A rapid detection tool for VT isolates of Citrus tristeza virus by immunocapture-reverse transcriptase loop-mediated isothermal amplification assay

Vijayanandraj Selvaraj; Yogita Maheshwari; Subhas Hajeri; Raymond Yokomi

doi:10.1371/journal.pone.0222170

Peer Review History

Original SubmissionMay 25, 2019
18 Jun 2019 Decision Letter - Ulrich Melcher, Editor PONE-D-19-14855 A rapid detection tool for VT isolates of Citrus tristeza virus by immunocapture-reverse transcriptase loop-mediated isothermal amplification assay PLOS ONE Dear Research Plant Pathologist Yokomi, 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 see the Academic Editor Comments below. We would appreciate receiving your revised manuscript by Aug 02 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: 1. When submitting your revision, we need you to address these additional requirements. 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 http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://apsjournals.apsnet.org/doi/10.1094/PHYTO-100-4-0319 https://www.nature.com/articles/s41598-017-13881-4 In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed." 3. In your Methods section, please provide additional location information, including geographic coordinates for the data set if available. 4.We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. Additional Editor Comments (if provided): Please could you address the following comments before your manuscript is sent out for external review: *********************************************** Generalities : The title mentions the VT strain, yet there are absolutely no references to VT genomic uniqueness especially in its 5'end as demonstrated already in 1996 following its complete sequencing (Mawassi et al 1996 ) and comparison with T36 (Karasev et al, 1995). Similarly nothing is mentioned on VT : unique biological characteristics, subdivision into different isolates reported which cause r both quick decline QD and stem pitting (SP), while others cause SP of grapefruits with minimal or no effects on orange trees grafted on sour oranges. On the specifics, the authors did mention previous reports on CTV genotyping by Northern Hybridization and sequential analyses of enzyme immunoassays and capillary electrophoresis-single-strand conformation polymorphisms. J Virol Methods. 181:139-47. Furthermore in the above JVM paper tests were conducted on RNA recovered from positively reacting ELISA wells , thus directing genotyping only for the positively reacting citrus trees A previous report on RT-LAMP assay for sensitive detection of CTV by Warghane in J Virol Methods. 2017 Dec;250:6-10. doi: 10.1016/j.jviromet.2017.09.018. Epub 2017 Sep 21 is also missing. **************************************************** [Note: HTML markup is below. Please do not edit.] Reviewers' comments: [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.0222170.r001
Revision 1
11 Jul 2019 Author Response 1. Address format corrected 2. overlapping text. I believe this was corrected by adding the appropriate reference 3. Rather than geographic coordinates, Township/Range/Section was added for each field collection. 4. We don't need repository information. The relevant data is included in our submission. 5. VT description expanded and references added. 6. VT phenotype variation was also added 7. CTV genotyping. This study was not to differentiate CTV genotypes, rather, to screen CTV isolates efficiently for potential severe phenotype which has a VT genotype. 8. Immunocapture. Yes, the CCTEA screens CTV samples from infected trees with MCA13 monoclonal antibody and extracts from MCA13-positive samples are sent to my ARS lab for molecular genotyping by RT-qPCR with strain discriminating primers/probes and selected isolates are biocharacterized in a virus index using graft inoculation to a citrus host range. 9. Warghane et al 2017 was mentioned in the introduction of the original submission and is still there. Attachments Attachment Submitted filename: Response to reviewer(s) PONE D-19-14855.docx https://doi.org/10.1371/journal.pone.0222170.r002
17 Jul 2019 Decision Letter - Ulrich Melcher, Editor PONE-D-19-14855R1 A rapid detection tool for VT isolates of Citrus tristeza virus by immunocapture-reverse transcriptase loop-mediated isothermal amplification assay PLOS ONE Dear Research Plant Pathologist Yokomi, 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 Aug 31 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 Additional Editor Comments (if provided): The manuscript has too many language errors to be accepted as is. Here is a list of necessary changes. A proof reader should be asked to deal with other possible problems. l. . 116 "leaf samples"l.121 number disagreement dara are l.121 Table S5 l. 124-5 temperatures l. 164 were used as negative L. 238 "extracts was grounded ???? were ground l. 245 used in further. l. 252 times were l.256 at different ratios New comments on second review: The language usage still requires considerable work before the manuscript is acceptable. Research is fine. l. 92 sequences...were used to l. 113 articles "the" or plural needed L. 129 change "at" to "in" l. 224 ia not a sentence l.226 number disagreement Primeres...doesn't also in line 259 l.238 "was ground" l.273 "data are shown" l. 287 l. 298-99 l.326 delete "an" [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.0222170.r003
Revision 2
24 Jul 2019 Author Response All editor call-outs in Additional Editor Comments and New Comments on Second Review corrected and additional grammar and missing information added. Time units for amplification time was standardized and express as min:sec. Attachments Attachment Submitted filename: Response to reviewer(s) PONE D-19-14855 ver4.docx https://doi.org/10.1371/journal.pone.0222170.r004
23 Aug 2019 Decision Letter - Ulrich Melcher, Editor A rapid detection tool for VT isolates of Citrus tristeza virus by immunocapture-reverse transcriptase loop-mediated isothermal amplification assay PONE-D-19-14855R2 Dear Dr. Yokomi, 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): I appreciate all the work on language improvement Reviewers' comments: https://doi.org/10.1371/journal.pone.0222170.r005
Formally Accepted
27 Aug 2019 Acceptance Letter - Ulrich Melcher, Editor PONE-D-19-14855R2 A rapid detection tool for VT isolates of Citrus tristeza virus by immunocapture-reverse transcriptase loop-mediated isothermal amplification assay Dear Dr. Yokomi: 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.0222170.r006

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