JOURNAL OF VIROLOGY

Use of Microbiological InformationThe 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 RequirementsManuscripts 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 “Authors’ Corrections” and “Retractions” below).

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, subject to requirements or limitations imposed by laws or governmental regulations of the United States, 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 PublicationA 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. Work, or its substance, presented as a meeting poster and subsequently reproduced or distributed as a “company white paper” is also unacceptable for submission 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. Similarly, posting for sale on a commercial or similar website of an original, unmodified thesis or dissertation (i.e., as submitted to, and accepted by, the thesis/dissertation committee) 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) where the sequence is posted 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/her 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 supplemental material.

Ultimately, it is an editorial decision whether the material constitutes the substance of a paper.

PermissionsThe 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.

Permission(s) must be obtained no later than the modification stage. The original signed permission(s) must be identified as to the relevant item in the ASM manuscript (e.g., “permissions for Fig. 1 in JVI00123-09”) and submitted to the ASM production editor on request. 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 “Supplemental Material” below), if the authors of the JVI manuscript are not also the owners 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.

AuthorshipAn 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 and must be agreed to by all of the authors. Other statements of attribution may be included in the Acknowledgments section.

A change in authorship (order of listing, addition or deletion of a name, or corresponding author designation) 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 or prevent review and/or publication of the manuscript. Should the individuals involved be unable to reach an accord, review and/or publication of the manuscript can proceed only after the matter is investigated and resolved by the authors’ institution(s) and an official report of such and signed statements of agreement are provided to ASM.

Conflict of InterestAll 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 manuscript. (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.

CopyrightTo 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 article.

In the copyright transfer agreement signed by an author, ASM grants to that author (and coauthors) the right to republish discrete portions of his/her (their) article in any other publication (print, CD-ROM, and other electronic forms) of which he/she 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., the copyright lines shown at the top of the first page).

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 “Supplemental Material” below) 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 RepositoriesThe 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 the 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 a 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 ResearchThe use of human subjects or 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 IdentificationWhen 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 SequencesIt 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 (online posting) date of the accepted manuscript. 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 as, e.g., January 2009. If relevant, the version of the software used should be specified.

See “Presentation of Nucleic Acid Sequences” below 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 Database (EMBL), http://www.ebi.ac.uk/embl/; and GenBank, National Center for Biotechnology Information (GenBank), http://www.ncbi.nlm.nih.gov/.

Structural DeterminationsIt is expected that coordinates for new structures of macromolecules determined by X-ray crystallography or cryo-electron microscopy 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 (online posting) date of the accepted manuscript. 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://rcsb-deposit.rutgers.edu/ and http://pdbdep.protein.osaka-u.ac.jp/.

Microarray DataIt 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 the publication (online posting) date of the accepted manuscript. 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/projects/geo/; ArrayExpress, http://www.ebi.ac.uk/microarray-as/ae/; and Center for Information Biology Gene Expression Database (CIBEX), http://cibex.nig.ac.jp/index.jsp.

Supplemental MaterialSupplemental material intended for posting by ASM should be restricted primarily to large or complex data sets or results that cannot readily be 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 as a separate Supplemental Material file(s) in Rapid Review and will be reviewed along with the manuscript. The maximum size permitted for an individual file is 25 MB. If your file exceeds this size, you must use a file compression utility (e.g., WinZip or Stuffit) to reduce the size below 25 MB. The decision to publish (i.e., post online only) the material with the article if it is accepted will be made by the editor. It is possible that a manuscript 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 manuscript, supplemental material will not be edited by the ASM Journals staff and proofs will not be made available. References related to supplemental material only should not be listed in the References section of an article; instead, include them with the supplemental material hosted by ASM or posted on a personal/institutional website.

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 material. Instead, the appropriate reference(s) to the original publication should be made in the manuscript 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.

ComplianceFailure 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.

Authors employed by companies whose policies do not permit them to comply with the ASM policies may be sanctioned as individuals and/or ASM may refuse to consider manuscripts having authors from such companies.

Warranties and ExclusionsArticles 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 ChargesAuthors 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 or corporate, etc.) are required to pay page charges (based on the number of typeset pages, including illustrations, in the article).

For a corresponding author who is an ASM member, page charges are currently $65 per page for the first eight pages and $125 per page for each page in excess of eight (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 eight pages and $250 for each page in excess of eight (subject to change without notice). 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 sent to the Journals Department, ASM, 1752 N St., N.W., Washington, DC 20036-2904, USA (fax, 202-942-9355; e-mail, aluckey{at}asmusa.org). The request must include the manuscript control number assigned by ASM and indicate how the work was supported.

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 StyleThe editorial style of ASM journals conforms to the ASM Style Manual for Journals (American Society for Microbiology, 2009, in-house document) and How To Write and Publish a Scientific Paper, 6th ed. (Greenwood Press, Westport, CT, 2006), 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 ProcessAll 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 must recommend at least five reviewers who have expertise in the field, who are not members of their institution(s), who have not recently been associated with their laboratory(ies), and who could not otherwise be considered to pose a conflict of interest regarding the submitted manuscript. At least three of the recommended reviewers must be editorial board members. Please provide, where indicated on the submission form, contact information for suggested reviewers who are not editorial board members.

Copies of in-press and submitted manuscripts that are important for judgment of the present manuscript should be included as supplemental material to facilitate the review.

When a manuscript is submitted to the journal, it is given a number (e.g., JVI00047-09 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 designated section of the Rapid Review submission form for the revised manuscript, and a compare copy of the manuscript (without figures) should be included as supplemental material if the editor requested one.

Manuscripts that have been rejected, or withdrawn after being returned for modification, may be resubmitted to the same ASM journal if the major criticisms have been addressed. 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; however, a manuscript rejected solely on the basis of scope may be “resubmitted” to a more appropriate ASM journal. A manuscript is considered a resubmission no matter how much (or little) it differs from the rejected or withdrawn manuscript and regardless of how much time has passed.

For all resubmissions (to the same or a different journal, and irrespective of the extent of the revisions and irrespective of the amount of time between rejection and resubmission), the cover letter must state that the manuscript is a resubmission, and the former manuscript number must be provided in the appropriate field on the submission form. A point-by-point response to the review(s) and a compare copy of the revised manuscript showing the changes must be included as supplemental material (the Rebuttal section appears in the submission form only if the manuscript is a modification). Manuscripts resubmitted to the same journal 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 AcceptanceWhen 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. A PDF version of the accepted manuscript is posted online as soon as possible (see below).

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.

Publish ahead of PrintFor its primary-research journals, ASM posts online PDF versions of manuscripts that have been peer reviewed and accepted but not yet copyedited. This feature is called “[journal acronym] Accepts” (e.g., JVI Accepts) and is accessible from the Journals website. The manuscripts are published online as soon as possible after acceptance, on a weekly basis, before the copyedited, typeset articles are published. They are posted “as is” (i.e., as submitted by the authors at the modification stage) and do not reflect ASM editorial changes. No corrections/changes to the PDF manuscripts are accepted. Accordingly, there likely will be differences between the JVI Accepts manuscripts and the final, typeset articles. The manuscripts remain listed on the JVI Accepts page until the final, typeset articles are posted. At that point, the manuscripts are removed from the JVI Accepts page and become available only through links from the final, typeset articles. The manuscripts are under subscription access control until 6 months after the typeset articles are posted, when free access is provided to everyone (subject to the applicable ASM license terms and conditions). Supplemental material intended, and accepted, for publication is not posted until publication of the final, typeset article.

Instructions on how to cite such manuscripts may be found in the “References” section below.

Page ProofsPage 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, 1752 N St., N.W., Washington, DC 20036-2904.

The proof stage is not the time to make extensive corrections, additions, or deletions. Figures as they appear in the proofs are for validation of content and placement, not quality of reproduction or color accuracy. Print output of figures in the PDF page proofs will be of lower quality than the same figures viewed on a monitor. Please avoid making changes to figures based on quality of color or reproduction in proof. Starting in 2009, the online version will be considered the journal of record for all ASM journals. If you submit RGB color files, the figures published online in the final version should be a very close color match to your figure source files; color figures in the printed issue may not look exactly like the online versions or the data as originally captured because the RGB files will be converted to CMYK color for print production. If you submit CMYK color files, the figures published in print should be a close color match to your source files, but CMYK files are not optimal for online color reproduction.

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 Communications at 804-261-3155 or gayk{at}cadmus.com.

ReprintsReprints (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 may 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 FilesA corresponding author who has included an e-mail address in his/her “corresponding author” footnote will have limited access (10 downloads, total) to the PDF file of his/her published article. An e-mail alert will automatically be sent to him/her 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).

Full-Length PapersFull-length papers should include the elements described in this section.

NotesThe Note format is intended for the presentation of brief observations that do not warrant full-length papers. Submit Notes in the same way as full-length papers. They receive the same review, they are not published more rapidly than full-length papers, and they are not considered preliminary communications.

Each Note must have an abstract of no more than 100 words. Do not use section headings in the body of the Note; combine methods, results, and discussion in a single section. Paragraph lead-ins are permissible. The text should be kept to a minimum and should not exceed 1,600 words (include the word count on the manuscript title page); the total number of figures and tables should not exceed four. Materials and methods should be described in the text, not in figure legends or table footnotes. Present acknowledgments as in full-length papers, but do not use a heading. The References section is identical to that of full-length papers.

MinireviewsMinireviews are brief (limit of six printed pages exclusive of references) summaries of important developments in virology research. They must be based on published articles and may address any subject within the scope of the journal.

Minireviews are solicited by the Minireview editor and are subject to review. Unsolicited reviews will not be considered. Ideas for Minireviews may be sent to the Minireview editor. Manuscripts should be submitted via Rapid Review.

Guest CommentariesGuest Commentaries are invited communications concerning topics relevant to the readership of JVI and are intended to engender discussion. Reviews of the literature, methods and other how-to papers, and responses targeted at a specific published paper are not appropriate. Guest Commentaries are subject to review.

The length may not exceed two printed pages, and the format is like that of a Minireview (see above). Guest Commentaries should be submitted via Rapid Review.

Letters to the EditorTwo types of Letters to the Editor may be submitted. The first type (Comment Letter) is intended for comments on final, typeset articles published in the journal (not on publish-ahead-of-print manuscripts) and must cite published references to support the writer's argument. The second type (New-Data Letter) may report new, concise findings that are not appropriate for publication as full-length papers or Notes.

Letters may be no more than 500 words long and must be typed double-spaced. Refer to a recently published Letter for correct formatting. Note that authors and affiliations are listed at the foot of the Letter. Provide only the primary affiliation for each author.

All Letters to the Editor must be submitted electronically, and the type of Letter (New Data or Comment) must be selected from the drop-down list in the submission form. For Letters commenting on published articles, the cover letter should state the volume and issue in which the article was published, the title of the article, and the last name of the first author. In the Abstract section of the submission form, put “Not Applicable.” Letters to the Editor do not have abstracts. Both types of Letter must have a title, which must appear on the manuscript and on the submission form. Figures and tables should be kept to a minimum.

If the Letter is related to a published article, it will be sent to the editor who handled the article in question. If the editor believes that publication is warranted, he/she will solicit a reply from the corresponding author of the article and make a recommendation to the editor in chief. Final approval for publication rests with the editor in chief.

New-Data Letters will be assigned to an editor according to subject matter and will be reviewed by that editor and the editor in chief. Final approval for publication rests with the editor in chief.

Please note that some indexing/abstracting services do not include Letters to the Editor in their databases.

ErrataThe Erratum section provides a means of correcting errors that occurred during the writing, typing, editing, or printing (e.g., a misspelling, a dropped word or line, or mislabeling in a figure) of a published article. Submit Errata via Rapid Review (see “How To Submit Manuscripts,” above). In the Abstract section of the submission form (a required field), put “Not Applicable.” Upload the text of your Erratum as an MS Word file. Please see a recent issue for correct formatting.

Authors’ CorrectionsThe Author's Correction section provides a means of correcting errors of omission (e.g., author names or citations) and errors of a scientific nature that do not alter the overall basic results or conclusions of a published article (e.g., an incorrect unit of measurement or order of magnitude used throughout, contamination of one of numerous cultures, or misidentification of a mutant strain, causing erroneous data for only a [noncritical] portion of the study). Note that the addition of new data is not permitted.

For corrections of a scientific nature or issues involving authorship, including contributions and use or ownership of data and/or materials, all disputing parties must agree, in writing, to publication of the Correction. For omission of an author's name, letters must be signed by the authors of the article and the author whose name was omitted. The editor who handled the article will be consulted if necessary.

Submit an Author's Correction via Rapid Review (see “How To Submit Manuscripts,” above). In the submission form, select Erratum as the manuscript type; there is no separate selection in Rapid Review for an Author's Correction, but your Correction will be published as such if appropriate. In the Abstract section of the submission form (a required field), put “Not Applicable.” Upload the text of your Author's Correction as an MS Word file. Please see a recent issue for correct formatting. Signed letters of agreement from all authors must be included as supplemental material (scanned and submitted as PDF files).

RetractionsRetractions are reserved for major errors or breaches of ethics that, for example, may call into question the source of the data or the validity of the results and conclusions of an article. Submit Retractions via Rapid Review (see “How To Submit Manuscripts,” above). In the Abstract section of the submission form (a required field), put “Not Applicable.” Upload the text of your Retraction as an MS Word file. Letters of agreement signed by all of the authors must be supplied as supplemental material (scanned and submitted as PDF files). The Retraction will be assigned to the editor in chief of the journal, and the editor who handled the paper and the chairman of the ASM Publications Board will be consulted. If all parties agree to the publication and content of the Retraction, it will be sent to the Journals Department for publication.

Image ManipulationComputer-generated images may be processed only minimally. Processing (e.g., changing contrast, brightness, or color balance) is acceptable only if applied to all parts of the image, as well as to the controls, equally, and descriptions of all such adjustments and the tools used (both hardware and software) must be provided in the manuscript. Unprocessed data and files must be retained by the authors and be provided to the editor on request.

DrawingsSubmit graphs, charts, complicated chemical or mathematical formulas, diagrams, and other drawings as finished products not requiring additional artwork or typesetting. All elements, including letters, numbers, and symbols, must be easily readable, and both axes of a graph must be labeled. Keep in mind that the journal is published both in print and online and that the same electronic files submitted by the authors are used to produce both.

When creating line art, please use the following guidelines:

1. All art must be submitted at its intended publication size. For acceptable dimensions, see “Size” above.

2. Avoid using screens (i.e., shading) in line art. It can be difficult and time-consuming to reproduce these images without moiré patterns. Various pattern backgrounds are preferable to screens as long as the patterns are not imported from another application. If you must use images containing screens,

   1. Generate the image at line screens of 85 lines per inch or lower.

   2. When applying multiple shades of gray, differentiate the gray levels by at least 20%.

   3. Never use levels of gray below 20% or above 70%, as they will fade out or become totally black upon scanning and reduction.

3. Use thick, solid lines that are no finer than 1 point in thickness.

4. No type should be smaller than 6 points at the final publication size.

5. Avoid layering type directly over shaded or textured areas.

6. Avoid the use of reversed type (white lettering on a black background).

7. Avoid heavy letters, which tend to close up, and unusual symbols, which the printer may not be able to reproduce in the legend.

8. If colors are used, avoid using similar shades of the same color and avoid very light colors.

In figure ordinate and abscissa scales (as well as table column headings), avoid the ambiguous use of numbers with exponents. Usually, it is preferable to use the Système International d'Unités (SI) symbols (μ for 10⁻⁶, m for 10⁻³, k for 10³, and M for 10⁶, etc.). A complete listing of SI symbols can be found in the International Union of Pure and Applied Chemistry (IUPAC) publication Quantities, Units and Symbols in Physical Chemistry (RSC Publishing, Cambridge, United Kingdom, 2007); an abbreviated list is available at http://www.old.iupac.org/reports/1993/homann/index.html. Thus, a representation of 20,000 cpm on a figure ordinate is to be made by the number 20 accompanied by the label kcpm.

When powers of 10 must be used, the journal requires that the exponent power be associated with the number shown. In representing 20,000 cells per ml, the numeral on the ordinate would be “2” and the label would be “10⁴ cells per ml” (not “cells per ml × 10⁻⁴”). Likewise, an enzyme activity of 0.06 U/ml would be shown as 6 accompanied by the label 10⁻² U/ml. The preferred designation would be 60 mU/ml (milliunits per milliliter).

Presentation of Nucleic Acid SequencesLong nucleic acid sequences must be presented as figures in the following format to conserve space. Print the sequence in lines of approximately 100 to 120 nucleotides in a nonproportional (monospace) font (e.g., Courier) that is easily legible when published with a line length of 6 inches (ca. 15.2 cm). If possible, lines of nucleic acid sequence should be further subdivided into blocks of 10 or 20 nucleotides by spaces within the sequence or by marks above it. Uppercase and lowercase letters may be used to designate the exon-intron structure or transcribed regions, etc., if the lowercase letters remain legible at a 6-inch (ca. 15.2-cm) line length. Number the sequence line by line; place numerals, representing the first base of each line, to the left of the lines. Minimize spacing between lines of sequence, leaving room only for annotation of the sequence. Annotation may include boldface, underlining, brackets, and boxes, etc. Encoded amino acid sequences may be presented, if necessary, immediately above or below the first nucleotide of each codon, by using the single-letter amino acid symbols. Comparisons of multiple nucleic acid sequences should conform as nearly as possible to the same format.

Figure LegendsLegends should provide enough information so that the figure is understandable without frequent reference to the text. However, detailed experimental methods must be described in the Materials and Methods section, not in a figure legend. A method that is unique to one of several experiments may be reported in a legend only if the discussion is very brief (one or two sentences). Define all symbols used in the figure and define all abbreviations that are not used in the text.

TablesTables that contain artwork, chemical structures, or shading must be submitted as illustrations in an acceptable format at the modification stage. The preferred format for regular tables is MS Word; however, WordPerfect and Acrobat PDF are also acceptable. Note that a straight Excel file is not currently an acceptable format. Excel files must be either embedded in a Word or WordPerfect document or converted to PDF before being uploaded. If your modified manuscript contains PDF tables, select “for reviewing purposes only” at the beginning of the file upload process.

Tables should be formatted as follows. Arrange the data so that columns of like material read down, not across. The headings should be sufficiently clear so that the meaning of the data is understandable without reference to the text. See the “Abbreviations” section (below) of these Instructions for those that should be used in tables. Explanatory footnotes are acceptable, but more-extensive table “legends” are not. Footnotes should not include detailed descriptions of the experiment. Tables must include enough information to warrant table format; those with fewer than six pieces of data will be incorporated into the text by the copy editor. Table 1 is an example of a well-constructed table.

Cover Photographs and DrawingsJVI publishes photographs and drawings on the front cover. Since we still want to optimize print presentation for covers even while making the online journal the journal of record (see above), color cover art must be prepared in the CMYK color space. Invitations are issued to authors whose manuscripts are returned for modification or whose manuscripts have been accepted for publication in JVI; material should be related to the work presented in the manuscript. Unsolicited photos will be considered in hard-copy format (two copies) only; if an unsolicited photo is chosen for the cover, the author may be asked to submit digital files. No material submitted for consideration will be returned to the author. Authors will be notified only if their cover art is selected. Copyright for the chosen material must be transferred to ASM. A short description of the cover material will be included at the end of the table of contents or the author index of the issue. Technical specifications are available from the cover editor, Daniel DiMaio (e-mail: daniel.dimaio{at}yale.edu).

Chemical and Biochemical NomenclatureThe recognized authority for the names of chemical compounds is Chemical Abstracts (CAS; http://www.cas.org/) and its indexes. The Merck Index, 14th ed. (Merck & Co., Inc., Whitehouse Station, NJ, 2006), is also an excellent source. For biochemical terminology, including abbreviations and symbols, consult Biochemical Nomenclature and Related Documents (Portland Press, London, United Kingdom, 1992), available at http://www.chem.qmul.ac.uk/iupac/bibliog/white.html, and the instructions to authors of the Journal of Biological Chemistry and the Archives of Biochemistry and Biophysics (first issues of each year).

Do not express molecular weight in daltons; molecular weight is a unitless ratio. Molecular mass is expressed in daltons.

For enzymes, use the recommended (trivial) name assigned by the Nomenclature Committee of the International Union of Biochemistry (IUB) as described in Enzyme Nomenclature (Academic Press, Inc., New York, NY, 1992) and its supplements and at http://www.chem.qmul.ac.uk/iubmb/enzyme/. If a nonrecommended name is used, place the proper (trivial) name in parentheses at first use in the abstract and text. Use the EC number when one has been assigned, and express enzyme activity either in katals (preferred) or in the older system of micromoles per minute.

For nomenclature of restriction enzymes, DNA methyltransferases, homing endonucleases, and their genes, refer to the article by Roberts et al. (Nucleic Acids Res. 31: 1805-1812, 2003).

Nomenclature of MiceFor mouse strain and genetic nomenclature, ASM encourages authors to refer to the guidelines set forth by the International Committee on Standardized Genetic Nomenclature for Mice, available on the Mouse Genome Database home page at http://www.informatics.jax.org/ and in Genetic Variants and Strains of the Laboratory Mouse, 3rd ed. (M. F. Lyon et al., ed., Oxford University Press, Oxford, England, 1996).

Nomenclature of VirusesNames used for viruses should be those approved by the International Committee on Taxonomy of Viruses (ICTV) and published in Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses (C. M. Fauquet et al., ed., Elsevier Academic Press, San Diego, CA, 2005). In addition, the recommendations of the ICTV regarding the use of species names should generally be followed: when the entire species is discussed as a taxonomic entity, the species name, like with other taxa, is italic and has the first letter and any proper nouns capitalized (e.g., Tobacco mosaic virus, Murray Valley encephalitis virus). When the behavior or manipulation of individual viruses is discussed, the vernacular (e.g., tobacco mosaic virus, Murray Valley encephalitis virus) should be used. If desired, synonyms may be added parenthetically when the name is first mentioned. Approved generic (or group) and family names may also be used.

Nomenclature of BacteriaBinary names, consisting of a generic name and a specific epithet (e.g., Escherichia coli), should be used for all bacteria. Names of categories at or above the genus level may be used alone, but specific and subspecific epithets may not. A specific epithet must be preceded by a generic name, written out in full the first time it is used in a paper. Thereafter, the generic name should be abbreviated to the initial capital letter (e.g., E. coli), provided there can be no confusion with other genera used in the paper. Names of all taxa (kingdoms, phyla, classes, orders, families, genera, species, and subspecies) are printed in italics; strain designations and numbers are not.

Genetic NomenclatureTo facilitate accurate communication, it is important that standard genetic nomenclature be used whenever possible and that deviations or proposals for new naming systems be endorsed by an appropriate authoritative body. Review and/or publication of submitted manuscripts that contain new or nonstandard nomenclature may be delayed by the editor or the Journals Department so that they may be reviewed by the Genetics and Genomics Committee of the ASM Publications Board.

Before submission of manuscripts, authors may direct questions on genetic nomenclature to the committee's chairman, Maria Costanzo (e-mail: maria{at}genome.stanford.edu). Such a consultation should be mentioned in the manuscript submission letter.

When appropriate for viral genetic systems, use the recommendations of Demerec et al. (Genetics 54: 61-76, 1966) as a guide.

(i) Phenotype designations must be employed when mutant loci have not been identified or mapped. They can also be used to identify the protein product of a gene, e.g., the OmpA protein. Phenotype designations generally consist of three-letter symbols; these are not italicized and the first letter of the symbol is capitalized. It is preferable to use Roman or Arabic numerals (instead of letters) to identify a series of related phenotypes. Thus, a series of bacteriocin-tolerant mutants might be designated TolI, TolII, and TolIII, etc., or a series of nucleic acid polymerase mutants might be designated Pol1, Pol2, and Pol3, etc. Wild-type characteristics can be designated Tol⁺ or Pol⁺, and, when necessary for clarity, negative superscripts (Tol⁻ Pol⁻) can be used to designate mutant characteristics. Lowercase superscript letters may be used to further delineate phenotypes (e.g., Str^r for streptomycin resistance). Phenotype designations should be defined.

(ii) Genotype designations are also indicated by three-letter locus symbols. These are lowercase italic (e.g., pol src). If several loci govern related functions, these are distinguished by italicized capital letters following the locus symbol.

(iii) Wild-type alleles are indicated with a superscript plus (ara⁺ his⁺). A superscript minus is not used to indicate a mutant locus; thus, one refers to an ara mutant rather than an ara⁻ strain.

(iv) The rules for genetic nomenclature of viruses (phages) differ from those of bacteria. As a general rule, the entire description of a virus is italicized, including the designations am or sus (amber suppressible) and ts (temperature sensitive). Superscripts are employed to indicate hybrid genomes. Genetic symbols may be one, two, or three letters. For example, a mutant strain of λ might be designated λ cI857 int2 red114 susA11; this strain carries mutations in genes cI, int, and red and a suppressible (sus) mutation in gene A. A strain designated λ imm²¹ att⁴³⁴ would represent a hybrid of phage λ that carries the immunity (imm) region of phage 21 and the attachment (att) region of phage 434. Host DNA insertions into viruses should be delineated by square brackets, and the genetic symbols and designations for such inserted DNA should conform to those employed for the host genome. Genetic symbols for phage λ can be found in reports by Echols and Murialdo (Microbiol. Rev. 42:577-591, 1978) and Szybalski and Szybalski (Gene 7:217-270, 1979).

Verb TenseASM strongly recommends that for clarity you use the past tense to narrate particular events in the past, including the procedures, observations, and data of the study that you are reporting. Use the present tense for your own general conclusions, the conclusions of previous researchers, and generally accepted facts. Thus, most of the abstract, Materials and Methods, and Results will be in the past tense, and most of the introduction and some of the Discussion will be in the present tense.

Be aware that it may be necessary to vary the tense in a single sentence. For example, it is correct to say “White (30) demonstrated that XYZ cells grow at pH 6.8,” “Figure 2 shows that ABC cells failed to grow at room temperature,” and “Air was removed from the chamber and the mice died, which proves that mice require air.” In reporting statistics and calculations, it is correct to say “The values for the ABC cells are statistically significant, indicating that the drug inhibited … .”

For an in-depth discussion of tense in scientific writing, see p. 191-193 in How To Write and Publish a Scientific Paper, 6th ed.

Drugs and Pharmaceutical AgentsChemical or generic names of drugs should be used; the use of trade names is not permitted. When code names or corporate proprietary numbers are to be used, either the chemical structure of the compound or a published literature reference illustrating the chemical structure, if known, must be provided at the first occurrence of the code name or number. For compounds not identified by generic nomenclature, all previous or concurrent identification numbers or appellations should be listed in the manuscript.

Reporting Numerical DataStandard metric units are used for reporting length, weight, and volume. For these units and for molarity, use the prefixes m, μ, n, and p for 10⁻³, 10⁻⁶, 10⁻⁹, and 10⁻¹², respectively. Likewise, use the prefixes c for 10⁻² and k for 10³. Avoid compound prefixes such as mμ or μμ. Use μg/ml or μg/g in place of the ambiguous ppm. Units of temperature are presented as follows: 37°C or 324 K.

When fractions are used to express units such as enzymatic activities, it is preferable to use whole units, such as g or min, in the denominator instead of fractional or multiple units, such as μg or 10 min. For example, “pmol/min” is preferable to “nmol/10 min,” and “μmol/g” is preferable to “nmol/μg.” It is also preferable that an unambiguous form such as exponential notation be used; for example, “μmol g⁻¹ min⁻¹” is preferable to “μmol/g/min.” Always report numerical data in the appropriate SI units.

For a review of some common errors associated with statistical analyses and reports, plus guidelines on how to avoid them, see the article by Olsen (Infect. Immun. 71:6689-6692, 2003).

For a review of basic statistical considerations for virology experiments, see the article by Richardson and Overbaugh (J. Virol. 79:669-676, 2005).

Isotopically Labeled CompoundsFor simple molecules, labeling is indicated in the chemical formula (e.g., ¹⁴CO₂, ³H₂O, and H₂³⁵SO₄). Brackets are not used when the isotopic symbol is attached to the name of a compound that in its natural state does not contain the element (e.g., ³²S-ATP) or to a word that is not a specific chemical name (e.g., ¹³¹I-labeled protein, ¹⁴C-amino acids, and ³H-ligands).

For specific chemicals, the symbol for the isotope introduced is placed in square brackets directly preceding the part of the name that describes the labeled entity. Note that configuration symbols and modifiers precede the isotopic symbol. The following examples illustrate correct usage:

• [¹⁴C]urea

• l-[methyl-¹⁴C]methionine

• [2,3-³H]serine

• [α-¹⁴C]lysine

• [γ-³²P]ATP

• UDP-[U-¹⁴C]glucose

• SV40 [³²P]DNA

• fructose 1,6-[1-³²P]bisphosphate

JVI follows the same conventions for isotopic labeling as the Journal of Biological Chemistry, and more-detailed information can be found in the instructions to authors of that journal (first issue of each year).