PONE-D-24-57722Induction of an early IFN-γ cellular response and high plasma levels of SDF-1α are inversely associated with COVID-19 severity and residence in rural areas in Kenyan patientsPLOS ONE

Dear Dr. Wanjiku,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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We look forward to receiving your revised manuscript.

Kind regards,

Ewurama Dedea Ampadu Owusu, PhD

Academic Editor

PLOS ONE

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Additional Editor Comments:

Authors should pay particular attention to the comments by Reviewer 2 in their revisions.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: I thoroughly enjoyed reading the manuscript. It is well-written, with findings clearly articulated and thoughtfully discussed. Only minor corrections are needed, along with a few adjustments to meet the publication criteria.

1. The abstract exceeds the 300-word limit required by the publication criteria. Please revise it to ensure compliance.

2. A minor grammatical error in the introduction (line 82).

3. According to the publication criteria, the introduction must include a brief statement of the overall aim of the study and a comment on whether the aim was achieved. While the aim is stated, there is no mention of its achievement. Please revise.

4. The study design is robust, with well-defined patient groups and clear cytokine/chemokine measurement methods. However, can you clarify how the missing data was handled in statistical analysis?

5. The experiment was conducted rigorously, with appropriate controls and sample sizes. The conclusion appropriately summarizes the results, emphasizing the association between IFN-gamma response, cytokine levels and COVID-19 severity. However, I suggest you include a discussion on potential confounding variables such as comorbidities. This could strengthen the argument.

6. The discussion is well-structured, but I suggest integrating more comparisons with similar studies outside Sub-Saharan Africa.

7. Figures and tables effectively present the data but should be closely examined for consistency in labeling (example: units, statistical significance markers).

8. References are comprehensive, but a few citations should be updated to include recent studies.

Reviewer #2: Summary:

The study investigates the immunological factors that might explain the lower severity of COVID-19 in Sub-Saharan Africa (SSA) compared to Europe and North America. It focuses on the levels of ex vivo SARS-CoV-2 peptide-specific IFN-γ producing cells and plasma cytokines and chemokines over the first month of COVID-19 diagnosis among Kenyan patients from urban (Nairobi) and rural (Kilifi) areas.

Methods:

• Participants: 188 COVID-19 patients from Nairobi (urban, n = 152) and Kilifi (rural, n = 36) were recruited and monitored longitudinally.

• Assays: IFN-γ secreting cells were enumerated using an ex vivo enzyme-linked immunospot (ELISpot) assay, and levels of 22 plasma cytokines and chemokines were measured using a multiplexed binding assay.

Results:

• IFN-γ Response: Higher frequencies of IFN-γ-secreting cells against SARS-CoV-2 spike peptides were observed on the day of diagnosis among asymptomatic patients compared to those with severe COVID-19.

• Cytokines and Chemokines: Higher concentrations of 17 out of 22 cytokines and chemokines were positively associated with severe disease, particularly IL-8, IL-18, and IL-1ra, while lower concentrations of SDF-1α were associated with severe disease.

• Geographical Differences: Concentrations of 8 and 16 cytokines and chemokines, including IL-18, were higher among Nairobi asymptomatic and mild patients compared to their Kilifi counterparts. Conversely, SDF-1α concentrations were higher in rural Kilifi compared to Nairobi.

Conclusion:

Pro-inflammatory cytokines and chemokines were associated with severe COVID-19, while an early IFN-γ cellular response to overlapping SARS-CoV-2 spike peptides was associated with reduced risk of disease. Living in urban Nairobi was associated with increased levels of pro-inflammatory cytokines/chemokines compared to rural Kilifi.

Loopholes in the Results and Discussion:

1. Sample Size and Recruitment Issues: The study faced difficulties recruiting asymptomatic patients in Nairobi and severe cases in Kilifi, leading to a relatively small sample size. This limitation could affect the generalizability of the findings.

2. Missing Data: Some data are incomplete for certain patients due to missed follow-ups or unavailability of adequate numbers of PBMCs to quantify IFN-γ cellular responses to the full spectrum of peptide pools.

3. Geographical Differences: The study suggests that the immune response to SARS-CoV-2 is less inflammatory among residents of rural areas. However, the differences in cytokine and chemokine levels between urban and rural patients might also be influenced by other factors such as environmental exposures and lifestyle differences.

4. The study does not provide a background on cellular response data against COVID-19 data available in the Kenyan population.

Other comments are in the attached draft.

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Reviewer #1: Yes:  Elizabeth Obeng-Aboagye

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-24-57722.pdf

PONE-D-24-57722R1Induction of an early IFN-γ cellular response and high plasma levels of SDF-1α are inversely associated with COVID-19 severity and residence in rural areas in Kenyan patientsPLOS ONE

Dear Dr. Wanjiku,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

==============================

ACADEMIC EDITOR: 

The revised version submitted by authors has strengthened the manuscript. However, the incorporation of these additional comments by the reviewer can make the manuscript ready for publication in Plos One. Authors should pay attention to the follow up questions/suggestions by the reviewer 2 in the attachment.

==============================

Please submit your revised manuscript by Aug 16 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Ewurama Dedea Ampadu Owusu, PhD

Academic Editor

PLOS ONE

Journal Requirements:

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.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: I thank the author’s for taking time to revise the manuscript. However, I do have some comments for the authors in the attached file.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy .

Reviewer #2: No

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[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment 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. Registration is free. 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 PLOS at figures@plos.org . Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: Reviewer 2 comments.docx

Induction of an early IFN-γ cellular response and high plasma levels of SDF-1α are inversely associated with COVID-19 severity and residence in rural areas in Kenyan patients

PONE-D-24-57722R2

Dear Dr. Wanjiku,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Ewurama Dedea Ampadu Owusu, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Dear Authors,

Responses to reviewer comments are satisfactory and relevant revisions have been effected.

But in line 73, the sentence begins with the same first two words as the sentence immediately following it in line 77 - "However, the...". Authors should endeavor to correct it before publication as it is repetitive and affects the comprehension of the conjunction between the two sentences.

Reviewers' comments: