Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals

Article activity feed

1. Version published to 10.1016/j.xcrm.2021.100355

   Jul 1, 2021
2. 

   ScreenIT

   Mar 15, 2021

   SciScore for 10.1101/2021.02.27.433180: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   : 96-well FluoroSpot plates were coated with anti-cytokine antibodies for IFNγ and IL-5 (mAbs 1-D1K and TRFK5, respectively; Mabtech, Stockholm, Sweden) at a concentration of 10μg/mL.	anti-cytokine suggested: None IL-5 suggested: None TRFK5 suggested: None
   After a 2-hour incubation, plates were washed again with PBS/0.05% Tween20 and incubated for 1 hour with fluorophore-conjugated antibodies (Anti-BAM-490 and Anti-WASP-640).	Anti-BAM-490 suggested: None Anti-WASP-640 suggested: None
   …

   SciScore for 10.1101/2021.02.27.433180: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   : 96-well FluoroSpot plates were coated with anti-cytokine antibodies for IFNγ and IL-5 (mAbs 1-D1K and TRFK5, respectively; Mabtech, Stockholm, Sweden) at a concentration of 10μg/mL.	anti-cytokine suggested: None IL-5 suggested: None TRFK5 suggested: None
   After a 2-hour incubation, plates were washed again with PBS/0.05% Tween20 and incubated for 1 hour with fluorophore-conjugated antibodies (Anti-BAM-490 and Anti-WASP-640).	Anti-BAM-490 suggested: None Anti-WASP-640 suggested: None
   Software and Algorithms
   Sentences	Resources
   All samples were acquired on a ZE5 5-laser or 4-laser cell analyzer (Bio-rad laboratories) and analyzed with FlowJo software (Tree Star).	FlowJo suggested: (FlowJo, RRID:SCR_008520)

   ---

   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: We detected the following sentences addressing limitations in the study:

   Limitations and future directions: The present study did not assess decreases in antibody reactivity, as several other studies have already investigated this matter (Edara et al., 2021; Greaney et al., 2021; Muik et al., 2021; Shen et al., 2021; Skelly et al., 2020; Stamatatos et al., 2021; Supasa et al., 2021; Wang et al., 2021a; Wang et al., 2021b; Wibmer et al., 2021; Wu et al., 2021). Further, our studies utilized overlapping peptide pools, and as such we could not exclude that some of the mutations might involve alterations in terms of antigen processing for either class I or class II, which would be undetected by using pools of “preprocessed” peptides. The number of donors studied was also limited, although variability in T cell reactivity suggestive of large variant-associated effects were not observed. While we have no reason to suspect that substantial differences might exist between the epitope specificity of responses elicited by different vaccines, our study did not address this point. Our study was designed to test for differences in overall response to the different variants and was not powered or designed to investigate differences between the mRNA vaccines. Furthermore, in our study we tested samples from convalescent donors infected before October 2020; thus, it is unlikely that any of the donors would have been infected by any of the variants, as this date precedes their diffusion to appreciable degree in the US and California. Finally, we have only investig...

   ---

   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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2021.02.27.433180 on bioRxiv

   Mar 1, 2021