Peer Review History

Original SubmissionMay 28, 2022
Decision Letter - Chiara Lazzeri, Editor

PONE-D-22-15286Severe COVID-19 with persistent respiratory failure- A retrospective cohort study in a tertiary centre in Malaysia.PLOS ONE

Dear Dr. Sia,

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.

We suggest to focus the discussion section on the novelty of the present investigation. Results should not be repeated in the Discussion, but evidence on this topic should be cited. The reason(s) why corticosteroids may or may have not been efficaceous shoudl be better explained. 

Please submit your revised manuscript by Sep 17 2022 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,

Chiara Lazzeri

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf  and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability.

Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized.

Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access.

We will update your Data Availability statement to reflect the information you provide in your cover letter.

3. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well.

[Note: HTML markup is below. Please do not edit.]

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: Partly

Reviewer #2: Yes

**********

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

Reviewer #1: No

Reviewer #2: Yes

**********

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: No

Reviewer #2: Yes

**********

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

**********

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: The present paper reported the retrospective study of severe COVID-19 patients who were admitted to a single tertiary centre from 1 January 2021 till 30 June 2021. Further, the study mainly focused on the persistent respiratory failure (PRF).

Among the patients who came for follow up all were in higher age group (mean 61.5+12.6). Of these patients 56.1% had hypertension followed by diabetes mellitus (47.6%), obesity (30.5%), CVD (14.4%), CKD (5.9%). The authors didn’t try to find any relation of these co-morbidities with the PRF and prolonged treatment of oral corticosteroid.

In addition, the authors have accepted in the study that they were unable to conclude that the use of oral corticosteroid maintenance has its beneficial effect in preventing the inflammatory sequelae, or if supportive care alone with oxygen support is sufficient to help in the process of patient’s recovery.

In conclusion this paper is not giving any conclusive findings for the usage corticosteroid for long term to the patients with severe COVID-19.

Reviewer #2: Very nice descriptive case series describing duration of organizing pneumonia in COVID19 survivors in a Malaysian hospital showing prolonged time to recovery, prolonged use of corticosteroids, and some TB reactivation and secondary infection.

**********

6. 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 #1: No

Reviewer #2: No

**********

[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.

Revision 1

Editor:

We thank you for the suggestion. We have made the changes to focus more on the novelty of findings by elaborating more on OP and the reasons of corticosteroid may or may not help in COVID-19 patients with PRF with two additional references [18,19] We also discussed more on the likely harmful effect of corticosteroid with opportunistic infection which has been reported in the literature. Apart from this, we have removed the repetition of result such as number of PRF, patients on prolonged corticosteroid with prednisolone and follow up outcome from the first paragraph of discussion.

We have changed the reference brackets to square brackets to meet the requirements.

Knowing the importance of minimal data set to be accessible to all the readers, we have uploaded the full dataset for the study population in Supporting Information file with identities being anonymised.

We have also added University Malaya Medical Centre ethics committee approval statement in method section.

Reviewer 1:

We truly appreciate the comment which has stimulated more analysis with some new findings. We have included the bivariate analysis between patient PRF with or without a prolonged treatment of oral corticosteroid and noted that there were no statistically significant differences in age, gender, ethnicity, comorbidities, laboratory result upon admission and inpatient complications between the two different groups. It was noted that prednisolone was frequently prescribed in patients with OP and DAD radiological changes, higher CT severity score, high requirement of oxygen, given pulse steroid or methylprednisolone, extended duration corticosteroid during acute treatment, longer hospital stays and given short term oxygen therapy upon discharge, There was no statistically significant of radiological improvement between these groups upon outpatient follow up.

We agree that retrospective design is difficult to conclude the benefit of corticosteroid in some group of patients. Our study was to show OP may be the cause of PRF in some patients and hopefully it can provide a framework for future study to explore the benefit of prolonged corticosteroid in certain group of patients as being shown in some case series and observational study. Prospective study is required to investigate any benefit of prolonged steroid in patients with PRF and OP changes.

Reviewer 2:

We thank the acknowledgment from the reviewer.

Overall, we have incorporated all the suggestions into the revision. Thanks for the help.

Decision Letter - Chiara Lazzeri, Editor

Severe COVID-19 with persistent respiratory failure- A retrospective cohort study in a tertiary centre in Malaysia.

PONE-D-22-15286R1

Dear Dr. Sia,

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.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Chiara Lazzeri

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Formally Accepted
Acceptance Letter - Chiara Lazzeri, Editor

PONE-D-22-15286R1

Severe COVID-19 with persistent respiratory failure - A retrospective cohort study in a tertiary centre in Malaysia.

Dear Dr. Sia:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Chiara Lazzeri

Academic Editor

PLOS ONE

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .