Use of Microbiological Information. The Council Policy Committee (CPC) of the American Society for Microbiology affirms the long-standing position of the Society that microbiologists will work for the proper and beneficent application of science and will call to the attention of the public or the appropriate authorities misuses of microbiology or of information derived from microbiology. ASM members are obligated to discourage any use of microbiology contrary to the welfare of humankind, including the use of microbes as biological weapons. Bioterrorism violates the fundamental principles expressed in the Code of Ethics of the Society and is abhorrent to ASM and its members.
ASM recognizes that there are valid concerns regarding the publication of information in scientific journals that could be put to inappropriate use as described in the CPC resolution mentioned above. Members of the ASM Publications Board will evaluate the rare manuscript that might raise such issues during the review process. However, as indicated elsewhere in these Instructions, research articles must contain sufficient detail, and material/information must be made available, to permit the work to be repeated by others. Supply of materials should be in accordance with laws and regulations governing the shipment, transfer, possession, and use of biological materials and must be for legitimate, bona fide research needs. Links to, and information regarding, these laws and regulations can be found at http://www.asm.org/Policy/index.asp.
General Requirements. Manuscripts submitted to the journal must represent reports of original research, and the original data must be available for review by the editor if necessary.
All authors of a manuscript must have agreed to its submission and are responsible for its content (initial submission and any subsequent versions), including appropriate citations and acknowledgments, and must also have agreed that the corresponding author has the authority to act on their behalf in all matters pertaining to publication of the manuscript. The corresponding author is responsible for obtaining such agreements and for informing the coauthors of the manuscript's status throughout the submission, review, and publication process. For Authors' Corrections and Retractions, signed letters of agreement from all of the authors must be submitted (see p. 11).
By submission of a manuscript to the journal, the authors guarantee that they have the authority to publish the work and that the manuscript, or one with substantially the same content, was not published previously, is not being considered or published elsewhere, and was not rejected on scientific grounds by another ASM journal.
It is expected that the authors will provide written assurance that permission to cite unpublished data or personal communications has been granted.
By publishing in the journal, the authors agree that any DNAs, viruses, microbial strains, mutant animal strains, cell lines, antibodies, and similar materials newly described in the article are available from a national collection or will be made available in a timely fashion, at reasonable cost, and in limited quantities to members of the scientific community for noncommercial purposes. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner.
Similarly, the authors agree to make available computer programs, originating in the authors' laboratory, that are the only means of confirming the conclusions reported in the article but that are not available commercially. The program(s) and suitable documentation regarding its (their) use may be provided by any of the following means: (i) as a program transmitted via the Internet, (ii) as an Internet server-based tool, or (iii) as a compiled or assembled form on a suitable medium (e.g., magnetic or optical). It is expected that the material will be provided in a timely fashion and at reasonable cost to members of the scientific community for noncommercial purposes. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner.
Primary Publication. A scientific paper or its substance published in a serial, periodical, book, conference report, symposium proceeding, or technical bulletin, posted on a nonpersonal website, or made available through any other retrievable source, including CD-ROM and other electronic forms, is unacceptable for submission to an ASM journal on grounds of prior publication.
Posting of a method/protocol on a nonpersonal website should not interfere with the author's ability to have a manuscript utilizing that technique considered for publication in an ASM journal; however, ultimately, it is an editorial decision whether the method constitutes the substance of a paper.
Posting of a limited amount of original data on a personal/university/company website or websites of small collaborative groups working on a problem does not preclude subsequent submission to, and publication by, an ASM journal. The posted data, however, may not constitute the substance of the submission. Specific questions about this policy may be referred to the Publications Board chairman on a case-by-case basis. Posting of theses and dissertations on a personal/university-hosted website does not preclude subsequent submission to, and publication by, an ASM journal.
Posting of unpublished sequence data on the Internet is usually not considered prior publication; however, the address (URL) of the source of the sequence should be included in the text.
Preliminary disclosures of research findings webcast as meeting presentations or published in abstract form as adjuncts to a meeting, e.g., part of a program, are not considered prior publication.
It is incumbent upon the author to acknowledge any prior publication, including his own articles, of the data contained in a manuscript submitted to an ASM journal. A copy of the relevant work should be submitted with the paper as supporting material.
Ultimately, it is an editorial decision whether the material constitutes the substance of a paper.
Permissions. The corresponding author is responsible for obtaining permission from both the original author and the original publisher (i.e., the copyright owner) to reproduce or modify figures and tables and to reproduce text (in whole or in part) from previous publications.
The original signed permission(s) must be submitted directly to the editor, outside the Rapid Review system, no later than the modification stage and should be identified as to the relevant item in the ASM manuscript (e.g., “permissions for Fig. 1 in JVI00123-06”). In addition, a statement indicating that the material is being reprinted with permission must be included in the relevant figure legend or table footnote of the manuscript. Reprinted text must be enclosed in quotation marks, and the permission statement must be included as running text or indicated parenthetically.
For supplemental material intended for posting by ASM (see p. 5), if the authors of the JVI manuscript are not also the owner of the supplemental material, the corresponding author must send to ASM signed permission from the copyright owner that allows posting of the material, as a supplement to the article, by ASM. The corresponding author is also responsible for incorporating in the supplemental material any copyright notices required by the owner.
Authorship. An author is one who made a substantial contribution to the overall design and execution of the experiments; therefore, ASM considers all authors responsible for the entire paper. Individuals who provided assistance, e.g., supplied strains or reagents or critiqued the paper, need not be listed as authors but may be recognized in the Acknowledgments section.
A study group, surveillance team, working group, consortium, or the like (e.g., the Active Bacterial Core Surveillance Team) may be listed as a coauthor in the byline if its contributing members satisfy the requirements for authorship and accountability as described in these Instructions. The names (and institutional affiliations if desired) of the contributing members only may be given in a footnote keyed to the study group name in the byline or as a separate paragraph in the Acknowledgments section.
If the contributing members of the group associated with the work do not fulfill the criteria of substantial contribution to and responsibility for the paper, the group may not be listed in the author byline. Instead, it and the names of its contributing members may be listed in the Acknowledgments section.
All authors must agree to the order in which their names are listed in the byline. Statements regarding equal contributions by two or more authors (e.g., X.J. and Y.S. contributed equally to
…
) are permitted as footnotes to bylines. Other statements of attribution may be included in the Acknowledgments section.
A change in authorship (order of listing or addition or deletion of a name) after submission of the manuscript will be implemented only after receipt of signed statements of agreement from all parties involved. Disputes about authorship may delay review and/or publication of the manuscript.
Conflict of Interest. All authors are expected to disclose, in the manuscript submittal letter, any commercial affiliations as well as consultancies, stock or equity interests, and patent-licensing arrangements that could be considered to pose a conflict of interest regarding the submitted article. (Inclusion of a company name in the author address lines of the manuscript does not constitute disclosure.) Details of the disclosure to the editor will remain confidential. However, it is the responsibility of authors to provide, in the Acknowledgments section, a general statement disclosing financial or other relationships that are relevant to the study. Examples of potentially conflicting interests that should be disclosed include relationships that might detract from an author's objectivity in presentation of study results, and interests whose value would be enhanced by the results presented. All funding sources for the project, institutional and corporate, should be credited in the Acknowledgments section, as described below. In addition, if a manuscript concerns a commercial product, the manufacturer's name must be indicated in the Materials and Methods section or elsewhere in the text, as appropriate, in an obvious manner.
Copyright. To maintain and protect the Society's ownership and rights and to continue to afford scientists the opportunity to publish in high-quality journals, ASM requires the corresponding author to sign a copyright transfer agreement on behalf of all the authors. This agreement is sent to the corresponding author when the manuscript is accepted and scheduled for publication. Unless this agreement is executed (without changes and/or addenda), ASM will not publish the manuscript.
In the copyright transfer agreement signed by an author, ASM grants to that author (and coauthors) the right to republish discrete portions of his (their) article in any other publication (print, CD-ROM, and other electronic forms) of which he is (they are) the author(s) or editor(s), on the condition that appropriate credit is given to the original ASM publication. This republication right also extends to posting on a host computer to which there is access via the Internet. Except as indicated below, significant portions of the article may not be reprinted/posted without ASM's prior written permission, however, as this would constitute duplicate publication.
Authors may post their own published articles on their personal or university-hosted (but not corporate, government, or similar) websites without ASM's prior written permission provided that appropriate credit is given (i.e., either the copyright lines shown on the top of the first page of the PDF version or “Copyright © American Society for Microbiology, [insert journal name, volume number, page numbers, and year]” for the HTML version).
The copyright transfer agreement asks that authors who were U.S. Government employees and who wrote the article as part of their employment duties be identified. This is because works authored solely by such U.S. Government employees are not subject to copyright protection, so there is no copyright to be transferred. The other provisions of the copyright transfer agreement, such as author representations of originality and authority to enter into the agreement, apply to U.S. Government employee-authors as well as to other authors.
ASM also requires that copyright transfer agreements be signed for cover artwork/photographs.
Copyright for supplemental material (see p. 5) remains with the author, but a license permitting the posting by ASM will be sent, along with the article copyright transfer agreement, to the corresponding author for signing at the acceptance stage. (If the author of the article is not also the copyright owner of the supplemental material, the corresponding author must send to ASM signed permission from the owner that allows posting of the material, as a supplement to the article, by ASM. The corresponding author is also responsible for incorporating into the supplemental material any copyright notices required by the owner.)
Funding Agency Repositories. The National Institutes of Health (NIH) requests that its grantee and intramural authors provide copies of their accepted manuscripts to PubMed Central (PMC) for posting in the PMC Public Access Repository. ASM allows such JVI authors to do so. ASM also allows JVI authors whose work was supported by similar funding agencies that have public access requirements like those of NIH (e.g., the Wellcome Trust) to post their accepted manuscripts in publicly accessible electronic repositories maintained by those funding agencies. If a funding agency does not itself maintain such a site, then ASM allows the author to fulfill that requirement by depositing the manuscript (not the typeset article) in an appropriate institutional or subject-based open repository established by a government or noncommercial entity.
Since ASM makes the final, typeset articles from its primary-research journals available free of charge on the ASM Journals and PMC websites 6 months after final publication, ASM recommends that when submitting the accepted manuscript to PMC or similar public access site, the author specify that the posting release date for the manuscript be no earlier than 6 months after publication of the typeset article by ASM.
Use of Human Subjects or Animals in Research. The use of human subjects or other animals for research purposes is regulated by the federal government and individual institutions. Manuscripts containing information related to human or animal use should clearly state that the research has complied with all relevant federal guidelines and institutional policies. Copies of these guidelines and policy statements must be available for review by the editor if necessary.
Patient Identification. When isolates are derived from patients in clinical studies, do not identify them by using the patients' initials, even as part of a strain designation. Change the initials to numerals or use randomly chosen letters. Do not give hospital unit numbers; if a designation is needed, use only the last two digits of the unit. (Note: Established designations of some viruses and cell lines, although they consist of initials, are acceptable [e.g., JC virus, BK virus, and HeLa cells].)
Nucleotide and Amino Acid Sequences. It is expected that newly determined nucleotide and/or amino acid sequence data will be deposited and GenBank/EMBL/DDBJ accession numbers will be included in the manuscript no later than the modification stage of the review process. It is also expected that the sequence data will be released to the public no later than the publication date of the article. The accession numbers should be included in a separate paragraph at the end of the Materials and Methods section for full-length papers or at the end of the text for Notes. If conclusions in a manuscript are based on the analysis of sequences and a GenBank/EMBL/DDBJ accession number is not provided at the time of the review, authors should provide the sequence data as supplemental material.
It is expected that, when previously published sequence accession numbers are cited in a manuscript, the original citations (e.g., journal articles) will be included in the References section when possible or reasonable.
Authors are also expected to do elementary searches and comparisons of nucleotide and amino acid sequences against the sequences in standard databases (e.g., GenBank) immediately before manuscripts are submitted and again at the proof stage.
Analyses should specify the database, and the date of each analysis should be indicated in the format MM/YY. If relevant, the version of the software used should be specified.
See p. 14 for nucleic acid sequence formatting instructions.
The URLs of the databases mentioned above are as follows: DNA Data Bank of Japan (DDBJ), http://www.ddbj.nig.ac.jp; EMBL Nucleotide Sequence Submission (EMBL), http://www.ebi.ac.uk; and GenBank, National Center for Biotechnology Information (GenBank), http://www.ncbi.nlm.nih.gov.
Structural Determinations. It is expected that coordinates for new structures of macromolecules will be deposited in the Protein Data Bank and that assigned identification codes will be included in the manuscript no later than the modification stage of the review process. It is also expected that the coordinates will be released to the public no later than the publication date of the article. Authors are encouraged to send coordinates with their original submission, however, so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph at the end of the Materials and Methods section for full-length papers or at the end of the text for Notes.
The URLs for coordinate deposition are http://pdb.rutgers.edu and http://pdbdep.protein.osaka-u.ac.jp.
Microarray Data. It is expected that the entire set of supporting microarray data will be deposited in the appropriate public database (e.g., GEO, ArrayExpress, or CIBEX) and that the assigned accession number(s) will be included in the manuscript no later than the modification stage of the review process. It is also expected that the data will be released to the public no later than 6 months after publication of the typeset article. Authors are encouraged to send the relevant data with their original submission, however, so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph at the end of the Materials and Methods section for full-length papers or at the end of the text for Notes.
The URLs of the databases mentioned above are as follows: Gene Expression Omnibus (GEO), http://www.ncbi.nlm.nih.gov/geo; ArrayExpress, http://www.ebi.ac.uk/arrayexpress; and Center for Information Biology Gene Expression Database (CIBEX), http://cibex.nig.ac.jp.
Supplemental Material. Supplemental material intended for posting by ASM may not include additional figures or tables that simply support the authors' conclusions. It must be restricted to large or complex data sets or results that cannot be readily displayed in printed form because of space or technical limitations. Such material may include data from microarray, structural, biochemical, or video imaging analyses. In such cases, the manuscript submitted for review should include a distillation of the results so that the principal conclusions are fully supported without referral to the supplemental material.
Supplemental material intended for posting by ASM must be uploaded in Rapid Review and will be reviewed along with the manuscript. The decision to publish (i.e., post online only) the material with the article if it is accepted will be made by the editor and conveyed to the corresponding author in the acceptance e-mail. Note, therefore, it is possible that an article will be accepted but that the supplemental material will not be.
If the software required for users to view/use the supplemental material is not embedded in the file, you are urged to use shareware or generally available/easily accessible programs.
Unlike the article, supplemental material will not be edited by the ASM Journals staff and proofs will not be made available.
Supplemental material will always remain associated with its article and is not subject to any modifications after publication.
Material that has been published previously (print or online) is not acceptable for posting as supplemental data. Instead, the appropriate reference(s) to the original publication should be made in the article text.
Copyright for the supplemental material remains with the author, but a license permitting the posting by ASM will be sent, along with the article copyright transfer agreement, to the corresponding author for signing. If you are not the copyright owner, you must provide to ASM signed permission from the owner that allows posting of the material, as a supplement to your article, by ASM. You are responsible for including in the supplemental material any copyright notices required by the owner.
A one-time charge (amount not yet determined) may be levied for posting of supplemental material. When instituted, the charge will be indicated in the ASM acceptance letter.
Compliance. Failure to comply with the policies described in these Instructions may result in a letter of reprimand, a suspension of publishing privileges in ASM journals, and/or notification of the authors' institutions.
Warranties and Exclusions. Articles published in this journal represent the opinions of the authors and do not necessarily represent the opinions of ASM. ASM does not warrant the fitness or suitability, for any purpose, of any methodology, kit, product, or device described or identified in an article. The use of trade names is for identification purposes only and does not constitute endorsement by ASM.
Page Charges. Authors whose research was supported by grants, special funds (including departmental and institutional), or contracts (including governmental) or whose research was done as part of their official duties (government, corporate, etc.) are required to pay page charges.
For a corresponding author who is an ASM member, page charges are currently $65 per page for the first six pages and $200 per page for each page in excess of six (subject to change without notice). To obtain the member rate, the corresponding author must be an ASM member.
For a nonmember corresponding author, page charges are currently $75 per page for the first six pages and $250 for each page in excess of six. A corresponding author who is not an ASM member may join ASM to obtain the member rate.
If the research was not supported by any of the means described above, a request to waive the charges may be mailed (Journals Department, ASM, 1752 N St., N.W., Washington, DC 20036-2904, USA) or faxed (202-942-9355) to the Journals Department. This request must indicate how the work was supported and should be accompanied by copies of the title page and Acknowledgments section.
Minireviews, Guest Commentaries, and Comment Letters to the Editor are not subject to page charges. New-Data Letters to the Editor are subject to page charges.
Editorial Style. The editorial style of ASM journals conforms to the ASM Style Manual for Journals (American Society for Microbiology, 2006, in-house document) and How To Write and Publish a Scientific Paper, 5th ed. (Oryx Press, 1998), as interpreted and modified by the editors and the ASM Journals Department.
The editors and the Journals Department reserve the privilege of editing manuscripts to conform with the stylistic conventions set forth in the aforesaid publications and in these Instructions.
Review Process. All manuscripts are considered to be confidential and are reviewed by the editors, members of the editorial board, or qualified ad hoc reviewers. To expedite the review process, authors should recommend at least two reviewers who are members of the JVI editorial board, are not members of their institution(s), and have never been associated with them or their laboratory(ies); please provide their contact information where indicated on the submission form.
Copies of in-press and submitted manuscripts that are important for judgment of the present manuscript should be included as supporting material to facilitate the review.
When a manuscript is submitted to the journal, it is given a number (e.g., JVI00047-06 version 1) and assigned to one of the editors. (Always refer to this number in communications with the editor and the Journals Department.) It is the responsibility of the corresponding author to inform the coauthors of the manuscript's status throughout the submission, review, and publication processes. The reviewers operate under strict guidelines set forth in “Guidelines for Reviewers” (http://www.journals.asm.org/misc/reviewguide.shtml) and are expected to complete their reviews expeditiously.
The corresponding author is notified, generally within 4 to 6 weeks after submission, of the editor's decision to accept, reject, or require modification. When modification is requested, the corresponding author must either submit the modified version within 2 months or withdraw the manuscript. A point-by-point response to the reviews must be provided in the Rebuttal section of the Rapid Review submission form for the revised manuscript, and a compare copy of the manuscript (without figures) should be included as supporting material if the editor requested one.
Manuscripts that have been rejected, or withdrawn after being returned for modification, may be resubmitted if the major criticisms have been addressed. (Note: A manuscript rejected by one ASM journal on scientific grounds or on the basis of its general suitability for publication is considered rejected by all other ASM journals.) The cover letter must state that the manuscript is a resubmission, and the former manuscript number should be provided in the appropriate field on the submission form. A point-by-point response to the reviews and a compare copy of the revised manuscript showing the changes must be included as supporting material (the Rebuttal section appears in the submission form only if the manuscript is a modification). Resubmitted manuscripts are normally handled by the original editor.
Rejected manuscripts may be resubmitted only once unless permission has been obtained from the original editor or from the editor in chief.
Notification of Acceptance. When an editor has decided that a manuscript is acceptable for publication on the basis of scientific merit, the author and the Journals Department are notified. The text files undergo an automated preediting, cleanup, and tagging process specific to the particular article type, and the illustrations are examined. If all files have been prepared according to the criteria set forth in these Instructions and those in Rapid Review, the acceptance procedure will be completed successfully. If there are problems that would cause extensive corrections to be made at the copyediting stage or if the files are not acceptable for production, ASM Journals staff will contact the corresponding author.
Once all the material intended for publication has been determined to be adequate, the manuscript is scheduled for the next available issue and an acceptance letter indicating the month of publication, approximate page proof dates, and table of contents section is mailed to the corresponding author; a copyright transfer agreement is also included, as is a license to permit posting of supplemental material (if applicable). The editorial staff of the ASM Journals Department completes the editing of the manuscript to bring it into conformity with prescribed standards.
Page Proofs. Page proofs, together with a query sheet and instructions for handling proofs, will be made available to the corresponding author electronically via a PDF file that can be accessed through a unique password. Since corresponding authors will be notified of the availability of their PDF proofs, instructed how to access information about page charges, reprints, and color figure charges (if applicable), and assigned their unique password via e-mail, an e-mail address must be supplied in the correspondent footnote. Failure to do so may result in a delay in publication. The PDF page proofs must be printed out, and corrections must be written on the hard copy. Queries must be answered on the query page or on a separate sheet of paper, and any changes related to the queries must be indicated on the proofs. Note that the copy editor does not query at every instance where a change has been made. Queries are written only to request necessary information or clarification of an unclear passage or to draw attention to edits that may have altered the sense. It is the author's responsibility to read the entire text, tables, and figure legends, not just items queried. As soon as the page proofs are corrected and signed by the person who proofread them (within 48 h), they should be mailed or sent by a courier service such as FedEx, not faxed or sent as an e-mail attachment, to the ASM Journals Department.
The proof stage is not the time to make extensive corrections, additions, or deletions. Important new information that has become available between acceptance of the manuscript and receipt of the proofs may be inserted as an addendum in proof with the permission of the editor. If references to unpublished data or personal communications are added, it is expected that written assurance granting permission for the citation will be included. Limit changes to correction of spelling errors, incorrect data, and grammatical errors and updated information for references to manuscripts that have been submitted or are in press. If URLs have been provided in the article, recheck the sites to ensure that the addresses are still accurate and the material that you expect the reader to find is indeed there.
Questions about late proofs and problems in the proofs should be directed to the ASM Journals Department (telephone, 202-942-9234). Questions about accessing or viewing your PDF proofs should be directed to Katie Gay of Cadmus Professional Communications at 804-261-3155 or gayk/at/cadmus.com.
Reprints. Reprints (in multiples of 100) may be purchased by all coauthors. In the proof notification e-mail, the corresponding author will be instructed how to access information about reprints.
The corresponding authors of Minireviews and Guest Commentaries will receive 100 free reprints of their contribution; additional reprints (in multiples of 100) may be purchased if desired. As for regular articles, the corresponding author will be instructed, in the proof notification e-mail, how to access information about reprints.
PDF Files. A corresponding author who has included an e-mail address in his “corresponding author” footnote will have limited access (10 downloads, total) to the PDF file of his published article. An e-mail alert will automatically be sent to him on the day the issue is posted. It will provide a URL, which will be required to obtain access, and instructions. An article may be viewed, printed, or stored, provided that it is for the author's own use.
Should coauthors or colleagues be interested in viewing the paper for their own use, the corresponding author may provide them with the URL; a copy of the article may not be forwarded electronically. However, they must be made aware of the terms and conditions of the ASM copyright. (For details, go to http://www.journals.asm.org/misc/terms.shtml.) Note that each such download will count toward the corresponding author's total of 10. After 10 downloads, access will be denied and can be obtained only through a subscription to the journal (either individual or institutional) or after the standard access control has been lifted (i.e., 6 months after publication).