DW-PBJ4-Harsha - Githubissues

Main Research Question?

The intended aim outlined by GeurtsvanKessel was to determine whether T cell neutralization and response efficacy varied across known SARS-CoV-2 variants compared to the wild-type (D614G) variant. The authors observed these changes early (28 days) and late (6 months) post-immunization (Pfizer, Moderna, Astrazeneca, Janssen, NovaVax) to elucidate the conservation or depletion of T cell immunity post-vaccination.

Methods & Data

The illustration for study designs (subfigures A) are great additions to the paper to demonstrate the timeline of the vaccination/collection stages.

Tabular layouts for participant characteristics (Tables 1 & 2) for vaccinations and boosters, respectively, do not need to be included as main diagrams. The only possible data measurement that could be shown are the vaccination intervals, as those demonstrate a independent variable factor that may contribute to the related results.

I am finding difficulty justifying the relevancy of the memory subset flow cytometry plot in figure 3B (bottom left). How does the distinction between these memory subsets support of consolidate the flow cytometry T cell figures under DMSO and Spike stimulation conditions?

Authors' interpretation

I see no faults in the author's outlined approach and their following interpretations.

Enhancement or next experiment?

Dendritic cell and other APC activity? The non-significance of T-cell response/neutralization activity could be in part to an attenuated APC (MHC I and II) activity due to SARS-CoV-2.

For the purpose of the paper, the controls were substantiated. However, I recommend comparing T-cell results in SARS-CoV-2 to other viruses, say, of the same type (coronaviruses) or other common viruses (rhinovirus, influenza, etc). This comparison would demonstrate severity differences across multiple viruses.

Have the authors considered variant-specific mutations affecting T-cell response? Another paper (Gaebler, 2022) determined that spike protein mutations correlates to affinity matured humoral antibodies. Could there be a similar maturation amongst T cells (Th1 and Th2) in their recognition of the spike protein?

confusion? Terms you don't understand?

Why bother looking at T[em] and T[emra] cells in flow cytometry? I am lost on that part.

For the ChAdOx-1 S (Astrazeneca) vaccine, I do not understand why the collection at day 28 appears after the vaccination day 56 (Fig 1A); this is chronologically out of order and breaks the flow of the diagram.

Have your own opinions or critiques?

I believe including a placebo vaccination would have benefited the controls of the experiment. Although the ethicality of this may be ambiguous, it could address how other agents antagonistic to SARS-CoV-2 could affect viral T cell responses. Such examples could be those patients who took the Influenza vaccination (or other vaccination), but not the Covid vaccination.

I hereby confirm that I have:

[x] I am still working on the worksheet
[x] I have finished the worksheet
[x] I have gone through the papers
[x] Check your peer if they have similar ideas. If it is, plz add their issue number to your comments.

Overall, this is a very nicely written worksheet that is very closed to a formal peer review! Great job!

The illustration for study designs (subfigures A) are great additions to the paper to demonstrate the timeline of the vaccination/collection stages.

Yes, this is one of the major strengths of this paper. It also demonstrates that giving reviewer easier life will help author get their papers published easier.

Tabular layouts for participant characteristics (Tables 1 & 2) for vaccinations and boosters, respectively, do not need to be included as main diagrams.

I think this is required because human T cell immunity is significantly influenced by age/gender. For example, CD4/CD8 T cells are proportionally decreased along ageing. Thus the relatively closed age/gender proportion should be explicit in the main text. Also see: https://www.science.org/doi/epdf/10.1126/sciimmunol.abj1750. Table 1.

I am finding difficulty justifying the relevancy of the memory subset flow cytometry plot in figure 3B (bottom left). How does the distinction between these memory subsets support of consolidate the flow cytometry T cell figures under DMSO and Spike stimulation conditions?

Excellent question. I have no clues as well. And their previous paper (citation 8) also did not include this memory cell panel. I also cannot find any relevant mentioning in the main text. So I will agree to remove it.

Dendritic cell and other APC activity? The non-significance of T-cell response/neutralization activity could be in part to an attenuated APC (MHC I and II) activity due to SARS-CoV-2.

This will be out of the scope but you are in the right direction. But there is one critical aspect that the peptide pools did not consider whether the mutations impact the processing of antigens in APCs. As such in vitro APC-T cell assay to allow APC naturally processing of natural form of S spike proteins and present antigens to CD4/CD8 T cells will be an ideal complementary assay.

This comparison would demonstrate severity differences across multiple viruses.

Good ideas. This is really thought for higher systematic level of understanding human Vaccinology. However, for this paper, it will be out of scope. But good that you mention it.

Could there be a similar maturation amongst T cells (Th1 and Th2) in their recognition of the spike protein?

T cells were selected in thymus but after they egress from thymus, they do not under somatic mutation to further "shuffle" their TCRs. Thus, there has no somatic mutation concept for T cell biology.