Normalized AUC for IgA suggested: None anti-RBD suggested: None
   The number of antibody sequences (IGVH and IGVL) evaluated for each participant are n=68 (MOD1), n=45 (MOD2), n=117 (MOD3), n=123 (MOD4), n=110 (MOD6), n=109 (MOD7), n=144 (MOD8), n=102 (MOD9), n=132 (PFZ10), n=109 (MOD11), n=91 (PFZ12), n=78 (C001), n=66 (C003), and n=115 (C004). b, Distribution of the hydrophobicity GRAVY scores at the IGH CDR3 compared to a public database (see Methods for statistical analysis).	MOD3 suggested: None MOD4 suggested: None MOD7 suggested: None MOD8 suggested: None MOD9 suggested: None PFZ10 suggested: None MOD11 suggested: None PFZ12 suggested: None C001 suggested: None C003 suggested: (GenWay Biotech Inc. Cat# GWB-22C003, RRID:AB_10283528) C004 suggested: (Creative Diagnostics Cat# DMABH-C004, RRID:AB_2528444)
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells were periodically tested for contamination with mycoplasma or retroviruses. rVSV/SARS-CoV-2/GFP chimeric virus stocks were generated by infecting 293T/ACE2.cl22 cells.	293T/ACE2.cl22 suggested: None
   Then, the virus-antibody mixtures were incubated with 5× 105 293T/ACE2cl.22 cells in 6-well plates.	293T/ACE2cl.22 suggested: None
   Briefly, 293T cells were transfected with pNL4-3DEnv-nanoluc and pSARS-CoV-2- SΔ19 and pseudotyped virus stocks were harvested 48 hours after transfection, filtered and stored at -80℃.	293T suggested: RRID:CVCL_H376)
   Software and Algorithms
   Sentences	Resources
   The study visits and blood draws were reviewed and approved under the National Institutes of Health’s Federalwide Assurance (FWA00005897), in accordance with Federal regulations 45 CFR 46 and 21 CFR 5 by the NIH Intramural Research Program IRB committee (IRB# 99CC0168, Collection and Distribution of Blood Components from Healthy Donors for In Vitro Research Use) and by the Institutional Review Board of the Rockefeller University (IRB# DRO-1006, Peripheral Blood of Coronavirus Survivors to Identify Virus-	NIH Intramural Research Program suggested: None
   The average of its signal was used for normalization of all of the other values on the same plate with Excel software before calculating the area under the curve using Prism V8.4 (GraphPad).	Excel suggested: None Prism suggested: (PRISM, RRID:SCR_005375)
   For monoclonal antibodies, the EC50 was determined using four-parameter nonlinear regression (GraphPad Prism V8.4).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   For analysis of the sequencing data, the raw paired-end reads were pre-processed to remove trim adapter sequences and to remove low-quality reads (Phred quality score < 20) using BBDuk.	Phred suggested: (Phred, RRID:SCR_001017)
   Single CD3−CD8−CD14−CD16−CD20+Ova−RBD-PE+RBD-AF647+ B cells were sorted into individual wells of 96-well plates containing 4 μl of lysis buffer (0.5× PBS, 10 mM DTT, 3,000 units/ml RNasin Ribonuclease Inhibitors (Promega, N2615) per well using a FACS Aria III and FACSDiva software (Becton Dickinson) for acquisition and FlowJo for analysis.	FACSDiva suggested: (BD FACSDiva Software, RRID:SCR_001456) FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Sequence analysis was performed using MacVector.	MacVector suggested: (MacVector, RRID:SCR_015700)
   Data were collected using SerialEM automated data collection software44 and movies were recorded with a K3 camera (Gatan).	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   For all datasets, cryo-EM movies were patch motion corrected for beam- induced motion including dose-weighting within cryoSPARC v2.1545 after binning super resolution movies.	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   Models were then refined into cryo-EM maps by rigid body and real space refinement in Phenix47 If the resolution allowed, partial CDR3 loops were built manually in Coot48 and then refined using real-space refinement in Phenix.	Phenix suggested: (Phenix, RRID:SCR_014224)
   Data availability statement: Data presentation Figures arranged in Adobe Illustrator 2020.	Adobe Illustrator suggested: (Adobe Illustrator, RRID:SCR_010279)

   ---

   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.

   ---

   About SciScore

   SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

   Read the original source
7. 

   Version published to 10.1101/2021.01.15.426911v1 on bioRxiv

   Jan 19, 2021