Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis

Jackson S. Musuuza; Lauren Watson; Vishala Parmasad; Nathan Putman-Buehler; Leslie Christensen; Nasia Safdar

doi:10.1371/journal.pone.0251170

Peer Review History

Original SubmissionOctober 22, 2020
22 Jan 2021 Decision Letter - Victor C Huber, Editor PONE-D-20-33286 Prevalence and outcomes of co-infection and super-infection with SARS-CoV-2 and other pathogens: A Systematic Review and Meta-analysis PLOS ONE Dear Dr. Musuuza, 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. During the revision process, please address the comments related to discussion of the findings in the context of the recent understanding of co- and super-infections with SARS-CoV-2. Please submit your revised manuscript by Mar 08 2021 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. 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Please upload copies of the completed PRISMA checklist as Supporting Information with a file name “PRISMA checklist”. [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: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know 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: Yes 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 article by Musuuza et al. investigates the prevalence and outcomes of co/ super-infection with SARS-CoV-2 as A Systematic Review and Meta-analysis. It is an interesting study and definitely important to bring attention to other infections among COVID-19 patients. Major comments -Due to the importance of the disease, the evaluation period of the articles is very short and many interesting and newly published articles have been ignored. For example (https://pubmed.ncbi.nlm.nih.gov/32873235/, https://pubmed.ncbi.nlm.nih.gov/32613024/ , https://pubmed.ncbi.nlm.nih.gov/32603803/ , etc). It is suggested that the author increase the time period for reviewing articles and add newer studies to the MS. - No data on the use of antibiotics in SARS-CoV-2 patients were found in this study. It is recommended to add some data about the treatment protocols used in patients. Discussion The results are not well discussed, especially the role of co/super infections in mortality of COVID patients. So, it needs to be improved. Conclusion The sentence " Our results have ………. virus season in the fall." cannot be concluded from this study. Major comment Method Page 4, Line 83 - change "Covid" to "COVID". Result In Table 2, change "Fungus" to "Fungi". Reviewer #2: This is well drafted manuscript on a very relevant question. Authors have done adequate work although due to dynamic nature of the ongoing pandemic the findings may vary in near future and further updates on this issue will be useful. ****** 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. https://doi.org/10.1371/journal.pone.0251170.r001
Revision 1
14 Apr 2021 Author Response April 14, 2021 RE: PONE-D-20-33286: “Prevalence and outcomes of co-infection and super-infection with SARS-CoV-2 and other pathogens: A Systematic Review and Meta-analysis.” Dear Dr. Huber, We thank you and the reviewers for the careful review and thoughtful feedback on our manuscript, “Prevalence and outcomes of co-infection and super-infection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis.” We have revised the manuscript according to the comments and believe that it is substantially improved with the incorporation of these edits. Below, we provide a point-by-point reply to the reviewers’ comments. We have included a marked copy of the revised manuscript that highlights changes, as well as a clean version. We have also ensured that our manuscript meets style requirements of PLOS ONE. Thank you for your consideration of our revised manuscript. EDITOR COMMENTS Comment 1: During the revision process, please address the comments related to discussion of the findings in the context of the recent understanding of co- and super-infections with SARS-CoV-2. Authors’ reply: We have revised the Discussion to place our findings in the context of the recent understanding of co- and super-infections with SARS-CoV-2. Comment 2: We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. In your revised cover letter, please address the following prompts: a) If there are set ethical or legal restrictions on sharing a de-identified data, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Please see http://www.bmj.com/content/340/bmj.c181.long for guidelines on how to de-identify and prepare clinical data for publication. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Authors’ reply: We have uploaded an anonymized dataset as one of the supporting information files. There are no ethical or legal restrictions on sharing our data. Comment 3: We note that this manuscript is a systematic review or meta-analysis; our author guidelines therefore require that you use PRISMA guidance to help improve reporting quality of this type of study. Please upload copies of the completed PRISMA checklist as Supporting Information with a file name “PRISMA checklist”. Authors’ reply: We have included a completed PRISMA checklist as a supporting information file (S3 File). REVIEWER #1 COMMENTS The article by Musuuza et al. investigates the prevalence and outcomes of co/ super-infection with SARS-CoV-2 as A Systematic Review and Meta-analysis. It is an interesting study and definitely important to bring attention to other infections among COVID-19 patients. Major comments Comment #1: Due to the importance of the disease, the evaluation period of the articles is very short and many interesting and newly published articles have been ignored. For example (https://pubmed.ncbi.nlm.nih.gov/32873235/, https://pubmed.ncbi.nlm.nih.gov/32613024/ , https://pubmed.ncbi.nlm.nih.gov/32603803/ , etc.). It is suggested that the author increase the time period for reviewing articles and add newer studies to the MS. Authors’ reply: As suggested, we have expanded the timeframe for the search to include eligible articles published since our last search date (June 11, 2020) through February 8, 2021. Comment #2: No data on the use of antibiotics in SARS-CoV-2 patients were found in this study. It is recommended to add some data about the treatment protocols used in patients. Authors’ reply: Seventy percent (83/118) of the studies reported data on antibiotic use. Of these, antibiotics were administered in 98% (81/83) of the studies. We have included this information in the revision. Discussion Comment #3: The results are not well discussed, especially the role of co/super-infections in mortality of COVID patients. So, it needs to be improved. Authors’ reply: We have revised the Discussion overall and included a paragraph on the role of co/super-infections in mortality of SARS-COV-2 infected patients. We believe the discussion is much improved with this revision. Conclusion Comment #4: The sentence " Our results have ………. virus season in the fall." cannot be concluded from this study. Authors’ reply: We agree with the reviewer and have removed this sentence and revised the Conclusion accordingly. Methods Comment #5: Page 4, Line 83 - change "Covid" to "COVID". Authors’ reply: We thank the reviewer for this comment, and we would like to clarify that the term “Covid” was used here as a search term since there some studies have used it in their reports. Throughout the paper, we use “COVID-19.” Results Comment #6: In Table 2, change "Fungus" to "Fungi". Authors’ reply: We have made this correction per the reviewer’s suggestion. REVIEWER #2 COMMENTS Reviewer #2: This is well drafted manuscript on a very relevant question. Authors have done adequate work although due to dynamic nature of the ongoing pandemic the findings may vary in near future and further updates on this issue will be useful. Authors’ reply: We thank the reviewer for this comment. Although, we have extended our article search dates in this revision, we agree that further updates of this work will be needed periodically. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0251170.r002
22 Apr 2021 Decision Letter - Victor C Huber, Editor Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis PONE-D-20-33286R1 Dear Dr. Musuuza, 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, Victor C Huber Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0251170.r003
Formally Accepted
28 Apr 2021 Acceptance Letter - Victor C Huber, Editor PONE-D-20-33286R1 Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis Dear Dr. Safdar: 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. Victor C Huber Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0251170.r004

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