PONE-D-23-08923Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and UgandaPLOS ONE

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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: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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: Yes

Reviewer #3: Yes

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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: Yes

Reviewer #3: Yes

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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: The paper for Dunay and collegues reports on viruses that are detected in saliva from chimpanzees housed in two sanctuaries in Africa, one in the Republic of Congo and the other in Uganda.

In both sanctuaries saliva was collected from 22 and 24 chimpanzees and subsequently analyzed by next generation metagenomic sequencing to document viral diversity in saliva, especially for the presence of viral families that include viruses that can be pathogenic for humans and and be transmitted to humans, especially animal keepers, via bites.

The methods are correct and are standard for this kind of studies. Moreover this is one of the first studies reporting on saliva. The authors identified around 20 viruses from 5 viral families, but none of them is currently associated with pathogenicity in chimpanzees or humans.

I have a few points that need to be clarified:

The authors mention also results on plasma or blood samples rom the same chimpanzee communities, can they specify whether this is also from the same animals for whom saliva samples are studies in this report?

Table 1 seems to contain important information, but the table is truncated and many information is not displayed. This should be rectified!!

The authors should provide more details on the number of reads for the different viruses they reported and the different gene fragments that are obtained. For some viruses , they obtained whole genomes, and for others they did phylogenetic analysis on genes fragments, but how much of the different virus genomes were recovered in the different samples?

Can the authors also provide information on what percentage of the total reads are represented by the viruses reported here, what is percentage of other viruses that were excluded and what was the overall diversity of viruses in saliva.

This can be useful information on whether saliva has a specific virome or whether some viruses are also observed in fecal samples from apes, which are more frequently studied, because these samples are easier to collect.

Reviewer #2: The authors present a manuscript based on the presence of viruses in saliva from african chimpanzees.

This manuscript explain that viruses found in saliva do not cause disease in chimpanzee and human. The authors used phylogenetic analysis for viruses identification and characterisation.

1- The authors have detected viruses in saliva but did not tell about the proviral load for all these viruses. This information is important to best understand the infectiosity of each virus and to best evaluate the risk for transmission to other non human primates and to human.

2- Some bibliographic references number are missed or used in duplicate or triplicate. The authors are requested to use a good logiciel for formating bibliography at the end of the manuscript.

3- Line 267, page 13: What does the sentence means:" Accesssion...this study."

4- Page 16, line 344: What does 70.8% represents? a CI?

5- At the line 419, the authors explain that "primates" include also humans. Is the word "primates" used several time in the manuscript include also "humans" or only animal? If so, the authors are requested to write NHPS and not only "primates".

6- Page 20, line 428: "...has been..." is written twice

Reviewer #3: The present study looks to use metagenomic methods to identify viruses in saliva samples from chimpanzees in two wildlife sanctuaries. I believe the study is interesting, well presented and valuable for practitioners in the field that work in wildlife rehabilitation facilities.

The abstract is succinct, and identifies the uniqueness of the study, as well as clearly summarizes the results and greater implications.

The authors do a great job introducing the subject material and highlighting the importance of the study.

The figures and tables visualize and support the findings well. There is a great number of both as supplementary material.

The methods are well detailed and comprehensively written so that others could repeat the methodology.

The discussion includes limitations and relevant comparisons with previous research. It presents relevant findings, and I believe the conclusions are within the realm of the results.

Minor revision: Please have a look over the reference list as some numbers are missing, repeated or out of order (5 and 6 missing, 21 repeated, 125 comes between 46 and 50).

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and Uganda

PONE-D-23-08923R1

Dear Dr. Dunay,

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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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,

Engin Berber

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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 #2: All comments have been addressed

Reviewer #3: 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 #2: Yes

Reviewer #3: Yes

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

Reviewer #2: Yes

Reviewer #3: 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 #2: Yes

Reviewer #3: 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 #2: Yes

Reviewer #3: 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 #2: (No Response)

Reviewer #3: (No Response)

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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 #2: No

Reviewer #3: No

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