PLoS Pathogens Guidelines for Reviewers

If you have been invited to review a manuscript, please use the online manuscript submission system.

1. About PLoS Pathogens

Bacteria, fungi, parasites, prions, and viruses cause a variety of diseases that have important medical, agricultural, and economic consequences. Moreover, the study of microbes continues to provide novel insights into such fundamental processes as the molecular basis of cellular and organismal function.

PLoS Pathogens reflects the full breadth of research in these areas by publishing outstanding original articles that significantly advance the understanding of pathogens and how they interact with their host organisms.

Topics include (but are not limited to) adaptive and innate immune defenses as well as pathogen countermeasures, emerging pathogens, evolution, genomics and gene regulation, model host organisms, pathogen-cell biology, pathogenesis, prions, proteomics and signal transduction, rational vaccine design, structural biology, and virulence factors.

2. Criteria for Publication

To be considered for publication in PLoS Pathogens, any given Research Article must satisfy the following criteria:

Originality
High importance and broad interest to the community of researchers studying pathogens and pathogen-host interactions
Rigorous methodology
Substantial evidence for its conclusions

Manuscripts also must be well written to ensure clear and effective presentation of the work and key findings.

Finally, all manuscripts submitted to PLoS Pathogens must adhere to our Editorial and Publishing Policies and Author Guidelines

3. The Review Process

Submitted manuscripts are first reviewed by the Editor-in-Chief (EIC), Deputy Editor, or one of the Section Editors, who may decide to reject the paper or send it on to an Associate Editor (AE) for further review. The AE is most often a member of the PLoS Pathogens Editorial Board, but occasionally a guest of the Board is invited to serve in this capacity. The AE evaluates the paper and decides whether it describes a sufficient body of work to support a major advance in a particular field. If the AE does not judge the manuscript to be suitable for the journal, alone or in consultation with other editors, the manuscript may be rejected outright, without external peer review, with the reasons outlined in the decision letter. If the AE does judge the manuscript to be suitable for the journal, it will then be subject to external peer review.

The opinions of up to 5 experts are sought to evaluate the manuscript fully with respect to its significance, relevance, quality, and clarity. On receipt of all reviewer comments, AEs, in consultation with other members of the Board and with the Editor-in-Chief or Deputy Editor, weigh all comments before rendering a decision.

Based on the review comments and potentially further consultation amongst other editors, a decision is rendered by the AE and co-signed by the EIC, Deputy, or one of the Section Editors, who will send the decision to the corresponding author.

Possible decisions include:

Reject
Major Revision
Minor Revision
Accept

If reviewers appear to disagree fundamentally, the editors may choose to share all the reviews with each of the reviewers and by this means elicit additional comments that may help to make a decision. The editor may also choose to consult with other editors on the Board. That said, although the reviewers' comments and opinions on the manuscript are very important, decisions are not necessarily made according to majority rule. Instead, the editors evaluate the recommendations and comments of the reviewers alongside comments by the authors and material that may not have been made available to those reviewers. The decision, along with the full set of review comments, is shared with the reviewers after a decision has been made.

When a paper has been revised in response to the review, or when authors appeal against a decision, we often ask the reviewers to offer additional comments. We request that reviewers make themselves available to provide such follow-up advice. We are nevertheless aware that reviewers do not wish to be involved in extended discussions over papers, and our goal is to keep such consultations to a minimum while still allowing authors a fair hearing.

4. Reviewer Selection

The selection of appropriate and responsive reviewers is paramount for the success of the review process. We decide on reviewers for a particular manuscript based on many factors, including expertise, reputation, specific recommendations of authors and academic editors, and the AE's own knowledge of a reviewer's past performance.

As part of our editorial procedure, we confer with potential reviewers before sending them manuscripts to review. Reviewers should bear in mind that even these initial messages or conversations contain confidential information, which should be regarded as such.

5. Writing the Review

The purpose of the review is to provide the editors with an expert opinion regarding the significance, quality, relevance, and clarity of the manuscript under consideration, based on the Criteria for Publication. The review should also supply authors with explicit feedback on how to improve their papers so that they are acceptable for publication in PLoS Pathogens.

Although reviewers are welcome to make a particular recommendation for its suitability for publication, they should do so with the understanding that other reviewers may offer other opinions. To assist the AEs and Editor-in-Chief or Deputy Editor who often must weigh disparate comments to arrive at a balanced decision, the reviewer should provide the editors with as much information as possible. A review that clearly outlines reasons both for and against publication is often of as much or even more value as one that makes a direct recommendation.

Although confidential comments to the editors are respected, any remarks that might help to strengthen the paper should be directed to the authors themselves.

The best possible review of a Research Article would answer the following questions:

What are the main claims of the paper and how significant are they? Is this paper important in its discipline?
Have the authors provided adequate proof for their claims?
Are these claims novel? If not, please specify papers that weaken the claims of originality of this one.
Would additional work improve the paper? How much better would the paper be if this work were performed and how difficult would it be to do this work?
Are the claims properly placed in the context of the previous literature? Have the authors treated the literature fairly?
Do the data and analyses support the claims? If not, what other evidence is required?
Are original data deposited in appropriate repositories and accession/version numbers provided for genes, proteins, mutants, diseases, etc.?
Does the study conform to any relevant guidelines such as CONSORT, MIAME, QUORUM, STROBE, and the Fort Lauderdale agreement?
Are details of the methodology sufficient to allow the experiments to be reproduced?
Is any software created by the authors freely available?
PLoS Pathogens encourages authors to publish detailed protocols and algorithms as supporting information online. Do any particular methods used in the manuscript warrant such treatment?
Is the manuscript well organized and written clearly enough to be accessible to non-specialists? Would you recommend the author seek the services of a professional science writer?^*
Have any parts of the paper been published elsewhere? Are there any copyright issues associated with this that conflict with the PLoS license?^*
Does the paper use standardized scientific nomenclature and abbreviations? If not, are these explained at the first usage?

^*Please alert the journal office: plospathogens [at] plos.org

6. Peer Review of Pearls, Review, and Opinion Articles

The best possible review of a Pearls article, Review, or Opinion would consider a different set of questions:

Is the article relevant and of interest to a broad pathogens readership?
Does this article take the discussion or debate on this topic in a novel direction?
Are the authors' statements focused and well supported?
Have the authors missed anything important — including important research findings – on the topic they’re writing about? Please provide details of anything important that is missing.
Is the article well written and engaging? Are there any specific sections that do not make sense?
If tables and figures have been included, do they help the reader, or are they unnecessary?
In what ways could the article be improved?

If you have any questions about the peer review of PLoS Pearls, Review, or Opinion articles, please contact us at plospathogens [at] plos.org.

7. Confidentiality

The review process is strictly confidential and should be treated as such by reviewers. Because the author may have chosen to exclude some people from this process, no one not directly involved with the manuscript, including colleagues or other experts in the field, should be consulted by the reviewer unless such consultations have first been discussed with the AE.

8. Timely Review

PLoS Pathogens believes that an efficient editorial process that results in timely publication provides a valuable service both to authors and to the scientific community at large. We therefore request that reviewers respond promptly, usually within 2 weeks of their receipt of a manuscript. If reviewers need more time, or are unable to perform the review, we request they provide prompt notice and suggestions for 2 or 3 alternate qualified reviewers.

9. Anonymity

We offer authors the possibility of having their manuscripts reviewed anonymously (i.e., "double blinded"). If authors choose this option, we do not provide to reviewers the authors' names and affiliations. PLoS Pathogens does not otherwise delete any self-referential text. Authors are responsible for removing this information themselves from the manuscript.

Unless reviewers have explicitly requested to be made known by signing their name at the end of their comments to the authors, we do not release their names either to authors or to other reviewers of the manuscript. We discourage any attempt on the part of authors to discover the identity of any reviewer or to contact this person directly. We encourage the reviewers to adopt the same policy. If authors have requested an anonymous review, a similar policy applies to reviewers who may wish to learn the identity of those authors; in these cases, we discourage any attempts by reviewers to discover the authors' identity and will neither confirm nor deny any conjectures.

10. Editing Reviewers' Reports

The editors and PLoS staff do not edit any comments made by reviewers that are intended to be read by the authors unless the language is deemed inappropriate for professional communication or the comments contain information considered confidential. Such remarks should be reserved for the confidential section of the review form, which is intended to be read by the editors only. In their comments to authors, reviewers are encouraged to be honest but not offensive in their language. On the other hand, authors should not confuse frank and perhaps even robust language with unfair criticism.

11. Competing Interests

As far as possible we respect requests by authors to exclude reviewers whom they consider to be unsuitable. We also, as much as possible, try to rule out those reviewers who may have an obvious competing interest, such as those who may have been collaborators on other projects with the authors of the manuscript under review, those who may be direct competitors, those who may have a known history of antipathy with the author(s), or those who might profit financially from the work. Because it is not possible for all such competing interests to be known by a particular editor, we request that reviewers who recognize a potential competing interest inform the editors or journal staff and recuse themselves if they feel that are unable to offer an impartial review.

Read more about the Public Library of Science's Competing Interests Policy. When submitting your review you must indicate whether or not you have any competing interests.

Occasionally, reviewers may be asked to offer their opinion on a manuscript that they may have reviewed for some other journal. This is not in itself a competing interest. That two journals have identified the same person as especially well qualified to judge the manuscript under consideration does not in any way decrease the validity of that opinion and may perhaps even enhance it.

12. Feedback to Reviewers

We send reviewers’ comments along with the decision letter to all reviewers of that manuscript. If reviewers have identified themselves, this information will be passed on to other reviewers. Reviewers who may have offered an opinion not in accordance with the final decision should not feel that their recommendation was not duly considered or their service not properly appreciated. Experts often disagree, and it is the job of the editorial team to make a final publication decision.

13. Sharing Reviews with Other PLoS Journals

PLoS publishes several journals. Occasionally, editors recommend after peer review that a particular article is more suitable for another PLoS journal. If the authors choose to pursue that option, we transfer the manuscript and the reviews to the other journal. We expect that reviewers for any PLoS journal are willing to have their reviews considered by the editors of another PLoS journal.