Molecular typing and epidemiology profiles of human adenovirus infection among hospitalized patients with severe acute respiratory infection in Huzhou, China

Deshun Xu; Liping Chen; Xiaofang Wu; Lei Ji

doi:10.1371/journal.pone.0265987

Peer Review History

Original SubmissionMarch 15, 2021
6 Oct 2021 Decision Letter - Rosa Maria Wong-Chew, Editor PONE-D-21-05692 Molecular Typing and Epidemiology Profiles of Human Adenovirus Infection among Hospitalized Patients with Severe Acute Respiratory Infection in Huzhou, China PLOS ONE Dear Dr. Lei Ji, 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 read the reviewers´comments. ============================== Please submit your revised manuscript by September 10th. 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. 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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: Yes ******** 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: 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 study assessed cases of severe acute respiratory infection in a hospital in Huzhou, China, for epidemiological analysis of human adenovirus (HAdV), including viral genotyping based on sequencing of the hexon gene and nested-PCR. Results add more information about the epidemiology of HAdV in China, complementing previous studies in the country. Considering that HAdV is an important respiratory virus worldwide, I suggest discussing the findings of the study with studies performed in other countries, such as in Europe (Price RHM et al., https://doi.org/10.1038/s41598-018-37481-y) and South America (Pscheidt et al., DOI: 10.1002/rmv.2189). There are several English and typing details that should be revised and corrected, as pointed in the pdf file. For example, symbols such as ~ to describe age group (0～, 2～, 5～,15～, 50～, 65～) does not make much sense. Please use 0≤2; 2≤5; 5≤15, etc. In the methodology, I believe there is a step missing in the PCR description. Isn't there an extension step at 72ºC after the annealing step? In Table 1, I suggest including the percentage in addition to the number of cases – N (%). In Table 2, use Sex instead of Gender. In the Results section, it is necessary to make a thorough revision of typing. Spaces missing, double spaces, typos etc. make it difficult to read the results, mainly between lines 192–209. When discussing HAdV seasonality, I suggest comparing the study with those from other geographic regions, as viral circulation has been associated with temperature and circulation of other respiratory viruses. Other comments and suggestions can be found in the pdf file (attached). Reviewer #2: Comments to the Author Xu et al., report valuable information on HAdV epidemiology including prevalence, seasonality, and molecular epidemiology in patients with SARI in China. The study methods are sound and the results are an important contribution to the field. I have only one comment: The authors were unable to type up to 42.3% (22/52) of the study samples. What could explain this high failure rate. ****** 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: Yes:** Ana Beatriz Gorini da Veiga 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-21-05692_reviewer.pdf https://doi.org/10.1371/journal.pone.0265987.r001
Revision 1
3 Nov 2021 Author Response Responses to the reviewers’ comments: (Q as comments, A as our responses) Reviewer 1 Q: Considering that HAdV is an important respiratory virus worldwide, I suggest discussing the findings of the study with studies performed in other countries, such as in Europe (Price RHM et al., https://doi.org/10.1038/s41598-018-37481-y) and South America (Pscheidt et al., DOI: 10.1002/rmv.2189). When discussing HAdV seasonality, I suggest comparing the study with those from other geographic regions, as viral circulation has been associated with temperature and circulation of other respiratory viruses. A: Thanks for the reviewer’s suggestion. The two references mentioned above have been added (see line 230, 239,242). “Most respiratory viral infections have seasonality, of note, this seasonality might vary according to geographical location. Price RHM et al. have investigated the relationship between meteorological factors and viral seasonality in Scotland over a 6.5-year period. In their study, HAdV is present throughout the year without a clear seasonality and prefer temperatures around 9 °C. In another study conducted in patients with respiratory infection in southern Brazil, HAdV circulated year‐round, with higher frequency during winter and early spring.” We have added these sentences to the manuscript, see line 238-245. Q: There are several English and typing details that should be revised and corrected, as pointed in the pdf file. For example, symbols such as ~ to describe age group (0～, 2～, 5～,15～, 50～, 65～) does not make much sense. Please use 0≤2; 2≤5; 5≤15, etc. A: Thanks for the reviewer’s suggestion. Corrections have been made in the revised version. Q: In the methodology, I believe there is a step missing in the PCR description. Isn't there an extension step at 72ºC after the annealing step? A: According to the multiplex real-time PCR kit’s instructions, the qPCR cycling program was as 50 °C for 10 min, 95 °C for 5min, followed by 40 cycles of 95 °C for 10 s, and 55 °C for 40 s. The same temperature (55 °C) is used for the annealing and extension steps. Q: In Table 1, I suggest including the percentage in addition to the number of cases – N (%). In Table 2, use Sex instead of Gender. A: Thanks for the reviewer’s suggestion. Corrections have been made in the revised version . Q: Other comments and suggestions can be found in the pdf file (attached). A: Thanks. Corrections have been made in the revised version according to comments and suggestions in the pdf file. Reviewer 2 Q: I have only one comment: The authors were unable to type up to 42.3% (22/52) of the study samples. What could explain this high failure rate. A: Thanks for the reviewer’s suggestion. Since the sensitivity of ordinary RT-PCR is lower than that of real-time RT-PCR, more accurate genotyping was only possible for 57.7% (30/52) of the HAdV-positive samples confirmed by real-time RT-PCR, the remaining 22 samples with most of them got a cycle threshold (Ct) ≥ 30 were failed to genotyped. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0265987.r002
3 Feb 2022 Decision Letter - Jianhong Zhou, Editor PONE-D-21-05692R1Molecular Typing and Epidemiology Profiles of Human Adenovirus Infection among Hospitalized Patients with Severe Acute Respiratory Infection in Huzhou, ChinaPLOS ONE Dear Dr. Ji, 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. Specifically, please address Reviewer 1's remaining concerns. Please submit your revised manuscript by Mar 19 2022 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Jianhong Zhou Associate Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. 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. 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: (No Response) 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 made significant changes in the manuscript according to the reviewers' comments. There are still a few things to correct regarding typing and other details. For example, for age groups 0≤2, 2≤5, 5≤15 etc. means that 2 years old are included in both groups 0-2 and 2-5. The correct is 0<2, 2<5, 5<15 and so on. With regards to HAdV in southern Brazil, it is more frequent during the winter, however, in relation to other respiratory viruses, HAdV is more prevalent in summer (Pscheidt et al, 2021). Other comments were made in the pdf file, attached. Reviewer #2: Nothing to report, all my comments have been adressed favorably. Thanks for the invitation. Best regards. ****** 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. Attachments Attachment Submitted filename: PONE-D-21-05692_R1_reviewer.pdf https://doi.org/10.1371/journal.pone.0265987.r003
Revision 2
2 Mar 2022 Author Response Dear Editor Jianhong Zhou, Thank you very much for giving us an opportunity to revise our manuscript. We also appreciate reviewers very much for their positive and constructive comments and suggestions on our manuscript entitled “Molecular Typing and Epidemiology Profiles of Human Adenovirus Infection among Hospitalized Patients with Severe Acute Respiratory Infection in Huzhou, China” (PONE-D-21-05692). We have carefully addressed all of the comments from the reviewers, as outlined in the point-by-point responses attached below. We hope that you find the revised manuscript now acceptable for publication in PLOS ONE. Updated statement: This work was supported by grants from Natural Science Foundation of Huzhou Science and Technology Bureau (grant number: 2021YZ23), the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Yours Sincerely Lei Ji Responses to the reviewers’ comments: (Q as comments, A as our responses) Reviewer 1 Q: for age groups 0≤2, 2≤5, 5≤15 etc. means that 2 years old are included in both groups 0-2 and 2-5. The correct is 0<2, 2<5, 5<15 and so on. A: Thanks for the reviewer’s suggestion. Corrections have been made in the revised version. Q: With regards to HAdV in southern Brazil, it is more frequent during the winter, however, in relation to other respiratory viruses, HAdV is more prevalent in summer A: Thanks for the reviewer’s suggestion. Corrections have been made in the revised version, see line 237-241. Q: Other comments and suggestions can be found in the pdf file (attached). A: Thanks. Corrections have been made in the revised version according to comments and suggestions in the pdf file. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0265987.r004
14 Mar 2022 Decision Letter - Luis Menéndez-Arias, Editor Molecular Typing and Epidemiology Profiles of Human Adenovirus Infection among Hospitalized Patients with Severe Acute Respiratory Infection in Huzhou, China PONE-D-21-05692R2 Dear Dr. Ji, 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, including a couple of minor corrections indicated by reviewer no. 1. 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, Luis Menéndez-Arias, Ph. D. 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 #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: There are only 2 corrections that have not beem made: Line 64: it should be "prevalent HAdV type" (not types) Line 232: should be "children aged 2 to 5 years", delete < Reviewer #2: The study methods are sound and the results are an important contribution to the field. All my comments have been addressed by the authors. ****** 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 https://doi.org/10.1371/journal.pone.0265987.r005
Formally Accepted
13 Apr 2022 Acceptance Letter - Luis Menéndez-Arias, Editor PONE-D-21-05692R2 Molecular Typing and Epidemiology Profiles of Human Adenovirus Infection among Hospitalized Patients with Severe Acute Respiratory Infection in Huzhou, China Dear Dr. Ji: 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. Luis Menéndez-Arias Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0265987.r006

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