Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19
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SciScore for 10.1101/2022.02.17.22271138: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization Thirty-two samples were randomly selected from each plate to measure the library size distribution. Blinding All SPR experiments were performed twice, and the researchers performing the assay were blinded to sample identity. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Samples were collected on subjects from three groups: 1) those with a prior history of symptomatic SARS-CoV-2 infection (defined as a history positive nasal PCR test and positive Food and Drug Administration (FDA) Emergency Use Authorization (EUA) SARS-CoV-2 antibody test at the time of protocol … SciScore for 10.1101/2022.02.17.22271138: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization Thirty-two samples were randomly selected from each plate to measure the library size distribution. Blinding All SPR experiments were performed twice, and the researchers performing the assay were blinded to sample identity. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Samples were collected on subjects from three groups: 1) those with a prior history of symptomatic SARS-CoV-2 infection (defined as a history positive nasal PCR test and positive Food and Drug Administration (FDA) Emergency Use Authorization (EUA) SARS-CoV-2 antibody test at the time of protocol screening), 2) those with a history of asymptomatic SARS-CoV-2 infection (defined as a positive FDA EUA SARS-CoV-2 antibody test at the time of protocol exam but no history of COVID-like symptoms), and 3) individuals with no history of SARS-CoV-2 infection (defined as a negative FDA EUA SARS-CoV-2 antibody test at the time of the protocol screening). SARS-CoV-2suggested: NoneExperimental Models: Cell Lines Sentences Resources Influenza microneutralization titers: Virus-neutralizing titers of pre- and post-vaccination sera were determined in a microneutralization assay based on the methods of the pandemic influenza reference laboratories of the Centers for Disease Control and Prevention (CDC) using low pathogenicity vaccine viruses and MDCK cells. MDCKsuggested: CLS Cat# 602280/p823_MDCK_(NBL-2, RRID:CVCL_0422)Pseudovirions were produced by co-transfection of Lenti-X 293T cells with psPAX2(gag/pol), 293Tsuggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)The supernatants were harvested at 48h post transfection and filtered through 0.45-µm membranes and titrated using 293T-ACE2 cells (HEK293T cells that express ACE2 protein). HEK293Tsuggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)For the neutralization assay, 50 µL of SARS-CoV-2 S pseudovirions were pre-incubated with an equal volume of varying dilutions of serum at room temperature for 1 h, then virus-antibody mixtures were added to 293T-ACE2 cells in a 96-well plate. 293T-ACE2suggested: NoneRecombinant DNA Sentences Resources SARS-CoV-2 pseudovirus production and neutralization assay3–5: Human codon-optimized cDNA encoding SARS-CoV-2 S glycoprotein (NC_045512) was cloned into eukaryotic cell expression vector pcDNA 3.1 between the BamHI and XhoI sites. pcDNA 3.1suggested: RRID:Addgene_20407)Pseudovirions were produced by co-transfection of Lenti-X 293T cells with psPAX2(gag/pol), psPAX2suggested: RRID:Addgene_12260)Software and Algorithms Sentences Resources Surveys were sent via email to the participants and responses were transferred from the REDCap system to the NIH Clinical Research Information Management System (CRIMSON) system by the study team. REDCapsuggested: (REDCap, RRID:SCR_003445)NIH Clinical Research Information Management Systemsuggested: NoneLymphocyte (T cell, B cell, NK cell) flow cytometry quantification was performed using the BD FACSCanto™ II flow cytometer (BD Biosciences, Franklin Lakes, NJ). BD FACSCanto™suggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Limitations of this study include most study subjects were younger than 65 and thus these findings may not apply to the elderly, an important population of COVID-19 recoverees. Additionally, our findings are largely associative in nature and the study design does not allow the linking of acute response phenotypes to the long-term imprints in the same individuals. Some of the imprints we considered as stable given lack of association with TSD may still be evolving slowly (or could be limited by statistical power for detecting association with TSD). And while there was no clear difference in disease severity or duration between the COVID-19-recovered males and females in our study (and no subjects were hospitalized), it is possible that our sex-specific findings reflect unappreciated clinical factors. It is possible that some of the post-vaccination reversal towards the healthy, pre-vaccination state by day 28 may also in part be due to ongoing disease resolution. However, this is unlikely the case for the vaccine-induced elevation in the expression of the reset genes towards the healthy state because those changes were clearly detectable on day 1 after vaccination and persisted through day 28, especially in females, indicating that this reversal was driven (or at least accelerated) by vaccination and could not be attributed to the “natural” resolution process alone. While it would be informative to further assess our findings in follow up cohorts, given our observation that va...
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04025580 Suspended Systems Analyses of the Immune Response to the Seasonal Infl… Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 43, 45 and 23. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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