PONE-D-21-31987Risk factors for bovine rotavirus infection and genotyping of bovine rotavirus in diarrheic calves in BangladeshPLOS ONE

Dear Dr. Alam,

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PLOS ONE

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Additional Editor Comments (if provided):

Dear Dr. Alam,

Please check the attached comments. As you can see that both the reviewers have suggested minor comments for the improvement of your manuscript.

Thanks

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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: Partly

Reviewer #2: Yes

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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: Minor comments

Abstract

1. The age of the calves should be preferably in weeks over months.

2. Crossbred calves details like types, distribution among types, etc. missing.

3. Comparison to Indian strain of G6 and G10 w.r.t. specific locations in genotype should be elaborated.

Introduction

1. There are lot of lines where space between words are missing. For example, Line 50. "Bovinerotavirus" should be "Bovine rotavirus"; Line 100. "...,breedand location..." should be "..., breed and ..."; Line 108. "..placedin.." should be "...placed in...". Similarly for Line 116. 153. 162. 171. 200. 201. 202. 214. 226. 258. 304.

2. Line 52. RV is not abbreviated before.

3. The flow of introduction should be re-looked.

4. Line 166. Details of Chromas 2.23 required.

5. Line 178. "ND: Note determined" should be "Not Determined"

6. Table 3. Age should be presented in weeks instead of month. Breed details are required. Are Cross Breed unique or represent non-indigenous as a whole?

7. Line 244. "This result...vice-versa" suggests transit of BRVs via established routes. Please revise the sentence appropriately.

8. Line 224. "Blast" should be "BLAST"

9. Line 314. "Legal and illegal...frequent". The author may substantiate this statement with reference.

10. What is the detection limit of the PCR-test used.

11. Different vaccines have been developed and deployed across the world. Serum Institute of India has made bovine rotavirus vaccine as well. The authors may comment upon the utility of known vaccines on the cohort tested.

12. What is the vaccination status of the cohort and that of the herd from which the calves were selected? What criteria was used to determine selection of calves in the herd?

13. How does the data correlate with Indian rotaviral reports like that of Tatte et a. 2019 (PMID: 30879319) and Kumar et al 2018 (PMID: 29464925), Chitambar 2011 (PMID: 20880637)?

14. Have the authors identified any similarities with the human rotaviruses?

Reviewer #2: In the present study, Ahmed et al. has tried to identify G and P genotypes of bovine rotavirus (BRV) strains in diarrheic calves as well as the major risk factors of BRV infection. In this study, Ahmed et al. noticed the predominant role of G6P[11] genotype (94.4%), followed by G10P[11] (5.6 %) in BRV infection. Further, their experimental evidence suggested age and breed of claves as major risk factors for the BRV infection.

Comments:

1. Authors should also discuss the impact of other factors particularly, season and sex in the abstract.

2. In the introduction section, authors have discussed more about the genotypes of BRV; it will be good, if they will reduce this part and include a paragraph on the impact of different parameters (such as Herd size, colostrum feeding, colostrum timing and colostrum amount) on the rate of BRV infection in calves.

3. If possible, authors should also examine the impact of other factors on BRV infection, which are also identified as one of the potential factors (such as Herd size, colostrum feeding, colostrum timing and colostrum amount) for BRV infection.

4. In this study, author found that female calves are more susceptible for BRV infection while studies have also shown that male calves are more susceptible for BRV infection, what could be the possible reason; please discuss this in to the discussion section.

6. Discuss the principle of rapid detection kit BIO K 152 behind the detection of BRV in the materials and methods.

7. Authors should elaborate the methods used in the study for better understanding of the readers.

8. In figure 1, authors have mentioned 11 RNA fragments but in the figure only 10 RNA segments are visible, 8th RNA segment in all groups is not visible. Please justify this. It will be good if authors will mention about the encoded proteins of different RNA fragments in figure as well as in the discussion section.

9. In figure 2, label the name of gene (VP7 and VP4) along with product length.

10. Author have stated two contradictory statements, Page 3, line No 3-4, and Page 12, line No 201-203, please clarify this.

11. The pattern of cited references in the list is not consistent, please do the needful corrections.

12. There are few grammatical and typographical mistakes in the manuscript, so authors should carefully read the manuscript and do the needful corrections.

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Reviewer #1: No

Reviewer #2: Yes: Dr. Ajay Kumar, Assistant Professor, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi-221005

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Attachments

Attachment

Submitted filename: Reviewer comments.docx

PONE-D-21-31987R1Risk factors for bovine rotavirus infection and genotyping of bovine rotavirus in diarrheic calves in BangladeshPLOS ONE

Dear Dr. Alam,

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 submit your revised manuscript by Mar 12 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,

Vibhav Gautam

Academic 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.

Additional Editor Comments (if provided):

Dear Dr. Alam:

I have received the reports from our advisors on your manuscript, "Risk factors for bovine rotavirus infection and genotyping of bovine rotavirus in diarrheic calves in Bangladesh.

Based on the advice received, I have decided that your manuscript could be reconsidered for publication should you be prepared to incorporate major revisions. When preparing your revised manuscript, you are asked to carefully consider the reviewer comments which are provided below, and submit a list of responses to the comments.

I look forward to receiving your revised manuscript.

Sincerely yours,

Vibhav Gautam

[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: (No Response)

Reviewer #3: (No Response)

**********

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: Partly

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: N/A

**********

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

Reviewer #3: 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: No

Reviewer #2: Yes

Reviewer #3: 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: All previous comments have been answered except for minor language corrections and need of citation at one place. Please refer to details here.

line 128 - centrification - should be centrifugation.

line 163 - Rephrase to "RT-PCR targeting the genes - VP7 and VP4 were used to detect BRV."

lines 216-7 - age is represented as months here while in previous sentences ages is mentioned in weeks. Please rectify.

line 232 - Correct "segemnts" to "segments".

Line 238-41 - Rephrase to "Based on the subtype-specific RT-PCR and we-based analysis, among the 18 amplicons evaluated, 17 were BRV G6 (94.4%) and 1 BRV G10 (5.6%). This indicates that G6 is the predominant genotype."

Line 345 - What percentage of the total land of the nation, do the 3 districts cover?

Line 346 - Give reference of the "another study".

Reviewer #2: Authors have not performed the suggested experiments and have also not properly modified the manuscript as per the suggestion. More so, they have not well responded to the comments.

Reviewer #3: Comments:

1) In the present study authors focused only on three districts, what was the status of diarrheic calves in other districts of Bangladesh?

2) As authors said they used BRV rapid detection kit_which only provides the information about the presence and absence of infection, what was the percentage of infection does any other method or technique to calculate the % of infection?

3) In the present study authors find the G and P genotypes in diarrheic calves, if authors prefer the HRM (high resolution melting) analysis in control and infected calves to find out the SNP (single nucleotide polymorphism) which is responsible for the diarrheic condtion??

4) In figure 2a lane no. four there is light amplified product , what represent this band??

Minor comments:

Line no.116,153,171,200,201,258,294 and 304 two-three words are combined ,this might be due to mac or windows please once check it.

**********

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

Reviewer #3: 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.

Risk factors for bovine rotavirus infection and genotyping of bovine rotavirus in diarrheic calves in Bangladesh

PONE-D-21-31987R2

Dear Dr. Alam,

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,

Vibhav Gautam

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: