The scientific chaos phase of the great pandemic: A longitudinal analysis and systematic review of the first surge of clinical research concerning COVID-19

Till Adami; Markus Ries

doi:10.1371/journal.pone.0289193

Peer Review History

Original SubmissionJuly 12, 2023
18 Sep 2023 Decision Letter - Ashraful Hoque, Editor PONE-D-23-21783The scientific chaos phase of the Great Pandemic: A longitudinal analysis and systematic review of the first surge of clinical research concerning COVID-19PLOS ONE Dear Dr. Adami, 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. Please submit your revised manuscript by Nov 02 2023 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. 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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. Thank you for stating the following in the Competing Interests section: “Markus Ries is a guest editor of the call for papers “Prediction and Mitigation of Natural Hazards”.” Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests). If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf. [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: Yes Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know ****** 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: Dear Authors, this is an interesting manuscript, but the Tables 1-6 are cutoff and thus not accessible/readable in the PDF file that I have received for review. Please reformat these items for further review. Reviewer #2: This manuscript has great potential to provide some insight into research patterns during the COVID-19 pandemic. The authors explained their methods in great detail, demonstrating the great care they took in identifying both intervention and observational studies. The authors demonstrated some very important research trends in this study and I think that the comparison to research in other pandemics and high-risk infectious diseases (eg, HIV) was important. I think the authors provide some sound advice to researchers and their research suggeests that there has been a great deal of "spinning wheels" as well as some poor quality research churned out, so I like that this paper takes the perspective that we need some caution with COVID-19 research. A few thoughts for improvement - one thing that was difficult for me was the description of the methods. The methods were very detailed, but a bit long. Are there ways to streamline this? Can the search terms be put into a table, perhaps? That would help the readability of the manuscript and make it easier to follow. I found myself re-reading the methods again and again to be sure I understood what was done. So a bit of streamline could be helpful here. I had tremendous difficulty with the tables, and honestly, it was a barrier to my providing my review. It was so hard to provide feedback when I couldn't read the full tables. Details are here: In the uploaded manuscript, table 1 was cut off after DEU column and I was not able to fully assess this table. In the uploaded manuscript, table 2 was cut off after the "other" column, so I was not able to fully assess this table. In the uploaded manuscript, table 3 as cutt off after the "other" column, so I was not fully able to assess this table. In the uploaded manuscript, table 4 was cut off after the EU column, so I was not able to fully assess this table. In the uploaded manuscript, table 5 was cut off after the EU-CTR column, so I was not fully able to assess this table. In the uploaded manuscript, table 6 was cut off after the "sequential" column; the column after that starts with the letter N but I could not see any more of this table and therefore I was not able to fully assess it. I think the issue is that once the Word (or whatever you used to write the manuscript) was converted to a PDF, the formatting of the tables was thrown off and everything was cut off. So that was very hard for me to give feedback on. I am uploading the PDF so you can see how they are cut off. For the graphs by country, is there any way to have one giant graph of all of the countries together, with different colors representing them? There are just so many tables and a lot to look at. A unified table with the countries together could be instuctive and interesting for comparison. I hope this is helpful and many apologies for my delayed review. ****** 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. Attachments Attachment Submitted filename: PONE-D-23-21783_reviewer.pdf Attachment Submitted filename: PONE-D-23-21783-tables cut off.pdf https://doi.org/10.1371/journal.pone.0289193.r001
Revision 1
27 Oct 2023 Author Response Journal requirements Comment 1: Thank you for stating the following in the Competing Interests section: “Markus Ries is a guest editor of the call for papers “Prediction and Mitigation of Natural Hazards”.” Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests). If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf. Answer: We included the updated competing interest statement in the cover letter. Reviewer #1 Comment 1: Dear Authors, this is an interesting manuscript, but the Tables 1-6 are cutoff and thus not accessible/readable in the PDF file that I have received for review. Please reformat these items for further review. Answer: In our initial submission we strictly complied with the submission guidelines, which state that tables should not be resized and shaped to fit the margins of the manuscript page. Tables that run of those margins can be seen using the “Draft View” of Microsoft Word. Unfortunately, it seems the reviewers have received an automatically created PDF version instead of the Microsoft Word file of the manuscript. We have immediately contacted the PLOS ONE staff team directly, asking for a technical resolution, but unfortunately have not received any answer or solution for this issue so far. To quickly facilitate your important review, we have adjusted all tables to fit the margins of the manuscript page. However, the tables now look very squashed and not as we would like to see in a published version. Reviewer #2 Comment 1: This manuscript has great potential to provide some insight into research patterns during the COVID-19 pandemic. The authors explained their methods in great detail, demonstrating the great care they took in identifying both intervention and observational studies. The authors demonstrated some very important research trends in this study and I think that the comparison to research in other pandemics and high-risk infectious diseases (eg, HIV) was important. I think the authors provide some sound advice to researchers and their research suggests that there has been a great deal of "spinning wheels" as well as some poor quality research churned out, so I like that this paper takes the perspective that we need some caution with COVID-19 research. Answer: We would like to express our gratitude for this comment and are extremely pleased for this encouraging statement. We could not agree more. Comment 2: A few thoughts for improvement - one thing that was difficult for me was the description of the methods. The methods were very detailed, but a bit long. Are there ways to streamline this? Can the search terms be put into a table, perhaps? That would help the readability of the manuscript and make it easier to follow. I found myself re-reading the methods again and again to be sure I understood what was done. So a bit of streamline could be helpful here. Answer: Thank you for this important comment. We totally agree with the reviewer and changed materials and methods to streamline this part. We changed the column of table 1 from “instruments” to “Data sources” and added a new column “variables”. All important information about which data was used on which objective can now be seen in one table. We also added an additional supporting file (S2) with the 22 items which were downloaded from the WHO in the original data set to prevent unnecessary listing of items. We feel that maintaining the reproducibility is very important, which is why we refrained from further streamlining of the methods. Comment 3: I had tremendous difficulty with the tables, and honestly, it was a barrier to my providing my review. It was so hard to provide feedback when I couldn't read the full tables. Details are here: In the uploaded manuscript, table 1 was cut off after DEU column and I was not able to fully assess this table. In the uploaded manuscript, table 2 was cut off after the "other" column, so I was not able to fully assess this table. In the uploaded manuscript, table 3 as cutt off after the "other" column, so I was not fully able to assess this table. In the uploaded manuscript, table 4 was cut off after the EU column, so I was not able to fully assess this table. In the uploaded manuscript, table 5 was cut off after the EU-CTR column, so I was not fully able to assess this table. In the uploaded manuscript, table 6 was cut off after the "sequential" column; the column after that starts with the letter N but I could not see any more of this table and therefore I was not able to fully assess it. I think the issue is that once the Word (or whatever you used to write the manuscript) was converted to a PDF, the formatting of the tables was thrown off and everything was cut off. So that was very hard for me to give feedback on. I am uploading the PDF so you can see how they are cut off. Answer: Please see our answer to Reviewer #1, comment 1. We altered the tables and they should now appear fully within the margins of the page. In addition, we are in contact with the PLOS ONE staff to identify the best possible technical solution for this technical conversion issue. Comment 4: For the graphs by country, is there any way to have one giant graph of all of the countries together, with different colors representing them? There are just so many tables and a lot to look at. A unified table with the countries together could be instructive and interesting for comparison. Answer: Thank you again for this important and helpful critique. We agree with the reviewer and have created one giant graph. Giving each country a different colour would have resulted in a convoluting 20 different colours. As an alternative we decided to work with two colours instead, blue representing the cumulative cases of COVID-19 and orange representing the cumulative trials. As the main message of this graph is to highlight the differences in cases and trial evolution between China and the rest of the world, we highlighted the Chinese graphs and dashed all other graphs. We are convinced that the new graph allows a much better comparison than the previous graphs. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0289193.r002
17 Nov 2023 Decision Letter - Ashraful Hoque, Editor The scientific chaos phase of the Great Pandemic: A longitudinal analysis and systematic review of the first surge of clinical research concerning COVID-19 PONE-D-23-21783R1 Dear Dr. Adami, 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, Ashraful Hoque, MD PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0289193.r003
Formally Accepted
22 Nov 2023 Acceptance Letter - Ashraful Hoque, Editor PONE-D-23-21783R1 The scientific chaos phase of the Great Pandemic: A longitudinal analysis and systematic review of the first surge of clinical research concerning COVID-19 Dear Dr. Adami: 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 customercare@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. Ashraful Hoque Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0289193.r004

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