Dear Dr Laguna,

Thank you very much for submitting your manuscript "Longitudinal dynamics of SARS-CoV-2-specific cellular and humoral immunity after natural infection or BNT162b2 vaccination" for consideration at PLOS Pathogens. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

Dear Dr. Laguna,

Thank you for submitting your manuscript. The reviewers appreciated your study and the need to validate findings in different cohorts. However, they had a major concern about the lack of novelty. If you are able to address this concern, perhaps by including additional data (such as the virologic parameters of infected patients, as suggested by Reviewer 1), or new immunologic results, we would be happy to reconsider this manuscript for publication.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the review comments and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Sujan Shresta

Associate Editor

PLOS Pathogens

Sonja Best

Section Editor

PLOS Pathogens

Kasturi Haldar

Editor-in-Chief

PLOS Pathogens

​orcid.org/0000-0001-5065-158X

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

***********************

Dear Dr. Laguna,

Thank you for submitting your manuscript. The reviewers appreciated your study and the need to validate findings in different cohorts. However, they had a major concern about the lack of novelty. If you are able to address this concern, perhaps by including additional data (such as the virologic parameters of infected patients, as suggested by Reviewer 1), or new immunologic results, we would be happy to reconsider this manuscript for publication.

Reviewer's Responses to Questions

Part I - Summary

Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship.

Reviewer #1: This manuscript describes the kinetic of the development of humoral and cellular immune response in a cohort of 88 patients with mild, moderate and severe COVID-19 immediately after symptoms onset until recovery or fatal outcome. They also analyzed the SARS-CoV-2 specific immune response in a large group of convalescents and n some vaccinated individuals.

The work provides evidences that a development of a coordinated functional T and B cell response is associated with mild disease. Even though these findings are not novel ( see ref 15 and 16) , I agree with the authors that previous work was done in limited number of patients and as such this work constitutes an important confirmation of such data.

Reviewer #2: Almendro-Vázquez and colleagues investigated longitudinal kinetics of SARS-CoV-2-specific humoral and cellular immunity after either natural infection or BNT162b2 vaccination.

The authors analyzed S1-, M- and N-specific IFN-γ and IL-2 T cell immune responses and anti-S total and neutralizing antibodies in mild, moderate or severe acute COVID-19 patients.

They compared immune responses in COVID-19 patients with mild and severe disease. They also found a robust Th1-driven immune response in uninfected blood donors following BNT162b2-vacination. While understanding immune responses in COVID-19 is of a great importance, the novelty aspects of this study are unclear.

Specific comments:

The authors should specify upfront the novel aspect of their study in context of the literature.

Abstract: “Description of the immune response elicited by real-world anti-SARS-CoV-2 vaccination is still lacking”: there are numerous publications on immune responses following COVID-19 vaccine. This sentence should be rephrased.

Statistics on the graphs: there is no need to show 'ns' for not significant differences as these subtract from clear visualisation of significant differences.

Representative T cell Fluorospots appear to be too dark thus lack clarity.

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Part II – Major Issues: Key Experiments Required for Acceptance

Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions.

Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject".

Reviewer #1: I have very little to say about the methods. Overall the data support the conclusions made.

A) However a weakness of the work is the lack of any virological quantification. It would be nice to add some virological parameters present in the studied patients. Quantity of virus present at the onset or a longitudinal analysis the persistence of SARS-CoV-2 +PCR over time in the different cohorts or in selected individuals might be a nice addition.

B) Figures quality is very poor. The impression i that the authors displayed all the data that they have but this doesn't increase the clarity of the message . The display of the results of Elispot are of very poor quality and they don't deliver any message, they are blacks dots identical in all the figures. It will be also nice to show some longitudinal data of selected patients in the different cohorts and make a direct comparison between mild, moderate and severe . The data are shown now as a sort of cross-sectional analysis an it is not clear whether some patients were analyzed sequentially. It will be more indicative and clear to show some of individual representative patients. Furthermore, there are 8 fatalities in their acute severe cohort according to their table, but they did not highlight them in their graphs. I think they should be highlighted, as it will be interesting to know if their immunological response is any difference from the other severe patients

Reviewer #2: (No Response)

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Part III – Minor Issues: Editorial and Data Presentation Modifications

Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity.

Reviewer #1: The T cell response to Spike was analysed only using peptides covering S1 regions. This should be discuss as a potential limitation of the analysis.

The authors should acknowledge in the results and not only in the introduction, the fact that their data confirmed previous works, I don't think the authors can state that" This is the first study analyzing the SARS-CoV-2-specific cellular and humoral immune response in patients upon ER arrival" . This was also done in ref 15-16

Reviewer #2: (No Response)

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Reviewer #1: Yes: Antonio Bertoletti

Reviewer #2: No

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

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Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example see here on PLOS Biology: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Dear Dr Laguna,

Thank you very much for submitting your manuscript "Longitudinal dynamics of SARS-CoV-2-specific cellular and humoral immunity after natural infection or BNT162b2 vaccination" for consideration at PLOS Pathogens. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

Thank you for responding to the reviewers’ comments by adding new data and highlighting how your study is different from published ones. However, the discussion of the literature could be improved. In particular, several groups have now examined the durability of vaccine-induced immune responses beyond 3 months.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Sujan Shresta

Associate Editor

PLOS Pathogens

Sonja Best

Section Editor

PLOS Pathogens

Kasturi Haldar

Editor-in-Chief

PLOS Pathogens

​orcid.org/0000-0001-5065-158X

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

***********************

Thank you for responding to the reviewers’ comments by adding new data and highlighting how your study is different from published ones. However, the discussion of the literature could be improved. In particular, several groups have now examined the durability of vaccine-induced immune responses beyond 3 months.

Reviewer Comments (if any, and for reference):

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

References:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Dear Dr Laguna,

We are pleased to inform you that your manuscript 'Longitudinal dynamics of SARS-CoV-2-specific cellular and humoral immunity after natural infection or BNT162b2 vaccination' has been provisionally accepted for publication in PLOS Pathogens.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Pathogens.

Best regards,

Sujan Shresta

Associate Editor

PLOS Pathogens

Sonja Best

Section Editor

PLOS Pathogens

Kasturi Haldar

Editor-in-Chief

PLOS Pathogens

​orcid.org/0000-0001-5065-158X

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

***********************************************************

Reviewer Comments (if any, and for reference):