SARS-CoV-2 viral load as a predictor for disease severity in outpatients and hospitalised patients with COVID-19: A prospective cohort study

Fredrikke Christie Knudtzen; Thøger Gorm Jensen; Susan Olaf Lindvig; Line Dahlerup Rasmussen; Lone Wulff Madsen; Silje Vermedal Hoegh; Malene Bek-Thomsen; Christian B. Laursen; Stig Lønberg Nielsen; Isik Somuncu Johansen

doi:10.1371/journal.pone.0258421

Peer Review History

Original SubmissionMarch 30, 2021
12 Jul 2021 Decision Letter - Giordano Madeddu, Editor PONE-D-21-10416 SARS-CoV-2 viral load as a predictor for disease severity in outpatients and hospitalised patients with COVID-19: a prospective cohort study PLOS ONE Dear Dr. Knudtzen, 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 Aug 26 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. 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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 move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. Additional Editor Comments (if provided): [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: 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: No ****** 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: assessing the viral load in Sars Cov 2 infection is very important as a predictor in hospitalized patients to evaluate their clinical and therapeutic progress over time. this publication allows us to correctly evaluate the parameters taken into consideration Reviewer #2: Introduction The authors evaluated the severity of the diseases with the initial viral load. I suggest adding in the introduction the main symptoms of COVID-19 and the common complication. I suggest some paper that you could read and use for the introduction: https://doi.org/10.26355/eurrev_202007_22291; https://doi.org/10.1371/journal.pone.0248009. Methods The study design is not clear. Therefore, I suggest re-writing it clearer (We conducted a retrospective case-control study […]). The authors wrote that they used as cases hospitalized patients and outpatients as control, but in the next sentence, they wrote that severe hospitalized patients are the cases, and moderate hospitalized patients are the control. Who performed the nasopharyngeal swabs? Was it always the same person? I am asking it because the swab is an operator-dependent procedure, and it could be an important bias. Have you considered as severe cases all people who died? Or have you excluded non COVID-19 related deaths? Results I suggest adding a table with the logistic regression in order to make the result more clear. Furthermore, in my opinion, Table S2 should be added in the manuscript and not in the supplemental material. It is not clear how they compare the different samples. In my opinion, the authors should compare only the samples coming from the same patients simultaneously; otherwise, too many biases are present. If it is not possible, I suggest removing this part. Discussion Some studies aimed that the presence of anosmia was correlated with a lower incidence of severe diseases. Other studies have not found this correlation. The authors could add a sentence about it considering the results. I suggest some paper that could be read and use: 10.1017/S0022215121001651; 10.1002/hed.26204 Figures The quality of the figures is poor, and it is not easy to evaluate them. Please upload high-resolution figures, better in .pdf Table 1. Some percentages are missing. The authors should add the captain explaining all abbreviations used in the tables. I suggest removing from the Table’s title “Continuous variables are given as medians with interquartile ranges (IQR), categorical variables as percentages”. ****** 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. 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Revision 1
16 Aug 2021 Author Response Dear reviewers, Thank you for taking the time to review our manuscript. We have altered the manuscript based on your constructive comments, and we believe the alterations have strengthened the manuscript. Here is a point-by-point response to the comments: 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: 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: No Reponse: the manuscript has been read and proofed by a native English speaker. 5. Comments from Reviewers Reviewer #1: assessing the viral load in Sars Cov 2 infection is very important as a predictor in hospitalized patients to evaluate their clinical and therapeutic progress over time. this publication allows us to correctly evaluate the parameters taken into consideration Response: thank you for this feedback. We agree that we present data worth taken into consideration when interpreting viral loads in patients with SARS-CoV-2. Reviewer #2: Introduction The authors evaluated the severity of the diseases with the initial viral load. I suggest adding in the introduction the main symptoms of COVID-19 and the common complication. I suggest some paper that you could read and use for the introduction: https://doi.org/10.26355/eurrev_202007_22291; https://doi.org/10.1371/journal.pone.0248009. Response: we thank the reviewer for this suggestion, and we have added information about symptoms and complications of COVID-19 in the introduction. We have read the suggested articles with great interest, and we have added the references to the articles in the introduction. Methods The study design is not clear. Therefore, I suggest re-writing it clearer (We conducted a retrospective case-control study […]). The authors wrote that they used as cases hospitalized patients and outpatients as control, but in the next sentence, they wrote that severe hospitalized patients are the cases, and moderate hospitalized patients are the control. Response: we thank the reviewer for this relevant comment. Under the sub-headline “Study design” in the Methods section, we have altered the text accordingly, to make it clearer what the study design consists of, and that there are two different case-control sub-studies within this study, with different cases and control-groups. Who performed the nasopharyngeal swabs? Was it always the same person? I am asking it because the swab is an operator-dependent procedure, and it could be an important bias. Response: we thank the reviewer for raising this relevant concern. As our study was retrospective, all swabs were performed on clinical indication by different medical personnel. We have added information about this to the Discussion section under the study limitations. Have you considered as severe cases all people who died? Or have you excluded non COVID-19 related deaths? Response: We define “severe diseases” in the Methods section under the sub-headline “Study Design”. Severe cases are defined as either ARDS, admittance to intensive care unit and/or death during admission. The mortality rate in our hospitalized cohort was low (only four deaths, all due to COVID-19), and this low mortality is discussed in detail in another publication by our group (Madsen LW et al. Low mortality of hospitalized patients with COVID-19 in a tertiary Danish hospital setting. https://doi.org/10.1016/j.ijid.2020.10.018). No non-COVID-19 related deaths were found in our cohort, so no patients were excluded on this basis. Results I suggest adding a table with the logistic regression in order to make the result more clear. Response: we thank you for this relevant comment. We have added a supplementary table displaying the univariate and multivariate logistic regression of risk factors associated with hospital admittance. Furthermore, in my opinion, Table S2 should be added in the manuscript and not in the supplemental material. Response: we appreciate this suggestion, and the table has been added to the manuscript. It is not clear how they compare the different samples. In my opinion, the authors should compare only the samples coming from the same patients simultaneously; otherwise, too many biases are present. If it is not possible, I suggest removing this part Response: in the Methods section, under the subline “Data collection” and “SARS-CoV-2 PCR assays” we have tried to explain both how the samples were taken, from whom, how they were compared, and how we included/excluded the different samples. As the main aim of this study was to compare all airway samples from different patients to see if they could determine hospital admission and severe disease, we chose to include all different airway samples available, to mimic the clinical reality we work in as medical doctors. We are aware that this complicates both the method and the results, but we believe this presents the most useful results. We have discussed this choice and the limitation it causes in the Discussion part of the paper. Discussion Some studies aimed that the presence of anosmia was correlated with a lower incidence of severe diseases. Other studies have not found this correlation. The authors could add a sentence about it considering the results. I suggest some paper that could be read and use: 10.1017/S0022215121001651; 10.1002/hed.26204 Response: this is a very interesting issue regarding SARS-CoV-2. We have followed the reviewer’s suggestion and included a section in the Results about symptoms including change in taste/smell. We have included the references by Vaira et al here. Figures The quality of the figures is poor, and it is not easy to evaluate them. Please upload high-resolution figures, better in .pdf Response: We thank you for this valuable response. We have altered the figures according to the PLOS ONE instructions, where they have all been uploaded to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool and altered to ensure they meet the PLOS quality requirements. Table 1. Some percentages are missing. The authors should add the captain explaining all abbreviations used in the tables. I suggest removing from the Table’s title “Continuous variables are given as medians with interquartile ranges (IQR), categorical variables as percentages”. Response: thank you for these suggestions. Table 1 has been altered accordingly. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0258421.r002
28 Sep 2021 Decision Letter - Giordano Madeddu, Editor SARS-CoV-2 viral load as a predictor for disease severity in outpatients and hospitalised patients with COVID-19: a prospective cohort study PONE-D-21-10416R1 Dear Dr. Knudtzen, 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, Giordano Madeddu Academic Editor PLOS ONE Additional Editor Comments (optional): 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: All comments have been addressed ******** 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 ****** 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: (No Response) ****** 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 https://doi.org/10.1371/journal.pone.0258421.r003
Formally Accepted
4 Oct 2021 Acceptance Letter - Giordano Madeddu, Editor PONE-D-21-10416R1 SARS-CoV-2 viral load as a predictor for disease severity in outpatients and hospitalised patients with COVID-19: a prospective cohort study Dear Dr. Knudtzen: 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. Giordano Madeddu Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0258421.r004

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