Relative Ratios of Human Seasonal Coronavirus Antibodies Predict the Efficiency of Cross-Neutralization of SARS-CoV-2 Spike Binding to ACE2
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SciScore for 10.1101/2021.07.16.21260079: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Study approval: Use of human samples for this study was approved by the University of Ottawa Ethics Review Board: Certificates H-04-20-5727, H-04-21-6643 and H-07-20-6009. 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 Antibody responses in pre-pandemic serum samples of all four cohorts were tested for the presence of antibody isotypes (IgA, IgM, IgG, and IgE) and IgG subtypes (IgG1, IgG2, IgG3, and IgG4) using this ELISA binding assay. IgAsuggested: NoneIgMsuggested: NoneIgGsuggested: NoneIgEsuggested: NoneIgG1suggested: NoneIgG2suggested…SciScore for 10.1101/2021.07.16.21260079: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Study approval: Use of human samples for this study was approved by the University of Ottawa Ethics Review Board: Certificates H-04-20-5727, H-04-21-6643 and H-07-20-6009. 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 Antibody responses in pre-pandemic serum samples of all four cohorts were tested for the presence of antibody isotypes (IgA, IgM, IgG, and IgE) and IgG subtypes (IgG1, IgG2, IgG3, and IgG4) using this ELISA binding assay. IgAsuggested: NoneIgMsuggested: NoneIgGsuggested: NoneIgEsuggested: NoneIgG1suggested: NoneIgG2suggested: NoneIgG3suggested: NoneIgG4suggested: NoneAccordingly, the control calibration antibodies were prepared with appropriate dilutions to generate the calibration curve (anti-COVID Ig). anti-COVID Ig) .suggested: NoneAfter two hours, plates were washed three times with 200uL PBS-T followed by the addition of secondary-HRP antibodies (1:3000) diluted in dilution buffer. secondary-HRPsuggested: None50uL of the appropriate diluted secondary antibody-HRP was added to each well and the plates were incubated at RT for one hour of shaking (700rpm). antibody-HRPsuggested: (Bioworld Technology Cat# MB001H, RRID:AB_2857326)Relieff is used to predict classification rank, i.e. within the group significance, for each feature in the training set classification, of serum antibody cross-reactivity to 4 different SARS-CoV-2 antigens (N, RBD, Spike) for IgA, IgM and IgG and separately for antibodies for seasonal viruses (OC43, HKU-1, 229E, NL63). antigens ( N , RBD , Spike ) for IgA , IgM and IgGsuggested: NoneNL63suggested: NoneSARS-CoV-2 ELISA Antigens and Antibodies: To evaluate the functional antibody responses of sCoV antibodies against different SARS-CoV-2 proteins, SARS-CoV-2 S, RBD, and N proteins were used as coating antigen (see antigen production). Antibodiessuggested: Noneantigen ( see antigen production) .suggested: NoneSecondary antibodies: Anti-human IgG-HRP (NRC anti-hIgG#5-HRP Anti-human IgG-HRPsuggested: NoneControl antibodies: Anti-SARS-CoV-2 S CR3022 Human IgG1 (Absolute Antibody, Ab01680-10.0), Anti-SARS-CoV-2 S CR3022 Human IgA (Absolute Antibody, Ab01680-16.0), Anti-SARS-CoV-2 S CR3022 Human IgM (Absolute Antibody, Ab01680-15.0), Anti-SARS-CoV-2 S CR3022 Human IgE (Absolute Antibody, Ab01680-14.0), Anti-SARS-CoV-2 S CR3022 Human IgG1 (Absolute Antibody Ab01680-10.0), Anti-SARS-CoV-2 S CR3022 Human IgG2 (Absolute Antibody Ab01680-11.0), Anti-SARS-CoV-2 S CR3022 Human IgG3 (Absolute Antibody Ab01680-12.1), and Anti-SARS-CoV-2 S CR3022 Human Ig4 (Absolute Antibody Ab01680-13.12). Anti-SARS-CoV-2 S CR3022 Human IgG1suggested: NoneHumansuggested: (Imported from the IEDB Cat# CR3022, RRID:AB_2848080)Anti-SARS-CoV-2 S CR3022 Human IgAsuggested: NoneAnti-SARS-CoV-2 S CR3022 Human IgMsuggested: NoneAnti-SARS-CoV-2 S CR3022 Human IgEsuggested: NoneAnti-SARS-CoV-2 S CR3022 Human IgG2suggested: NoneAnti-SARS-CoV-2 S CR3022 Human IgG3suggested: NoneAnti-SARS-CoV-2suggested: (Abcam Cat# ab273074, RRID:AB_2847846)The concentration of antigen, antibodies, and sample diluents were kept as above, although the volume was reduced to 10uL per well. antigen ,suggested: NoneExperimental Models: Cell Lines Sentences Resources The 229E RBD (P15423) was cloned in pCAGGs plasmid with a hexa-his Tag (C-term) with secretory signal (N-term) and transfected into 293F cells maintained in Freestyle 293 expression media (Thermo Fisher, 12338018) at 37°C, 7% CO2, with shaking (125rpm). 293Fsuggested: None6 – FLAG tag was synthesized by Genscript with codon-optimization for expression in CHO cells.A biotin acceptor peptide sequence (BAP: GLNDIFEAQKIEWHE) was added in-frame at the C-terminus of ACE2. CHOsuggested: CLS Cat# 603479/p746_CHO, RRID:CVCL_0213)The cDNA was cloned into pTT5 and ACE2-BAP cDNA was expressed by transient gene expression in CHO55E1 cells as described above with the addition of 5% (w:w) of pTT5-BirA (E. coli biotin ligase) expression plasmid. CHO55E1suggested: NoneRecombinant DNA Sentences Resources The 229E RBD (P15423) was cloned in pCAGGs plasmid with a hexa-his Tag (C-term) with secretory signal (N-term) and transfected into 293F cells maintained in Freestyle 293 expression media (Thermo Fisher, 12338018) at 37°C, 7% CO2, with shaking (125rpm). pCAGGssuggested: RRID:Addgene_127347)The spike ectodomain (SARS2: MN908947; OC43: AAT84362.1; HKU1: Q0ZME7.1) cDNA constructs with furin site mutated, two stabilizing prefusion proline mutations, the human resistin as trimerization partner and a C-terminal FLAG-(His)6 (SARS2) or FLAG-Twin Strep Tag-(His)6 (OC43 and HKU1) tag were cloned into pTT241 vector and transfected in CHO2353 to generate stable pools. pTT241suggested: NoneThe nucleocapsid (SARS2: YP_009724397; OC43: AY391777; HKU1: HM034837) cDNAs with a C-terminal FLAG-Twin Strep Tag-(HisG)6 tag were synthesized by Genscript (Cricetulus griseus codon bias) and cloned in the cDNA into pTT5™ expression plasmid. pTT5™suggested: NoneThe cDNA was cloned into pTT5 and ACE2-BAP cDNA was expressed by transient gene expression in CHO55E1 cells as described above with the addition of 5% (w:w) of pTT5-BirA (E. coli biotin ligase) expression plasmid. pTT5suggested: RRID:Addgene_52326)pTT5-BirAsuggested: NoneSoftware and Algorithms Sentences Resources Neutralizing activity was determined by calculating the % inhibition against SARS-CoV-2 S proteins using the following equation: Statistical and Machine learning analyses: Data analysis was conducted using GraphPad Prism v9, R and Matlab 2021a (Matworks Inc.).
GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Sample clustering was performed using fuzzy c-means (FCM) clustering method (fcm function running under Matlab). Matlabsuggested: (MATLAB, RRID:SCR_001622)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).
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.
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