Estimation of the incubation period of COVID-19 in Vietnam

Long V. Bui; Ha T. Nguyen; Hagai Levine; Ha N. Nguyen; Thu-Anh Nguyen; Thuy P. Nguyen; Truong T. Nguyen; Toan T. T. Do; Ngoc T. Pham; My Hanh Bui

doi:10.1371/journal.pone.0243889

Peer Review History

Original SubmissionMay 12, 2020
25 Aug 2020 Decision Letter - Ka Chun Chong, Editor PONE-D-20-14137 Estimation of the incubation period of SARS-CoV-2 in Vietnam PLOS ONE Dear Dr. Bui, 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 Oct 09 2020 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. 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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: The manuscript is well written and has a practical implications for addressing the COVID-19 response in Vietnam. The authors use small number of confirmed cases to estimate the incubation period and I have some comments for this manuscript. Minor comments 1. The analyses were highly dependent on the epidemiological investigations for each case. Please describe the process of the data generation such as epidemiological investigations briefly to show the validity of the data such as the date of exposure and illness onset. 2. The author compared the incubation period in other studies using the data from China. Can you please add the other studies using the data from out of china? For example, Korea (Lee H et al. Journal of Infection and Chemotherapy 2020), France (Slje H, hal-pasteur.achieve 2020), etc). 3. Please provide more detail of the limitation of this study, particularly on the small sample size to analyse. Reviewer #2: The authors estimated the incubation period of Vietnamese confirmed COVID-19 cases from a subsample of 19 of the 102 locally infected cases for the period 23 Jan to 13 Apr 2020. My review comments are: 1. How representative is the subsample? Data on age range and sex of the subsample was mentioned in the article, but not for the parent sample of 102 patients. Were their age/sex data comparable? 2. The authors attributed the large variation in incubation periods in their study to small sample size, but can these be contributed also by variations in exposure period and uncertainties in the date of infection (Figure 2)? 3. The authors commented that “Only one study by Leung [13] estimated longer incubation periods than our estimation”. But there are three other studies that gave estimates of longer mean incubation periods of COVID-19 in the order of 8 days: Kong T-K. Longer incubation period of coronavirus disease 2019 (COVID-19) in older adults. Aging Medicine 2020;3:102-109. Qin J, You C, Lin Q, Hu T, Yu S, Zhou X-H. Estimation of incubation period distribution of COVID-19 using disease onset forward time: a novel cross-sectional and forward follow-up study. Sci Adv. 2020. https://advances.sciencemag.org/content/early/2020/08/07/sciadv.abc1202 Tindale LC, Stockdale JE, Coombe M, et al. Evidence for transmission of COVID-19 prior to symptom onset. eLife 2020;9:e57149. https://doi.org/10.7554/eLife.57149 4. The authors recommended the quarantine period should be extended up to three weeks based on their study finding of 97.5th percentile 13.0, CI 10.6–20.7. But would they also comment on the wide CI of 10.6-20.7 and the reason for the uncertainty? ****** 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
20 Oct 2020 Author Response Dear Reviewer, Thank you for your helpful comments. We have revised our paper accordingly and feel that your comments helped clarify and improve our paper. Please find our response (in blue) to reviewer’s specific comments (in black) below. Reviewer #1: 1. The analyses were highly dependent on the epidemiological investigations for each case. Please describe the process of the data generation such as epidemiological investigations briefly to show the validity of the data such as the date of exposure and illness onset. Response: Thank you for your comment. I have added details on the data generation: According to the report flow of the Ministry of Health and National Steering Committee for COVID-19 response, information of all laboratory-confirmed COVID-19 cases in Vietnam, which include patient number, travelling history, contact tracing and clusters, date of laboratory-confirmed, date of assertion, date and status of discharge was collected by the local centers for disease control and hospitals where patients were being admitted. The information then was reported daily to the Ministry of Health and officially made publicly available on the website httpp://ncov.moh.gov.vn. This method was also used by several articles on COVID-19 in Vietnam, which were cited in our manuscript. 2. The author compared the incubation period in other studies using the data from China. Can you please add the other studies using the data from out of china? For example, Korea (Lee H et al. Journal of Infection and Chemotherapy 2020), France (Slje H, hal-pasteur.achieve 2020), etc). Reponse: Thank you very much. We have added relevant citation as you suggested. We did not cite Slje H, hal-pasteur.achieve 2020 because the article did not estimate the incubation period of COVID-19 in France, instead, the author used the incubation period of 5 days in a deterministic compartmental model stratified by age to describe the transmission of SARSCoV-2 in the French population. 3. Please provide more detail of the limitation of this study, particularly on the small sample size to analyse. Response: Thank you very much. We have added “In addition, the study could not analyze the differences in incubation period between age groups due to small sample size”. Reviewer #2: 1. How representative is the subsample? Data on age range and sex of the subsample was mentioned in the article, but not for the parent sample of 102 patients. Were their age/sex data comparable? Response: Thank you very much for your comment. We have added some lines that compare the age/sex of subgroup to the parent sample. “There was no statistical difference in mean age and sex distribution between sub-group for analysis and the entire group (p<0.05).” 2. The authors attributed the large variation in incubation periods in their study to small sample size, but can these be contributed also by variations in exposure period and uncertainties in the date of infection (Figure 2)? Response: Thank you very much. We’ve added this issue in the limitations: “The large variation in incubation periods in our study can also be attributed by variations in exposure period and uncertainties in the date of infection”. 3. The authors commented that “Only one study by Leung [13] estimated longer incubation periods than our estimation”. But there are three other studies that gave estimates of longer mean incubation periods of COVID-19 in the order of 8 days: Kong T-K. Longer incubation period of coronavirus disease 2019 (COVID-19) in older adults. Aging Medicine 2020;3:102-109. Qin J, You C, Lin Q, Hu T, Yu S, Zhou X-H. Estimation of incubation period distribution of COVID-19 using disease onset forward time: a novel cross-sectional and forward follow-up study. Sci Adv. 2020. https://advances.sciencemag.org/content/early/2020/08/07/sciadv.abc1202 Response: Thank you very much. We have added relevant citation as you suggested. We did not cite (Slje H, hal-pasteur.achieve 2020) because the article did not estimate the incubation period of COVID-19 in France, instead, the author used the incubation period of 5 days in a deterministic compartmental model stratified by age to describe the transmission of SARSCoV-2 in the French population. 4. The authors recommended the quarantine period should be extended up to three weeks based on their study finding of 97.5th percentile 13.0, CI 10.6–20.7. But would they also comment on the wide CI of 10.6-20.7 and the reason for the uncertainty? Response: Thank you very much. We’ve added one reference, suggesting that the incubation period of CVOID-19 may be up to 24 days “Prior studies also suggested that the incubation period in some cases can be up to 24 days [24]”. Thank you again for your constructive manuscript, that absolutely improve our manuscript. We hope reviewers take our revised version into your consideration. We look forward to hearing positive feedback from you. Sincerely Yours Bui My Hanh Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0243889.r002
12 Nov 2020 Decision Letter - Ka Chun Chong, Editor PONE-D-20-14137R1 Estimation of the incubation period of COVID-19 in Vietnam PLOS ONE Dear Dr. Bui, 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. ============================== ACADEMIC EDITOR: Please address the remaining comments. ============================== Please submit your revised manuscript by Dec 27 2020 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Ka Chun Chong Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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 #1: All comments have been addressed 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 #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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 #1: Yes 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 #1: Yes 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 #1: The authors reflect all of the comments in the revised manuscript; The readibility is improved and looks better. Reviewer #2: My review comments have been addressed and the manuscript is acceptable for publication after correction of one error and a typo: Line 157 error: Lee et al [10] should not be quoted as a study showing longer incubation period than the authors' study finding, because the median incubation period of Lee et al [10] is shorter at 3 days. It can nevertheless be quoted under Line 155 together with other studies showing shorter incubation period compared with the authors' finding. Line 112 typo: "of those" is duplicated. ****** 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 #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.0243889.r003
Revision 2
17 Nov 2020 Author Response Dear Reviewers, Thank you for your helpful comments. We have revised our paper accordingly and feel that your comments helped clarify and improve our paper. Please find our response to reviewer’s specific comments below. Reviewer #1: The authors reflect all of the comments in the revised manuscript; The readibility is improved and looks better. Response: Thank you for your comment. Reviewer #2: My review comments have been addressed and the manuscript is acceptable for publication after correction of one error and a typo: Line 157 error: Lee et al [10] should not be quoted as a study showing longer incubation period than the authors' study finding, because the median incubation period of Lee et al [10] is shorter at 3 days. It can nevertheless be quoted under Line 155 together with other studies showing shorter incubation period compared with the authors' finding. Line 112 typo: "of those" is duplicated. Response: Thank you for your comment. We have deleted the duplicated “of those”. We have moved the reference of Lee et al. to studies estimating shorter incubation time than ours and revised the range of shorter estimation from 3 – 5.6 days. We have made overall editing to the manuscript to make sure all typos and wordings are correct. Thank you again for your constructive manuscript, that absolutely improve our manuscript. We hope reviewers take our revised version into your consideration. We look forward to hearing positive feedback from you. Sincerely Yours Bui My Hanh Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0243889.r004
1 Dec 2020 Decision Letter - Ka Chun Chong, Editor Estimation of the incubation period of COVID-19 in Vietnam PONE-D-20-14137R2 Dear Dr. Bui, 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, Ka Chun Chong Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0243889.r005
Formally Accepted
10 Dec 2020 Acceptance Letter - Ka Chun Chong, Editor PONE-D-20-14137R2 Estimation of the incubation period of COVID-19 in Vietnam Dear Dr. Bui: 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. Ka Chun Chong Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0243889.r006

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