PONE-D-21-37085Novel RNA viruses associated with avian haemosporidian parasitesPLOS ONE

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(RS

This work was supported by the grant to RNMS, NIH 1SC3GM118210-01A. 

Ravinder Sehgal

grants.nih.gov

JRR

This work was supported by the Genentech Foundation Scholarship of the SEO office at San Francisco State University 

Jose Roberto Rodrigues

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Comments to the Author

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Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: N/A

Reviewer #2: N/A

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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

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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: The overall design of the study is acceptable and can conduct to the conclusion that new MaRNAV-like signals are identified as narna-like viruses and very likely infect bird hosts. Nevertheless, I would recommend to the authors to be more careful with the virus/host relationship establishment because, as well explained in the Discussion part, this study and the previous one from Charon et al are both based on bioinformatic identification. The use of "confirm" l. 197 is thus not adapted. On the other hand, some Narnaviridae are not only "suspected" fungal viruses as indicated l. 217 but have been clearly and experimentally associated to host infection (especially in S. cerevisiae).

Discussion of the identification of second segment is missing, as well as the discussion of the potential presence of the virus in the host genome. I would recommend to the authors to conduct a Blastn of their newly identified sequences to the nt NCBI to ensure the newly identified viruses are not EVEs, i.e. viral elements integrated into host genomes.

Please see below for minor comments/corrections :

l.25 : Precise the taxon of parasites here ? (Apicomplexa/Haemosporidian)

l.29 : Does it mean MaRNAV-3 share 40% with MaRNAV-1 and MaRNAV3 share 60% with MaRNAV-2 ? Unclear...

l.56 : I would add another ref for the protist definition and phylogeny... Perhaps Burki F. et al. (2020) ‘The New Tree of Eukaryotes’, Trends in Ecology & Evolution, 35: 43–55.

l.76 : RdRp cannot be considered as "highly" conserved but constitutes the most conserved protein in RNA viruses.

l.83 : Narnaviruses have been previously identified in protists (Oomycetes and Leishmania).

l.141: Indicate the parameters of ORF Finder (which genetic codes have been used for example). it can be critical when searching for protist viruses related to Lenarviricota as some could be mitochondria-associated.

l.161 : I would not use the the term "infection" but rather "presence", "association". As detailed in the Discussion part, bioinfo-based virus identification do not formally demonstrate host infection...

l.184 : What is the level of ID shared between the second segments of MaRNAV1 and 2 ? S2 table mention only one percentage for both MaRNAV1 and 2... No additional segments could be found for MaRNAV4 ?

l.197 : Replace "confirm" by "strongly suggest" ?

l.252 : The study in Charon et al has screened several SRA files from P. vivax Bioprojects to conclude that MaRNAV1 is widespread in P. vivax samples worldwide (not only in Malaysian samples).

Table1 : Percent of identity with what ?

Figure1: The quality is bad. Is the tree rooted ? What is the scale at the bottom ?

Supplemental material : I would suggest sharing the alignment in fasta format. Could you share the Phyre2 info tables as well ?

Reviewer #2: This is an interesting report. Perhaps the discussion is a little speculative, but I understand the need of providing a general context of otherwise a descriptive study. Some minor changes

The phrase: “Even though protists are no less evolved than more complex multicellular eukaryotes, they play an important role in deducing the origins of RNA viruses today”

I understand the intention, but even mentioning a “scala naturae” to dismiss it without arguing against do not assist the reader without background in evolutionary biology. This is not the place to discuss it, but it is not simply a stylistic matter so I found such a phrase a little unsettling. The issue could be addressed by simply stating that the most recent common ancestor between protists and multicellular eukaryotes likely was part of the origin of eukaryotes and as such, study the RNA viruses in the extant lineages of protist and multicellular eukaryotes may inform about the common ancestor of the RNA viruses observed today.

Lines between 255-275 are too speculative, I suggest changing it by emphasizing, briefly, the need of experimental work to establish the viruses effect, if any, in their hosts (in this case the Haemosporida parasites).

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Reviewer #2: No

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Novel RNA viruses associated with avian haemosporidian parasites

PONE-D-21-37085R1

Dear Dr. Rodrigues,

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.

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Kind regards,

Maria Andreína Pacheco, Ph.D.

Academic Editor

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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

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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

**********

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

Reviewer #2: Yes

**********

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

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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

**********

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: There are still a typos in the first page. I do not understand the use of the statement "These authors contributed equally to this work" and only appears one, which happen to be the corresponding. Perhaps it was intended for the other two authors.

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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.

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Reviewer #2: No