Competent immune responses to SARS-CoV-2 variants in older adults following mRNA vaccination

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1. 

   Version published to 10.1101/2021.07.22.453287v2 on bioRxiv

   Jan 19, 2022
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   ScreenIT

   Jul 26, 2021

   SciScore for 10.1101/2021.07.22.453287: (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	Following day cells were stimulated in X-VIVO 15 media with 5% male human AB serum containing ~1 nmol of peptide pool corresponding of SARS-CoV-2 Prot S of US-WA (wild-type), Gamma (P.1./B1.1.28) and Delta (B.1.617.2) variants or positive control anti-CD3 mAb CD3-2 from or blank media as negative control.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: Stocks of SARS-CoV-2 were generated as a single passage from received stock vial (USA-WA1/2020 and P.1.) or primary culture (B.1.595) on mycoplasma negative Vero cells (ATCC #CCL-81) at a MOI of 0.005 for 48 h.

   Table 2: Resources

   …

   SciScore for 10.1101/2021.07.22.453287: (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	Following day cells were stimulated in X-VIVO 15 media with 5% male human AB serum containing ~1 nmol of peptide pool corresponding of SARS-CoV-2 Prot S of US-WA (wild-type), Gamma (P.1./B1.1.28) and Delta (B.1.617.2) variants or positive control anti-CD3 mAb CD3-2 from or blank media as negative control.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: Stocks of SARS-CoV-2 were generated as a single passage from received stock vial (USA-WA1/2020 and P.1.) or primary culture (B.1.595) on mycoplasma negative Vero cells (ATCC #CCL-81) at a MOI of 0.005 for 48 h.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   AZ-E484Q, a B.1.595 virus (GISAID: EPI_ISL_765942) was grown from a nasopharyngeal swab on Calu-3 cells for 48 hours.	Calu-3 suggested: None
   Stocks of SARS-CoV-2 were generated as a single passage from received stock vial (USA-WA1/2020 and P.1.) or primary culture (B.1.595) on mycoplasma negative Vero cells (ATCC #CCL-81) at a MOI of 0.005 for 48 h.	Vero suggested: ATCC Cat# CCL-81, RRID:CVCL_0059)
   Software and Algorithms
   Sentences	Resources
   Blood for peripheral blood mononuclear cells (PBMCs) and plasma was collected in BD Vacutainer with sodium heparin.	BD Vacutainer suggested: None
   Area under the curve (AUC) values were calculated using R version 4.0.3 (R Core Team, 2020) and the DescTools package (Signorelli, 2021).	DescTools suggested: None
   Samples were acquired using a Cytek Aurora cytometer (Cytek) and analyzed by FlowJo software (Tree Star).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Statistical analysis: SPSS and Graph Pad Prism were used for statistical analysis.	SPSS suggested: (SPSS, RRID:SCR_002865)

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   The only limitation of ELISpot, as compared to flow cytometry based enumeration, is that total T cell responses are measured without separate quantification of CD4 and CD8 responses. We also analyzed Ag-specific T cell responses to stimulation with Spike protein peptide pools from WA1 versus two variants of concern by ELISpot. Participant PBMC’s were stimulated with 16-mer overlapping peptide pools corresponding to the spike protein of WA1, P.1. (Gamma) and B.1.617.2 (Delta). In accordance with previously published results (Sahin et al., 2020), mRNA vaccines induced a robust T cell response to WA1, an early 2020 virus, which did not differ for Gamma and Delta variants, as evidenced by a 10-fold increase in ELISpots from post-vaccination samples stimulated by S peptide pools compared to unstimulated wells (Figure 4A). Next, we analyzed T cell responses of both groups at different time points. Given that some samples had high responses in the unstimulated wells we subtracted the number of ELISpots from the unstimulated well to calculate the number of Ag-specific ELISpots for each time point. Data from aged mice (Brien et al., 2009; Fulton et al., 2013; Jergović et al., 2019) showed that induction of Ag-specific T cell responses becomes delayed and decreased with age. In our data, there was a slightly lower response in the older cohort at day 7 post first dose with all three variants but it was not statistically significant (Figure 4B). However, after a second (booster) dose bot...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 17, 20 and 21. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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   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.

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

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   Read the original source
3. 

   Version published to 10.1101/2021.07.22.453287v1 on bioRxiv

   Jul 22, 2021