Both COVID-19 infection and vaccination induce high-affinity cross-clade responses to SARS-CoV-2 variants
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SciScore for 10.1101/2022.04.07.22273545: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: All experiments and analyses involving samples from human donors were conducted with the approval of the ethics committee of the canton Zurich, Switzerland (KEK-ZH-Nr. 2015-0561, BASEC-Nr. 2018-01042, and BASEC-Nr. 2020-01731), in accordance with the provisions of the Declaration of Helsinki and the Good Clinical Practice guidelines of the International Conference on Harmonisation. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources After the sample incubation for 2 h at RT, the wells were washed five times with wash buffer, and the presence of anti–SARS-CoV-2 antibodies was … SciScore for 10.1101/2022.04.07.22273545: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: All experiments and analyses involving samples from human donors were conducted with the approval of the ethics committee of the canton Zurich, Switzerland (KEK-ZH-Nr. 2015-0561, BASEC-Nr. 2018-01042, and BASEC-Nr. 2020-01731), in accordance with the provisions of the Declaration of Helsinki and the Good Clinical Practice guidelines of the International Conference on Harmonisation. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources After the sample incubation for 2 h at RT, the wells were washed five times with wash buffer, and the presence of anti–SARS-CoV-2 antibodies was detected using horseradish peroxidase (HRP)-linked antibodies (1. anti-human IgG antibody: Peroxidase AffiniPure Goat Anti-Human IgG, Fcγ Fragment Specific; Jackson; 109-035-098 at 1:4,000 dilution. 2. anti-human IgA antibody: Goat Anti-Human IgA Heavy Chain Secondary Antibody, HRP; Thermo Fisher Scientific; 31417 at 1:750 dilution. 3. anti-human IgM antibody: anti-human IgM μ-chain–specific antibody; Sigma-Aldrich; A6907 at 1:3,000 dilution. 4. anti-human IgG1 antibody: mouse anti-human IgG1 Fc-HRP; Southern Biotech; 9054-05 at 1:3,000 dilution. 5. anti-human IgG2 antibody: mouse anti-human IgG2 Fc-HRP; Southern Biotech; 9060-05 at 1:3,000 dilution. 6. anti-human IgG3 antibody: mouse anti-human IgG3 Hinge-HRP; Southern Biotech; 9210-05 at 1:3,000 dilution. 7. anti-human IgG4 antibody: mouse anti-human IgG4 Fc-HRP; Southern Biotech; 9200-05 at 1:3,000 dilution), all of them diluted in sample buffer at 3 μL per well dispensed on Biotek Multiflo FX. anti–SARS-CoV-2suggested: Noneanti-human IgGsuggested: (Jackson ImmunoResearch Labs Cat# 109-035-098, RRID:AB_2337586)anti-human IgAsuggested: (Thermo Fisher Scientific Cat# 31417, RRID:AB_228253)Anti-Human IgA Heavy Chain Secondary Antibody,suggested: (Thermo Fisher Scientific Cat# 31417, RRID:AB_228253)anti-human IgMsuggested: (Sigma-Aldrich Cat# A6907, RRID:AB_258318)anti-human IgM μ-chain–specificsuggested: Noneanti-human IgG3suggested: (SouthernBiotech Cat# 9200-05, RRID:AB_2796691)For quality testing, the same procedure was applied as above using the same clone (HP6025) of the HRP-linked secondary antibody but from a different vendor, including a different storage buffer: mouse anti-human IgG4; Invitrogen; A-10654 at 1:500 dilution. anti-human IgG4suggested: (Thermo Fisher Scientific Cat# A-10654, RRID:AB_2534054)Software and Algorithms Sentences Resources Fisher’s test was conducted in Graph Pad Prism, with α < 0.01. Graph Pad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)For visualisation of individual data points in boxplots, violin plots, ridge plots (ggridges package), density plots (with geom_density_2d where a 2D kernel density estimation was performed on the X and Y coordinates of the input data and the results were displayed with contours), heatmaps (using heatmap.2, a part of the gplots 3.1.1 library), and as scatter dot plots, ggplot2 (version 3.3.5) functions were used. ggplot2suggested: (ggplot2, RRID:SCR_014601)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The limitations of our investigations reside in the number of patients enrolled in the study and the vast number of variables reported, which may constrain the generalizability of results and conclusions. Therefore, all variables underlying this study are available for further studies and for comparison with future cohorts. On the other hand, our findings describing the antibody response of pre-omicron convalescent or post-vaccination sera to the SARS-CoV-2 omicron variant are congruent with those found by others with other methods, including viral neutralization and clinical observations. In conclusion, we have investigated antibody affinity and concentration following infection and/or vaccination in the presence of an antigenic drift. We found that the tolerance to the omicron drift was surprisingly robust, whereas the currently approved therapeutic monoclonal antibodies lost much of their affinity. The most plausible scenario is that antibodies are selected in vivo for immunodominant spike domains that are invariant between clades of virus, whereas therapeutic monoclonals were presumably selected in vitro for highest affinity but not for cross-clade protection. Ultimately, our finding, along with others, suggests that the B-cell-mediated immunity, possibly concomitant with a T-cell response, elicited upon infection and/or vaccination might be broad enough to confer a layer of protection in the event of further waves of mutated SARS-CoV-2 variants.
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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