A novel immunofluorescent test system for SARS-CoV-2 detection in infected cells

Alexandra Rak; Victoria Matyushenko; Polina Prokopenko; Arina Kostromitina; Dmitry Polyakov; Alexey Sokolov; Larisa Rudenko; Irina Isakova-Sivak

doi:10.1371/journal.pone.0304534

Peer Review History

Original SubmissionFebruary 26, 2024
27 Mar 2024 Decision Letter - Boyan Grigorov, Editor PONE-D-24-07586A novel immunofluorescent test system for SARS-CoV-2 detection in infected cellsPLOS ONE Dear Dr. Rak, 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. As suggested by the reviewer, you need to improve the figures and to extend the number of participants in the study. Please submit your revised manuscript by May 11 2024 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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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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. 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Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: 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: This publication proposes the development of a new analytical tool to detect SARS-CoV-2 by a two-component test system with high sensitivity, a reduced number of analytical steps and low cost. The manuscript is well written and understandable. # minor recomendations: The population of vaccinated candidates could be extended to people vaccinated with other vaccines as Astra Zeneca, BioNtech or Moderna. L100: "Thirty serum samples were collected during the period from 2 December 2020 to 12 December100 2023 from five subjects fully vaccinated with Sputnik V and twenty-three COVID-19 convalescents101 aged 31 to 84 years, who participated in the study of humoral and T-cell responses to SARS-CoV-2." For statistical reasons, the number of patients should be greater to validate the study. Figure 1 could be improved with particular annotations on Westerblot (figure1C,D,E) for ease of reading. Figure2 : the letters and numbers are not sufficiently legible on the tables (modification of size of letters for example). An explanation on negative and positive controls is to be added (in the text or on figures). ****** 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. 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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.0304534.r001
Revision 1
9 May 2024 Author Response Thank you for consideration of our manuscript entitled "A novel immunofluorescent test system for SARS-CoV-2 detection in infected cells”. We appreciate the time and effort dedicated by the reviewer to provide insightful feedback on ways to strengthen our paper. Thus, it is with great pleasure that we resubmit for further consideration our article containing the changes that reflect the suggestions provided. We hope that our edits and responses which are provided below satisfactorily address all the issues and concerns the reviewer has noted. To facilitate your review of our revisions, the following is a point-by-point response to the referee’s questions and comments. Comments from Referee: Reviewer #1: This publication proposes the development of a new analytical tool to detect SARS-CoV-2 by a two-component test system with high sensitivity, a reduced number of analytical steps and low cost. The manuscript is well written and understandable. Authors’ response: Thank you very much for a such positive feedback. # minor recomendations: The population of vaccinated candidates could be extended to people vaccinated with other vaccines as Astra Zeneca, BioNtech or Moderna. L100: "Thirty serum samples were collected during the period from 2 December 2020 to 12 December 2023 from five subjects fully vaccinated with Sputnik V and twenty-three COVID-19 convalescents aged 31 to 84 years, who participated in the study of humoral and T-cell responses to SARS-CoV-2." For statistical reasons, the number of patients should be greater to validate the study. Authors’ response: We thank the reviewer for this important note. We agree with the reviewer regarding the comment about the small sample size of the subjects. However, due to the very limited availability of imported COVID-19 vaccines in our country, we were unable to add serum samples from such vaccinated individuals to the screening. Therefore, we conducted additional studies of neutralizing activity of sera from individuals vaccinated with Sputnik V vaccine (35 samples) and from individuals who had recovered from COVID-19 caused by SARS-CoV-2 (B.1) (36 patients). New results were also obtained side-by-side using the two test systems and a correlation was found for the calculated IC50 values as well as for the previously screened samples. Given these results, the expanded experimental sample included serum samples from 59 COVID-19 convalescents and 40 vaccinated individuals. Figure 1 could be improved with particular annotations on Westerblot (figure1C,D,E) for ease of reading. Authors’ response: We thank the reviewer for noting this. The figure was corrected accordingly. To better illustrate the agreement between the theoretical and observed mass of the streptavidin-eGFP protein, we added SDS-PAGE with a protein molecular weight marker to Figure 1 (panel C). In addition, in Figure 1, D ,E, F, bands corresponding to the active form of EGFP-SA and incorrectly folded aggregates formed during inadequate storage were indicated. Figure2 : the letters and numbers are not sufficiently legible on the tables (modification of size of letters for example). An explanation on negative and positive controls is to be added (in the text or on figures). Authors’ response: We thank the reviewer for this critique. Unfortunately, we cannot increase the size of well letters and the numbers indicating the number of FFUs in the resulting images obtained with the vSpot Spectrum Reader. Nevertheless, we added a description of the controls to the corresponding paragraph of the Materials and Methods chapter on performing the microneutralization assay. 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 Authors’ response: We checked the manuscript for the PLOS ONE's style requirements. 2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://pdfs.semanticscholar.org/755b/684fa2e81cfa38957ed82f7fb90ee6d88405.pdf https://www.mdpi.com/2076-393X/11/12/1810 Authors’ response: We revised our manuscript to reduce similarities with our previous publications. 3. Thank you for stating the following financial disclosure: “This research was funded by the RSCF grant 21-75-30003.” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. Authors’ response: We included the following statement to the manuscript: «The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”. 4. We note that your Data Availability Statement is currently as follows: [All relevant data are within the manuscript and its Supporting Information files.] Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. For example, authors should submit the following data: - The values behind the means, standard deviations and other measures reported; - The values used to build graphs; - The points extracted from images for analysis. Authors do not need to submit their entire data set if only a portion of the data was used in the reported study. If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Authors’ response: We changed the Data Availability Statement for «Data are available from corresponding author who may be contacted by email». 5. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please delete it from any other section. Authors’ response: This statement is now only in the Methods section. 6. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. Authors’ response: We included raw blot photos to the submission. 7. Please review your reference list to ensure that it is complete and correct. Authors’ response: The list of references was revised and corrected. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0304534.r002
14 May 2024 Decision Letter - Boyan Grigorov, Editor A novel immunofluorescent test system for SARS-CoV-2 detection in infected cells PONE-D-24-07586R1 Dear Dr. Rak, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Boyan Grigorov Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0304534.r003
Formally Accepted
20 May 2024 Acceptance Letter - Boyan Grigorov, Editor PONE-D-24-07586R1 PLOS ONE Dear Dr. Rak, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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. Boyan Grigorov Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0304534.r004

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