Peer Review History

Original SubmissionJuly 24, 2021
Decision Letter - Simon Clegg, Editor

PONE-D-21-20980

Lumpy skin disease outbreaks in Egypt during 2017-2018 among sheeppox vaccinated cattle: Epidemiological, pathological, and molecular findings

PLOS ONE

Dear Dr. Rouby,

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.

==============================

Many thanks for submitting your manuscript to PLOS One

It was reviewed by two experts in the field, and they have recommended some modifications be made prior to acceptance

I therefore invite you to make these changes and to write a response to reviewers which will expedite revision upon resubmission

I wish you the best of luck with your modifications

Hope you are keeping safe and well in these difficult times

Thanks

Simon

==============================

Please submit your revised manuscript by Oct 16 2021 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. 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,

Simon Clegg, PhD

Academic Editor

PLOS ONE

Journal requirements:

When submitting your revision, we need you to address these additional requirements.

1. 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

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. You indicated that you had ethical approval for your study. In your Methods section, please ensure you have also stated whether you obtained consent from farmers whose animals were included in the study or whether the research ethics committee or IRB specifically waived the need for their consent.

3. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability.

Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized.

Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access.

We will update your Data Availability statement to reflect the information you provide in your cover letter.

4. Please note that in order to use the direct billing option the corresponding author must be affiliated with the chosen institute. Please either amend your manuscript to change the affiliation or corresponding author, or email us at plosone@plos.org with a request to remove this option.

5. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

6. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels.

In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions.

7. 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.

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: Partly

Reviewer #2: Yes

**********

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

Reviewer #1: N/A

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 authors describe the substantial outbreak of LSD in SPPV-vaccinated cattle in Egypt.

In general, the manuscript is easy to read and the presented data support the conclusions. Nevertheless, some additional information would be improve the manuscript. If the according information are not available, it should be clearly stated out.

Major comments:

• In total, 1050 clinically affected cattle were screened, but it is not clear what susceptible cattle population is available in the Beni-Suef, Sohag and Aswan Governorates and how many of the cattle were vaccinated with the SPPV vaccine.

• Furthermore, it is not clear for me, at what time the SPPV vaccination was performed and how the vaccination procedure was recorded for each individual cattle.

• In this context, it would be helpful to know, how many of the verified SPPV vaccinated cattle produced an immunological response against the SPPV vaccine (humoral and/or cellular). If such data are not available for these cattle population, the authors should screen the literature for according data.

• It is not clear if the Egypt SPPV Romanian vaccine produce no immune response in cattle, in general. Alternatively, the heterologous immune response based on the SPPV vaccine could be not sufficient to protect for the LSDV infection. This problem should be discussed more intensive.

• An interesting study would be the analysis of the serological response after the SPV vaccination. Here, cattle from the field should be tested before and 6-8 weeks after vaccination to evaluate the rate of successful immunised cattle. But this experiment can be also the part of one of the next studies.

Minor comments:

• Page3, line 9: a dot after 4] is missing

• P3, l21: RPO-30

• P7, l12: RPO-30

• P7, l14: Fig. 4G is described here at the first time, thus the legend Fig. 4A would be better.

• P7, l18: Why only one of 10 PCR amplicons for the p32 sequence showed readable sequences. A confirmation of the p32 sequence for other LSDV-field strains from 2017/18 would be more robust for the conclusion.

Reviewer #2: This is a nice and interesting article which is simple to read and well presented which described LSDV in Egypt.

I have made a few comments- line numbers start from the first text line of the intro as there were none on the submitted manuscript.

It would be nice to know some figures for the areas- number of cows, % vaccinated etc, and how recent the vaccination was for the cattle.

Also, is it that the vaccination hasn’t produced a response? Or is it some other reason why the animal has become diseased?

A few minor comments are below.

Line 1- comma after devastating

Line 3- delete a

Line 6- reword to ..related to the genus ….

Line 24- I may be incorrect, but isn’t this the RPO-30? Please check throughout

Line 27 and 28- this is repetitive, please modify

Line 38- delete the second ‘of’

Line 63- please include full PCR reagents

Please ensure that all reagents have the manufacturer in the methods section

Line 77- remove brackets from dilution

Line 78- please define AP

P32 PCR- please include PCR reagents

Line 107- how were these samples chosen?

Line 117- please use similarities when not 100% identical

Line 148- comma after LSDV

Line 159-160= you don’t show this data- unless I missed it, and this is quite important

Not sure that figures 3 or 6 are needed but up to the authors

**********

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. 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.

Revision 1

I'd like to thank you for your valuable suggestions. All recommendations will be considered.

Reviewer 1:

Q1: In total, 1050 clinically affected cattle were screened, but it is not clear what susceptible cattle population is available in the Beni-Suef, Sohag and Aswan Governorates and how many of the cattle were vaccinated with the SPPV vaccine.

Response:

Thank you for your kind comment, the study only concerned with the animals showing the typical signs of the disease. The numbers of suspected animals in each governorate are shown in and under figure 1. Regarding the susceptibility of cattle and the number of vaccinated cattle, it was assumed that these animals are not susceptible because vaccination in cattle is compulsory all over the country where all animals are vaccinated regularly every 6 months since years. However, disease outbreaks still occur.

Q2: Furthermore, it is not clear for me, at what time the SPPV vaccination was performed and how the vaccination procedure was recorded for each individual cattle.

Response:

Thank you for your kind comment, all animals in this investigation were vaccinated (3 months) prior to developing the disease. As mentioned in method section “All affected animals were vaccinated within the national annual vaccination program with the Romanian SPPV vaccine (103 TCID50, Veterinary Serum and Vaccine Research Institute [VSVRI], Egypt). The development of the disease was reported three months after vaccination.”

Q3: In this context, it would be helpful to know, how many of the verified SPPV vaccinated cattle produced an immunological response against the SPPV vaccine (humoral and/or cellular). If such data are not available for these cattle population, the authors should screen the literature for according data.

-It is not clear if the Egypt SPPV Romanian vaccine produce no immune response in cattle, in general. Alternatively, the heterologous immune response based on the SPPV vaccine could be not sufficient to protect for the LSDV infection. This problem should be discussed more intensive.

-An interesting study would be the analysis of the serological response after the SPV vaccination. Here, cattle from the field should be tested before and 6-8 weeks after vaccination to evaluate the rate of successful immunised cattle. But this experiment can be also the part of one of the next studies.

Response:

Thank you for your kind comment, animals were not assessed for their immunological response. We have added a paragraph regarding the immunological response to SPPV in cattle.

Q4: It is not clear if the Egypt SPPV Romanian vaccine produce no immune response in cattle, in general. Alternatively, the heterologous immune response based on the SPPV vaccine could be not sufficient to protect for the LSDV infection. This problem should be discussed more intensive.

Response:

This is the fact in Egypt and therefore it was an important purpose to perform this study. This was stated in the manuscript: (Since 1988, LSD has been persistently reported in Egypt, with severe outbreaks until 2018 despite vaccination campaigns using heterologous vaccine (Romanian sheeppox vaccine). In addition, we have added a paragraph regarding the immunological response to SPPV in cattle.

Minor comments:

• Page3, line 9: a dot after 4] is missing

• P3, l21: RPO-30

• P7, l12: RPO-30

• P7, l14: Fig. 4G is described here at the first time, thus the legend Fig. 4A would be better.

• P7, l18: Why only one of 10 PCR amplicons for the p32 sequence showed readable sequences. A confirmation of the p32 sequence for other LSDV-field strains from 2017/18 would be more robust for the conclusion.

Response:

All were changed as recommended

P7, l14: Fig. 4G: it was changed to Fig. 4g not A as it is the best figure confirm the presence of a viral antigen “Describe the Red viral particles in macrophage of connective tissue of the dermal layer (black arrows) using alkaline phosphatase immunohistochemistry”

-Why only one of 10 PCR amplicons for the p32 sequence showed readable sequences. A confirmation of the p32 sequence for other LSDV-field strains from 2017/18 would be more robust for the conclusion.

Response:

Sequences was done to prove the stability of LSDV DNA by comparing the current circulating strain with 2012 LSDV strain. Results confirm the stability of LSDV DNA and came in accordance with that mentioned by Tuppurainen et al., 2017 “ There is only one serological type of LSDV, The large, double-stranded DNA virus is very stable, and very little genetic variability occurs. Therefore, for LSDV, farm-to-farm spread cannot be followed by sequencing the virus isolates, as is done with other TADs, e.g. foot-and-mouth disease (FMD).

Tuppurainen, E., Alexandrov, T. & Beltrán-Alcrudo, D. 2017. Lumpy skin disease field manual –

A manual for veterinarians. FAO Animal Production and Health Manual No. 20. Rome. Food and Agriculture Organization of the United Nations (FAO). 60 pages.

Reviewer: 2:

Reviewer #2: This is a nice and interesting article which is simple to read and well-presented which described LSDV in Egypt.

I have made a few comments- line numbers start from the first text line of the intro as there were none on the submitted manuscript.

It would be nice to know some figures for the areas- number of cows, % vaccinated etc, and how recent the vaccination was for the cattle.

Thank you for your kind comment, such figures are available in the Map (Fig. 1) and Table 1. All animals are vaccinated (Mandatory vaccination). Vaccination in this study as cited was 3 months prior to developing of the disease.

Also, is it that the vaccination hasn’t produced a response? Or is it some other reason why the animal has become diseased?

Insufficient immunity produced but this was not a target in this study.

The drastic effect of the virus.

The presence of pre-existing immunosuppressive diseases.

Pregnancy and blood parasites (Babesia and Theileria species infections), pneumonia and enteritis were considered potential risk factors associated with increased fatality.

A few minor comments are below.

Line 1- comma after devastating

Line 3- delete a

Line 6- reword to ..related to the genus ….

Line 24- I may be incorrect, but isn’t this the RPO-30? Please check throughout

Line 27 and 28- this is repetitive, please modify

Line 38- delete the second ‘of’

Line 63- please include full PCR reagents

Please ensure that all reagents have the manufacturer in the methods section

Line 77- remove brackets from dilution

Line 78- please define AP

P32 PCR- please include PCR reagents

Line 107- how were these samples chosen?

Line 117- please use similarities when not 100% identical

Line 148- comma after LSDV

Line 159-160= you don’t show this data- unless I missed it, and this is quite important

Not sure that figures 3 or 6 are needed but up to the authors

Response: thank you for your valuable suggestions. All recommendations will be considered.

I have attached a copy that highlights changes made to the original version

Journal requirements:

You indicated that you had ethical approval for your study. In your Methods section, please ensure you have also stated whether you obtained consent from farmers whose animals were included in the study or whether the research ethics committee or IRB specifically waived the need for their consent.

Response:

It was added as recommended “The animal ethical committee of the Faculty of Veterinary Medicine, Beni-Suef University, Egypt, approved the present study. Clinical samples used in this study were collected after approval of all the animals’ owners.”

Study’s minimal underlying data

Accession numbers

MN418201

MN418202

MN418200

Attachments
Attachment
Submitted filename: Response to Reviewers.docx
Decision Letter - Simon Clegg, Editor

Lumpy skin disease outbreaks in Egypt during 2017-2018 among sheeppox vaccinated cattle: Epidemiological, pathological, and molecular findings

PONE-D-21-20980R1

Dear Dr. Rouby,

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,

Simon Clegg, PhD

Academic Editor

PLOS ONE

Additional Editor Comments:

Many thanks for resubmitting your manuscript to PLOS One

As you have addressed all the comments and the manuscript reads well, I have recommended it for publication

You should hear from the Editorial Office shortly.

It was a pleasure working with you and I wish you the best of luck for your future research

Hope you are keeping safe and well in these difficult times

Thanks

Simon

Formally Accepted
Acceptance Letter - Simon Clegg, Editor

PONE-D-21-20980R1

Lumpy skin disease outbreaks in Egypt during 2017-2018 among sheeppox vaccinated cattle: Epidemiological, pathological, and molecular findings

Dear Dr. Rouby:

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. Simon Clegg

Academic Editor

PLOS ONE

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .