Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay

Shih-hua Tan; Fatima Osman; Sohrab Bodaghi; Tyler Dang; Greg Greer; Amy Huang; Sarah Hammado; Shurooq Abu-Hajar; Roya Campos; Georgios Vidalakis

doi:10.1371/journal.pone.0223958

Peer Review History

Original SubmissionJune 10, 2019
19 Aug 2019 Decision Letter - Ulrich Melcher, Editor PONE-D-19-16252 Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay PLOS ONE Dear Ms. Tan, 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. We would appreciate receiving your revised manuscript by Oct 01 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols 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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Ulrich Melcher Academic Editor PLOS ONE Journal Requirements: Additional Editor Comments (if provided): I was only able to obtain an evaluation of this manuscript from one reviewerbusy time of year). Consequently, I read the submission carefully myself. The manuscript describes an excellent description of analysis of viral genomic datasets. I did find a few places for which I think changes are needed. I am assuming the authors will make these small changes and those suggested by Reviewer1 on the way to production. Missing spaces: l. 33 Analysis/highlighted l. 125 the/3’ end Wherever quantities of units are displayed, a space is usually required between the quantity and the unit. I object to use of the term % homology. A pair of sequences are homologous or they are not. There is no in between. They may be a certain percentage identical or % simoilar. [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. 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 ****** 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 ****** 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: General Comments: The manuscript titled “Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay” presents data on full-length genome sequences of 12 CTLV isolates from different geographical areas, intercepted and maintained for the past 60 years at the Citrus Clonal Protection Program (CCPP), University of California, Riverside. The manuscript is well written and provides useful information and a good reference point for future works regarding design and validation of plant virus detection assays. Specific comments: minor corrections needed. Page 9, Line 165: introduce comma (,) after “citrus tissues” and before “an RT-qPCR” Page 10, Line 190: replace “annealing cycle” with “amplification cycle” Page 12, Line 232: start the sentence with “Twenty-two” instead of “22” Page 21, Table 7: Cq Values of COX are consistently different between true positive samples to true negative samples. Though, the COX results presented here does not have any significant bearing on this data analysis but out of curiosity, I would like to know any explanation for the different Cq values observed. Page 27, Line 441-442: Authors talk about Liu assay. However, I do not see the Cq values of Liu assay. It is possible that the Table 7 is incomplete or a column (for Liu assay) is missing in the reviewer’s copy. Page 21, Table 7: Similarly, Lab B data is not displayed in the Reviewer’s copy or it is missing from the table. Page 33, Line 469: Since the center of origin for citrus is Asia, it is not only surprising to find diverse citrus cultivars but also high genetic diversity of CTLV from Asia. Authors may want to add a sentence or so to reflect the point. ****** 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 [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0223958.r001
Revision 1
6 Sep 2019 Author Response Dear Editor and Reviwer, We wish to submit the revised manuscript, PONE-D-19-16252 “Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay” by Tan et al. to the PLOS ONE. We took in consideration all the comments from you and the Reviewer and made the changes accordingly in the manuscript and summarized in the attached response to your review. Due to the PLOS ONE table format requirements, Table 7 and some of the other tables may not be viewed properly in “Print Layout” mode of the word file. Please select “Draft” mode under “View” section in the Microsoft Word to view tables properly. We also attached Table 7 in the last page of the cover letter for your and the Reviewer’s convenience. We would like to thank you and the Reviewer again for your excellent recommendations and we trust that the revisions made to the manuscript are sufficient to warrant publication. Best Regards, Shih-hua Tan & Georgios Vidalakis Department of Microbiology and Plant Pathology University of California, Riverside Note: For detailed info, please find the pdf file with title "Rebuttal Letter with Response to Reviewers" in the re-submission package. Thank you. -- Response to Reviewers Journal Requirements: Additional Editor Comments (if provided): I was only able to obtain an evaluation of this manuscript from one reviewer*busy time of year). Consequently, I read the submission carefully myself. The manuscript describes an excellent description of analysis of viral genomic datasets. I did find a few places for which I think changes are needed. I am assuming the authors will make these small changes and those suggested by Reviewer1 on the way to production. Missing spaces: l. 33 Analysis/highlighted l. 125 the/3’ end Wherever quantities of units are displayed, a space is usually required between the quantity and the unit. I object to use of the term % homology. A pair of sequences are homologous or they are not. There is no in between. They may be a certain percentage identical or % similar. Authors: We thank the Editor for his time and effort in reviewing this manuscript during this busy time of the year as well as for providing useful comments. We have made the recommended changes and used the “sequence identity analysis” with % identical instead of homology analysis or homologous throughout the revised manuscript indicated with track changes. Reviewers' comments: (Question 5. Review Comments to the Author) Reviewer #1: General Comments: The manuscript titled “Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay” presents data on full-length genome sequences of 12 CTLV isolates from different geographical areas, intercepted and maintained for the past 60 years at the Citrus Clonal Protection Program (CCPP), University of California, Riverside. The manuscript is well written and provides useful information and a good reference point for future works regarding design and validation of plant virus detection assays. Specific comments: minor corrections needed. • Page 9, Line 165: introduce comma (,) after “citrus tissues” and before “an RT-qPCR” • Page 10, Line 190: replace “annealing cycle” with “amplification cycle” • Page 12, Line 232: start the sentence with “Twenty-two” instead of “22” Authors: We thank the reviewer for his comments and recommended corrections. We have made the recommended changes in the revised manuscript. Note: For detailed info, please find the pdf file of "Rebuttal Letter with Response to Reviewers" in the re-submission package. Thank you. • Page 21, Table 7: Cq Values of COX are consistently different between true positive samples to true negative samples. Though, the COX results presented here does not have any significant bearing on this data analysis but out of curiosity, I would like to know any explanation for the different Cq values observed. Authors: This is an interesting observation. We thank the reviewer for his comment. We agree that COX Cq values have no significant bearing on the data analysis of true positive and true negative. We are using the COX assay as designed by Osman et al. (2015) based on the housekeeping gene, cytochrome oxidase (COX; GenBank Accession No. CX297817), to assess the integrity and quality of the nucleic acids after the CCPP developed semi-automatic nucleic acid extraction procedure for citrus tissue. From our experience, testing hundreds of samples from different citrus species, COX Cq values between 12 and 24 give reliable PCR results for citrus virus detection as we experienced with CTLV in this study and other viruses in previous work (Osman et al. 2015). In addition, we have observed that similar range of Cq values for other citrus housekeeping genes (e.g. NADH) provided reliable citrus viroids detection when testing tens of thousands of samples in our lab for the California Department of Food and Agriculture (CDFA) Citrus Nursery Stock Pest Cleanliness Program (CDFA data). We hope we provided some good information to the Reviewer. If you need any additional information, please let us know. • Page 27, Line 441-442: Authors talk about Liu assay. However, I do not see the Cq values of Liu assay. It is possible that the Table 7 is incomplete or a column (for Liu assay) is missing in the reviewer’s copy. • Page 21, Table 7: Similarly, Lab B data is not displayed in the Reviewer’s copy or it is missing from the table. Authors: We apologize to the Reviewer for the inadequate presentation of Table 7. Unfortunately, this was the PLOS ONE format issue. In some cases, tables cannot be viewed properly in “Print Layout” mode of Word file. Please select “Draft” mode under “View” section in Microsoft Word to see the full table. We are also attaching Table 7 at the end of this response for your convenience. • Page 33, Line 469: Since the center of origin for citrus is Asia, it is not only surprising to find diverse citrus cultivars but also high genetic diversity of CTLV from Asia. Authors may want to add a sentence or so to reflect the point. Authors: We thank the Reviewer for his recommendation. We have made the recommended addition in the revised manuscript: page 28 line 638 “This finding also indicated that the origin and diversity of CTLV coincided with the origin of the citrus host”. Note: For detailed info, please find the pdf file with title "Rebuttal Letter with Response to Reviewers" in the re-submission package. Thank you. https://doi.org/10.1371/journal.pone.0223958.r002
3 Oct 2019 Decision Letter - Ulrich Melcher, Editor Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay PONE-D-19-16252R1 Dear Dr. Tan, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Ulrich Melcher Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0223958.r003
Formally Accepted
8 Oct 2019 Acceptance Letter - Ulrich Melcher, Editor PONE-D-19-16252R1 Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay Dear Dr. Tan: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Ulrich Melcher Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0223958.r004

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