PONE-D-22-30012Rational design of a sampling protocol for detection of a subcellular plant pathogen to demonstrate area freedom in commercial orchardsPLOS ONE

Dear Dr. Bonnéry,

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.

This is a research protocol paper. I expect widely acceptable details on method(s). It seems to me you had it but needs to clarify some details as one of the reviewers showed. I think your title is beyond what you suggest in general although the method might be used for other crops but needs to be verified as a protocol. I hope you will be able to make clearer statements.

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Kind regards,

Ahmet Uludag, Ph.D.

Academic Editor

PLOS ONE

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2. Thank you for stating the following in the Acknowledgments Section of your manuscript:

“This project has been funded by Hort Innovation, using the avocado research and

development levy and contributions from the Australian Government under Project

AV18007 – Avocado sunblotch viroid survey. Hort Innovation is the grower owned, not-forprofit research and development corporation for Australian horticulture.”

We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please note that funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

“This project has been funded by Hort Innovation (https://www.horticulture.com.au/), using the avocado research and development levy and contributions from the Australian Government under Project AV18007 – Avocado sunblotch viroid survey. Hort Innovation is the grower owned, not-for-profit research and development corporation for Australian horticulture.  The  grant was received by A. G.  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”

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Additional Editor Comments:

Two reviewers have suggested different decisions deeply. I would like to have your responds on reviewers' comments, especially from one who has rejected. I definitely agree with editor on too broad title you have. I think you need to explain methodic problems carefully.

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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

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: I Don't Know

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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: No

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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

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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: Dear Editor,

The study presents the results of original research and its results reported have not been published elsewhere. Experiments, statistics, and other analyses are performed to a high technical standard and are described in sufficient detail. Conclusions are presented in an appropriate fashion and are supported by the data. The article is presented in an intelligible fashion and is written in good English. The research meets all applicable standards for the ethics of experimentation and research integrity. The article adheres to appropriate reporting guidelines and community standards for data availability. However, I suggest some minor revisions. Introduction of the paper is too long and readers can get bored/tired. Please, shorten it if applicable. And, my decision is to accept the article after the minor revisions.

Reviewer #2: This manuscript describes a protocol for field sampling and detection of ASBVd that can be used as a regulatory procedure which, if samples from a field or region are negative for ASBVd, can support export of avocado to a country that does not accept import of avocado from a region or field that has ASBVd. I believe the title is too broad (e.g. subcellular plant pathogen) and should be specific for avocado and ASBVd. Many other viruses and viroids can be considered subcellular and the filter disk capture of the nucleic acid template may not be considered robust enough as part of a regulatory detection platform. Moreover, the molecular description of ASBVd is not adequately described to provide background needed to evaluate template preparation and RT-qPCR methods used. I do not like the term “negotiable” regarding an export protocol. Rather, it is based on solid data or a series of criteria that are “mutually” accepted. This and specific comments included in the attachment

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-22-30012 Review comments.pdf

Rational design of a survey protocol for avocado sunblotch viroid in commercial orchards to demonstrate pest freedom

PONE-D-22-30012R1

Dear Dr. Bonnery,

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.

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Kind regards,

Ahmet Uludag, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Thank you very much for your very good revision. Please consider some editorial points by a reviewer when you have received a copy before publishing.

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

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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

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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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

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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

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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: Unlike the other referee, I have previously stated that the make can be accepted after minor revision. However, the constructive suggestions of both the other referee and the editorial office on the article cannot be ignored. It is seen that the authors responded to all the points mentioned and revised the article as desired. I think the article can be published in this state.

Reviewer #2: This manuscript has been adequately revised from the original submission. It describes a protocol for field sampling and detection of ASBVd that can be used as a regulatory procedure which, if samples from a field or region are negative for ASBVd, can support export of avocado to a country that does not accept import of avocado from a region or field that has ASBVd. This reviewer does understand novelty of this work is in the design, development, and implementation of a statistical protocol to optimize sampling for pest freedom and not the standard qRT-PCR protocols for its detection. My comments are either to bring out methods that were used but not mentioned or to improve the final procedures that will be presented to the regulatory bodies for adaptation. This paper is acceptable for publication.

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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

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