Guide for Authors

About the Journal

Pathogens publishes original research that advances understanding of pathogens, pathogen–host interactions, and the mechanisms of infectious disease. The journal welcomes submissions across bacteriology, virology, mycology, parasitology, and prion biology, including studies of pathogenesis, immunity, epidemiology, evolution, diagnostics, therapeutics, and vaccine development.
Consistent with the founding mission of SKLS — Still Know Little Science — the journal operates on a non-profit basis with article processing charges set at the minimum level necessary to sustain basic operations. We are committed to fair, accessible, and quality-oriented publishing without imposing the financial barriers that characterize much of the commercial publishing sector.
The name Still Know Little Science reflects our intellectual orientation: scientific knowledge remains radically incomplete, certainty is often premature, and scholarship should proceed with humility rather than pretension. We welcome work that advances understanding while acknowledging the provisional nature of scientific claims.

Aims and Scope

Pathogens provides a forum for studies of pathogens and the diseases they cause. The journal publishes Research Articles, Brief Communications, and Reviews.
The journal welcomes basic, translational, and pre-clinical research. Studies reporting negative findings, replication studies, and multidisciplinary work are considered, provided they are scientifically rigorous and of value to the field. Manuscripts describing pathogen sequences without a significant advance in pathogen biology are not appropriate.
Submissions of broad interest to the community of pathologists, microbiologists, immunologists, and infectious disease researchers will be considered. The journal does not rank jurisdictions, assign scores, or endorse normative reform agendas.

Article Types

Research Articles report original experimental, clinical, or computational investigations. There is no strict word limit; authors are encouraged to be concise. Full methodological detail must be provided to permit replication. The structure should include an Abstract, Keywords, Introduction, Materials and Methods, Results, Discussion, and Conclusions (optional).
Brief Communications are short, self-contained studies of timely significance. They should not exceed four presentation items (figures and tables combined) and should be organized like a Research Article. The review process accounts for their more limited scope. Manuscripts describing pathogen sequences without a significant advance in pathogen biology are not appropriate as Brief Communications.
Reviews address sharply defined topics of interest to researchers across pathogen biology. Reviews should not attempt comprehensive coverage; they should focus on fundamental concepts, recent findings, and unresolved questions. Reviews may include an Abstract, Keywords, Introduction, relevant sections, Discussion, Conclusions, and Future Directions. No new, unpublished data should be presented.

Peer Review

Pathogens operates a single-anonymized review process. Submissions are first assessed by the editors. Those deemed suitable are sent to a minimum of two independent reviewers for expert assessment. The editors make the final decision.
Editors are not involved in decisions on manuscripts they authored, that were written by family members or colleagues, or that relate to products or services in which they have an interest. Such submissions follow the journal's standard procedures, with peer review handled independently.
Authors may submit a formal appeal of an editorial decision in accordance with the journal's appeal procedure. Only one appeal per submission is considered, and the appeal decision is final.

Submission

Manuscripts should be submitted through the journal's online submission system. The submitting author, generally the corresponding author, is responsible for the manuscript throughout submission and peer review, must ensure that all eligible co-authors are included, and must confirm that all authors have read and approved the submitted version.
A cover letter must accompany each submission. It should be concise (ideally under one page), state the study's aim and main findings, explain how the work fits the journal's scope, and emphasize its novelty and implications. Funding information, author declarations, and suggested or opposed reviewers should not be included in the cover letter; these are requested separately.

Manuscript Preparation

General Principles

Manuscripts must be written in clear, concise English (American or British usage, not a mixture). There are no strict formatting requirements at initial submission, provided the manuscript contains all elements necessary for editorial assessment and review. At revision, authors must supply editable source files formatted according to journal style.
Manuscripts should comprise:

• Front matter: Title, author list, affiliations, abstract, keywords
• Body: Introduction, Materials and Methods, Results, Discussion, Conclusions (optional)
• Back matter: Author contributions, funding, data availability, acknowledgments, conflicts of interest, references

The Results and Discussion may be combined. Materials and Methods may appear before Results or before Discussion, depending on the manuscript's logic.

Title Page

The title page should include:

• A concise, specific, and informative article title. Avoid abbreviations and formulae unless widely understood (e.g., DNA).
• Full given and family names of all authors, in the order they appear in the submission system.
• Affiliations indicating where the work was carried out, with full postal addresses and country names, marked by lower-case superscript letters.
• A clearly designated corresponding author, with email address, who will handle correspondence at all stages of review and publication.
• Present or permanent addresses for authors who have changed affiliation since the work was conducted, marked by superscript Arabic numerals.

Abstract

The abstract must not exceed 250 words. It should state the purpose of the research, principal results, and major conclusions, and must stand alone. References should be avoided; if essential, cite author and year. Non-standard abbreviations should be avoided or defined at first mention.

Keywords

Provide 1 to 7 keywords in English for indexing. Avoid multi-word keywords containing "and" or "of." Abbreviations should be used only if firmly established in the field.

Highlights

Authors are encouraged to provide 3 to 5 bullet points, each no more than 85 characters including spaces, capturing novel results and any new methods. Highlights should be submitted as a separate editable file with "highlights" in the file name.

Graphical Abstract

A graphical abstract is encouraged. It should summarize the article's content concisely and pictorially, appealing to an interdisciplinary audience. Image dimensions should be 531 × 1328 pixels (height × width) or proportionally larger, readable at 5 × 13 cm. Preferred formats are TIFF, EPS, PDF, or MS Office files. Third-party material requires permission. Generative AI use in graphical abstracts must comply with the journal's AI policy.

Units, Nomenclature, and Symbols

Use the International System of Units (SI). If other units are mentioned, provide SI equivalents. Follow established international nomenclature for genes, proteins, species, and pathogens. Genetic loci should be italicized; protein products should not be. Species names should be italicized and written in full at first mention.

Tables

Tables must be submitted as editable text, not images. Place tables next to the relevant text or at the end of the manuscript. Cite all tables in the text and number them consecutively. Provide captions and place notes below the table body. Avoid vertical rules and shading.

Figures and Artwork

Figures, images, diagrams, and other artwork must be supplied as separate files and cited in the manuscript text. Number images in the order they appear. Use a logical naming convention (e.g., Figure_1, Figure_2).

Do not submit low-resolution files, artwork with disproportionately small text, or multiple images combined into one file. An exception may be made for a small number of directly related images, such as before/during/after photographs.
Every figure requires a caption consisting of a brief title and a description. Symbols and abbreviations must be explained. Keep caption text to a minimum.

Supplementary Material

Supplementary materials should be accurate, relevant, and cited in the manuscript text. Submit all supplementary files with the manuscript, each with a concise descriptive caption. Supplementary files are published as received and are not checked, formatted, or typeset. After submission, supplementary files may be added or replaced only at revision.

Video

The journal accepts video and animation files. Provide a note in the text indicating where each file should be placed, label files clearly, and supply "stills" for each file to serve as icons. Preferred maximum file size is 150 MB per file and 1 GB total. Descriptive text should accompany video content to ensure accessibility.

Research Data

The journal is committed to the storage, access, and discovery of research data. Research data includes observations or experimentation results that validate findings, as well as software, code, models, algorithms, protocols, and methods.
Authors are encouraged to:

• Deposit research data in a relevant data repository
• Cite and link to the dataset in the article
• If deposition is not possible, provide a statement explaining why

A data statement should be provided at submission, stating the availability of any data. Where data cannot be shared due to sensitive or confidential information, the reason should be stated. Data statements appear with the published article.
Data may be linked to the article by providing a repository link during submission, through repository banners on the article page, or by using identifiers within the text in the format: Database: 12345 (e.g., PDB: 1XFN).

Article Structure

Divide the manuscript into clearly defined sections using headings. Limit heading levels to three.
Acknowledgements should appear in a separate section directly before the reference list. Do not include acknowledgements on the title page or as a footnote.
Author Contributions must use the CRediT taxonomy. Corresponding authors are required to acknowledge co-author contributions using the standard roles: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing.
Appendices should be identified as A, B, etc. Equations and tables within appendices should be numbered separately (Eq. A.1, Table A.1).

References

Citation in Text

References are cited in the text by superscript Arabic numerals in the order of their first appearance. The superscript number is placed after punctuation, with a period following the reference number where it concludes a sentence or clause.
Examples:

• The mechanism was first described in 1998.¹.
• Several studies have confirmed this observation.²⁻⁴.
• The role of interferon in viral clearance has been reviewed.⁵,⁶.
• As reported by Smith et al.,⁷. the response was dose-dependent.
• Recent work has challenged this model.⁸⁻¹⁰.

When citing multiple references, use commas for discrete numbers and en dashes for ranges: ¹,³,⁵. or ²⁻⁴.
References cited only in tables or figure legends should be numbered according to the first mention of the table or figure in the text.

Reference List

The reference list appears at the end of the manuscript, numbered in the order of first citation in the text. All references cited in the text must appear in the list, and vice versa.
The journal uses a Vancouver-style, numbered reference format. Journal names are abbreviated according to Index Medicus/MEDLINE. List all authors when there are six or fewer; when there are seven or more, list the first six followed by "et al." Each reference entry concludes with a period.

Reference Types and Examples

1. Journal Article (standard)

Author AA, Author BB, Author CC. Title of the article. Abbreviated Journal Name. Year;Volume:Page range.

Halpern SD, Ubel PA, Caplan AL. Solid-organ transplantation in HIV-infected patients. N Engl J Med. 2002;347:284-287.

2. Journal Article (more than six authors)

Author AA, Author BB, Author CC, Author DD, Author EE, Author FF, et al. Title of the article. Abbreviated Journal Name. Year;Volume:Page range.

Rose ME, Huerbin MB, Melick J, Marion DW, Palmer AM, Schiding JK, et al. Regulation of interstitial excitatory amino acid concentrations after cortical contusion injury. Brain Res. 2002;935:40-46.

3. Journal Article with DOI

Author AA, Author BB. Title of the article. Abbreviated Journal Name. Year;Volume:Page range. doi:xx.xxxx/xxxxx

Devaraju P, Gulati R, Antony PT, Mithun CB, Negi VS. Susceptibility to SLE in South Indian Tamils may be influenced by genetic selection pressure on TLR2 and TLR9 genes. Mol Immunol. 2014;63:123-128. doi:10.1016/j.molimm.2014.11.005

4. Journal Article (online ahead of print)

Author AA, Author BB. Title of the article. Abbreviated Journal Name. Published online Month Day, Year. doi:xx.xxxx/xxxxx

Smith JN, Jones AB. Emerging arboviruses in urban environments. Emerg Infect Dis. Published online March 15, 2026. doi:10.3201/eid2603.250123

5. Book

Author AA. Title of the Book. Edition. Publisher; Year.

Bates B. Bargaining for Life: A Social History of Tuberculosis. 1st ed. University of Pennsylvania Press; 1992.

6. Book Chapter

Author AA. Title of the chapter. In: Editor AA, Editor BB, eds. Title of the Book. Edition. Publisher; Year:Page range.

Hansen B. New York City epidemics and history for the public. In: Harden VA, Risse GB, eds. AIDS and the Historian. National Institutes of Health; 1991:21-28.

7. Edited Book

Editor AA, Editor BB, eds. Title of the Book. Edition. Publisher; Year.

Cohen J, Powderly WG, eds. Infectious Diseases. 4th ed. Elsevier; 2020.

8. Conference Paper or Abstract

Author AA, Author BB. Title of the presentation. In: Proceedings of the Name of the Conference; Date of Conference; Location. Publisher; Year:Page range.

Lee SH, Park JY. Genomic surveillance of influenza A in wastewater. In: Proceedings of the 12th International Conference on Emerging Infectious Diseases; March 3-6, 2025; Seoul, Korea. International Society for Infectious Diseases; 2025:45-46.

9. Thesis or Dissertation

Author AA. Title of Thesis. Level of thesis. Degree-Granting University; Year.

Wells A. Exploring the Development of the Independent, Electronic, Scholarly Journal. M.Sc. thesis. The University of Sheffield; 1999.

10. Website

Title of Site. Available at: URL. Accessed Month Day, Year.

World Health Organization. Global tuberculosis report 2025. Available at: https://www.who.int/publications/global-tuberculosis-report-2025. Accessed January 10, 2026.

11. Dataset

Author AA, Author BB. Title of the dataset. Repository Name. Version. Year. doi:xx.xxxx/xxxxx

Oguro M, Imahiro S, Saito S, Nakashizuka T. Mortality data for Japanese oak wilt disease and surrounding forest compositions. Mendeley Data. Version 1. 2015. doi:10.17632/xwj98nb39r.1

12. Preprint

Author AA, Author BB. Title of the preprint. Preprint. Posted Month Day, Year. doi:xx.xxxx/xxxxx

Kording KP, Mensh B. Ten simple rules for structuring papers. bioRxiv. Preprint posted November 28, 2016. doi:10.1101/088278

13. Government or Institutional Report

Name of Agency. Title of the Report. Report Number. Publisher; Year.

Centers for Disease Control and Prevention. Antibiotic Resistance Threats in the United States, 2019. US Department of Health and Human Services; 2019.

14. Newspaper or Magazine Article

Author AA. Title of the article. Name of Newspaper. Month Day, Year:Section/Page.

Fountain H. For already vulnerable penguins, study finds climate change is another danger. The New York Times. January 29, 2014:A3.

15. Package Insert or Product Monograph

Name of Product. Package insert. Name of Manufacturer; Year.

Remdesivir. Package insert. Gilead Sciences; 2020.

EndNote Model

An EndNote style template compatible with this journal is available for download from the journal's website. The style is based on the Vancouver numbered output style with the following adjustments:

• Citation type: Superscript number, no brackets or parentheses
• Citation punctuation: Period after the reference number where it concludes a sentence or clause
• Multiple citations: Comma-separated for discrete references; en dash for ranges
• Citation placement: After punctuation
• Author list: All authors if ≤6; first six followed by "et al." if ≥7
• Journal name: Abbreviated per Index Medicus/MEDLINE
• DOI: Included at end of reference when available
• Page ranges: Full page ranges, not abbreviated
• Reference list: Each entry concludes with a period

To use the template:

1. Download the Pathogens.ens style file from the journal's website.
2. In EndNote, go to Edit → Output Styles → Open Style Manager.
3. Click Install and select the downloaded style file.
4. In your Word document, select Pathogens from the style dropdown in the EndNote toolbar.
5. Insert citations as superscript numbers in the order of first appearance.

If the EndNote style is not available, authors may use the standard Vancouver style and manually convert the citation format to superscript at revision.

Citation Examples in Context

Single citation:

The viral load declined rapidly after treatment initiation.¹.

Two discrete citations:

Similar findings have been reported in other cohorts.²,³.

Range of citations:

The role of neutralizing antibodies has been extensively reviewed.⁴⁻⁷.

Citation with author name:

As demonstrated by Zhang et al.,⁸. the NS1 protein suppresses interferon induction.

Citation in figure legend:

Figure 1. Phylogenetic analysis of emerging isolates.¹²,¹³.

Citation in table footnote:

Data adapted from the Global Pathogen Surveillance Network.¹⁵.

Research and Publication Ethics

Authors must follow the ethical guidelines of the journal's publishing ethics policy.

Submission Declaration

Submission implies that:

• The work has not been published previously, except as a preprint, abstract, published lecture, academic thesis, or registered report.
• The article is not under consideration elsewhere.
• Publication is approved by all authors and by the responsible authorities where the work was carried out.
• If accepted, the article will not be published elsewhere in the same form without written consent of the copyright holder.

The journal may screen manuscripts to verify compliance with publishing policies.

Authorship

All authors must have made substantial contributions to:

• The conception and design of the study, or acquisition of data, or analysis and interpretation of data
• Drafting the article or revising it critically for important intellectual content
• Final approval of the version to be submitted

All authors are accountable for all aspects of the work. A single corresponding author must be appointed to communicate with the journal.
Changes to authorship are generally not considered after submission. Changes require approval by the journal editor, with written confirmation from all authors, and are not permitted after acceptance.

Declaration of Competing Interests

All authors must disclose any financial and personal relationships that could inappropriately influence or bias their work, including employment, consultancies, stock ownership, honoraria, paid expert testimony, patent applications, grants, and journal affiliations. Authors with no competing interests should state: "The authors declare no competing interests."

Funding Sources

Authors must disclose all funding sources and the role of sponsors in study design, data collection, analysis, interpretation, writing, and the decision to submit. If funders had no involvement, this should be stated.

Declaration of Generative AI Use

Authors must declare the use of generative AI tools in manuscript preparation at submission. AI tools must not be used as a substitute for human critical thinking, expertise, or evaluation, and may only be applied with human oversight. Authors are responsible for verifying accuracy, ensuring originality, and safeguarding data privacy. AI tools must not be listed as authors.
The declaration should be placed in a new section before the reference list:

During the preparation of this work, the author(s) used [NAME OF TOOL / SERVICE] in order to [REASON]. After using this tool/service, the author(s) reviewed and edited the content as needed and take(s) full responsibility for the content of the published article.

The declaration does not apply to basic tools used for grammar, spelling, and reference checking, or to disability-related assistive technology used solely for accessibility. If there is nothing to disclose, no statement is required.
Editors and reviewers are not permitted to upload unpublished manuscripts into generative AI tools. AI tools may be used in a supportive capacity to improve structure and language of review reports or to conduct background literature searches.

Preprints

Authors may share preprints in line with the journal's article sharing policy. Preprint sharing does not count as prior publication. The decision to post or not post has no effect on the editorial process.

Inclusive Language

Authors should use inclusive language throughout, acknowledging diversity, conveying respect, and avoiding anything that implies superiority on the grounds of age, gender, race, ethnicity, culture, sexual orientation, disability, or health condition. Write for gender neutrality using plural nouns as default and avoid "he," "she," or "he/she."

Reporting Sex- and Gender-Based Analyses

Sex and gender-based analyses (SGBA) should be integrated into research design when research involves humans, animals, or eukaryotic cells. Sex and/or gender dimensions should be addressed in the article or declared as a limitation. Definitions of sex and gender applied should be explicitly stated. Authors are advised to consult the SAGER guidelines.

Image Manipulation

Authors may adjust images for clarity, but manipulation for deception or fraud is scientific ethical abuse. No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. Brightness, contrast, and color balance adjustments are acceptable only if they do not obscure or eliminate original information. Nonlinear adjustments such as gamma changes must be disclosed in the figure legend. AI tools must not be used to create or manipulate primary research images, including western blots, microscopy images, histology images, or patient images.
The journal may send images to a secure third-party tool for screening. Editors may request original data or images. The final decision on image acceptability rests with the editors.

Jurisdictional Claims

The journal takes a neutral position on territorial disputes and jurisdictional claims, including maps and institutional affiliations. Maps should show only the area studied and include a note stating that map lines delineate study areas and do not necessarily depict accepted national boundaries.

Studies in Humans

Authors must follow ethical guidelines for research involving humans, their data, and their biological materials.
All studies must comply with relevant laws, regulations, and institutional guidelines, and must be approved by the appropriate institutional committee(s). Medical research involving humans should be carried out in accordance with the Declaration of Helsinki and should follow ICMJE recommendations.
Informed consent must be obtained for research with human participants, including their data and biological materials. Consent must be given without coercion, and privacy rights must always be observed. Written or electronic consent is required for certain studies under national laws. Where only verbal consent was obtained, authors must justify the absence of written consent, name the approving ethics committee, and state how verbal consent was recorded.
Consent for publication must also be obtained. Explicit written consent is required for identifiable participant materials, including case details, videos, recordings, images, photographs, and illustrations. All participant information must be de-identified. Case reports always require consent.
Written consents must be retained by the authors and provided to the journal only on request. Appropriate consents and safeguards are required for research with vulnerable populations.
All studies involving human participants require a statement detailing ethical approval(s), guidelines followed, confirmation of informed consent, and other necessary information, including the date and reference number of any ethical approval.

Human Biological Material

For studies using human organs or tissues, evidence must be provided that they were procured in line with WHO Guiding Principles on Human Cell, Tissue and Organ Transplantation. The source must be transparent and traceable and must not be from executed prisoners or prisoners of conscience.
Manuscripts describing organ transplantation must declare that autonomous consent was obtained from the donor or next of kin and that organs or tissues were not sourced from executed prisoners or prisoners of conscience.

Studies in Animals

All animal experiments should comply with the ARRIVE guidelines (or national equivalent) and relevant animal welfare laws, which may include the U.K. Animals (Scientific Procedures) Act 1986, EU Directive 2010/63/EU, or the National Research Council Guide for the Care and Use of Laboratory Animals.
Manuscripts must contain a statement confirming which guidelines were followed, including the ethics committee approval number where available. If a study was exempt or did not require ethics approval, a statement detailing this should be included.
The sex of animals and, where appropriate, the influence of sex on results should be indicated. Researchers are encouraged to document informed consent from clients or owners in studies involving client-owned animals. For research on threatened or endangered species, authors should consult international best practice guidelines.

Clinical Trials

The journal follows ICMJE clinical trials registration guidelines. Clinical trials must be registered in a public trials registry at or before the onset of patient enrolment. Purely observational studies do not require registration.
The clinical trial registration number must be included in the manuscript, preferably at the end of the abstract. A clinical trial is defined as any research study that prospectively assigns human participants or groups to one or more health-related interventions to evaluate effects on health outcomes.
Authors are required to disclose all postings in registries of results of the same or closely related work. Results previously posted in the same registry as a brief structured abstract (fewer than 500 words) or table are not considered prior publication.
Authors are encouraged to follow CONSORT guidelines when presenting randomized controlled trials and to provide the CONSORT checklist at submission, with a flow diagram illustrating patient progress.

Delayed Publication, Withdrawal, Correction, and Retraction

Authors needing to delay publication should contact the editorial office as early as possible. The journal will attempt to honor timely requests but cannot guarantee them.
For questions about withdrawal, correction, or retraction, consult the journal's article correction, retraction, and removal policy.

After Acceptance

Publishing Agreement

Authors complete a publishing agreement after acceptance. The corresponding author receives a link to the online agreement.

License Options

Authors are offered open access user license options determining how the article may be reused. Authors should review these options and any funding body license requirements before selecting.

Permission for Copyrighted Works

Written permission from copyright owners is required for excerpts from other copyrighted works, with credit given in the article using the journal's permission request and license form.

Proof Correction

Corresponding authors receive an email with a link to the online proofing system. Proof corrections should be provided within two days. The purpose of proofing is to check typesetting, editing, completeness, and correctness. Significant changes at this stage require journal editor approval.

Share Link

A customized Share Link providing 50 days of free access to the final published article will be sent to the corresponding author. It can be shared by email or social media. Share Links are not provided for open access articles, which are freely available via the DOI link.

Resources for Authors

The journal offers free e-learning modules, webinars, downloadable guides, and resources on research writing and peer review. Language editing services are available for authors who wish to eliminate grammatical or spelling errors and conform to correct scientific English.

Getting Help and Support

For questions about the editorial process or technical support, authors should consult the journal's publishing support center.

SKLS — Still Know Little Science
Advancing knowledge with humility.