The Journal of Virology (JVI) is devoted to the timely dissemination of significant knowledge concerning the viruses of plants, fungi, bacteria, protozoa, and animals. Investigators in areas of basic virology are invited to submit reports of original research that uses the approaches of biochemistry, biophysics, cell biology, epidemiology, genetics, genomics, immunology, molecular biology, morphology, proteomics, physiology, and pathogenesis and immunity. The original articles should contain experimental observations that address a hypothesis, lead to new concepts, and indicate new directions in research. Computational analyses of viruses, virus-like sequences, or viral proteins that advance the field are also appropriate. The journal will not publish papers that simply provide a new restriction map or nucleotide sequence; identify new immunodominant peptides representing T- or B-cell epitopes; or report the isolation or characterization of monoclonal antibodies, a viral variant, or a new strain or type. Such information or reagents must instead be used in further experimentation to test an idea or relate a clear set of novel conclusions that derive from the data.

JVI specifically encourages publications relating the viruses under study to their host cells or organisms. In recognition of this emphasis, the sections of the journal relating to viral pathogenesis and immunity and to virus-cell interactions have been specifically set aside and identified in the table of contents. The editors wish to promote the publication of research done at the cell biology-virology-organismic biology interface.

JVI also encourages the submission of manuscripts detailing studies in which viruses or viral genetic elements are used as components of vectors for the delivery of therapeutic genes into animals and plants. These original articles should contain experimental observations that lead to new concepts and understanding relevant to gene delivery, regulated expression of therapeutic genes, or viral pathogenesis. To promote publications in this area, the editors have established a section of the journal for articles relating to gene therapy.

JVI encourages manuscripts that include microarrays and similar parallel profiling analyses of viral or cellular gene expression. However, such manuscripts will be published only if they provide novel insight into the biology of the virus or the infected cell, or if they form the basis for additional experiments that provide such insights. It is expected that the primary data from such analyses will be incorporated into the text or figures or will be made available as supplementary material on the ASM website, a publicly accessible laboratory website, or a public repository (such as the National Center for Biotechnology Information).

ASM publishes a number of journals covering various aspects of microbiology. Each journal has a prescribed scope that must be considered in determining where to publish each manuscript. The following guidelines may be of assistance.

(i) JVI will consider papers that describe the use of antiviral agents in elucidating the basic biological processes of viruses and host cells. Papers dealing with other aspects of antiviral agents and chemotherapy will be considered for Antimicrobial Agents and Chemotherapy.

(ii) JVI will consider all papers dealing with the biology of bacteriophages. Studies involving the use of bacteriophages as a diagnostic typing system will be considered by the Journal of Clinical Microbiology. Those dealing with phages in relation to industrial microbiology will be considered by Applied and Environmental Microbiology.

(iii) Manuscripts describing new methods or improvements in media and culture conditions will not be considered by JVI unless the procedures are applied to the study of basic problems in virology or cell biology. Such manuscripts are more appropriate for Applied and Environmental Microbiology or the Journal of Clinical Microbiology. By the same token, manuscripts dealing with methods for the production of monoclonal antibodies will not be considered unless the methods have been used to address fundamental questions.

(iv) Manuscripts dealing with clinical investigations, excluding those concerned with the activities of antiviral agents, should be submitted to the Journal of Clinical Microbiology. Manuscripts dealing with ecology or environmental studies are more appropriate for Applied and Environmental Microbiology.

Questions about these guidelines may be directed to the editor in chief of the journal being considered.

If transfer to another ASM journal is recommended by an editor, the corresponding author will be contacted.

Note that 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.

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).

All submissions to JVI must be made electronically via the Rapid Review online submission and peer review system at the following URL: www.rapidreview.com/ASM2/author.html. (E-mailed submissions will not be accepted.) First-time users must create an Author account, which may be used for submitting to all ASM journals. Instructions for creating an Author account are available at the above URL under the Create Account button. The person from whose account a submission is made will be recorded as the corresponding author, and any correspondence will be sent to the e-mail address in that account. Step-by-step instructions for submitting a manuscript via Rapid Review are available from the account holder's My Manuscripts page. Information on file types acceptable for electronic submission can be found under the More About File Formats button.

On receipt at ASM, an accepted manuscript undergoes an automated preediting, cleanup, and tagging process specific to the particular article type. To optimize this process, manuscripts must be supplied in the correct format and with the appropriate sections and headings.

Type every portion of the manuscript double spaced (a minimum of 6 mm between lines), including figure legends, table footnotes, and References, and number all pages in sequence, including the abstract, figure legends, and tables. Place the last two items after the References section. Manuscript pages should have line numbers; manuscripts without line numbers may be editorially rejected by the editor, with a suggestion of resubmission after line numbers are added. The font size should be no smaller than 12 points. It is recommended that the following sets of characters be easily distinguishable in the manuscript: the numeral zero (0) and the letter “oh” (O); the numeral one (1), the letter “el” (l), and the letter “eye” (I); and a multiplication sign (×) and the letter “ex” (x). Do not create symbols as graphics or use special fonts that are external to your word processing program; use the “insert symbol” function. Set the page size to 8½ by 11 inches (ca. 21.6 by 28 cm). Italicize or underline any words that should appear in italics, and indicate paragraph lead-ins in bold type.

Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language.

Manuscripts may be editorially rejected, without review, on the basis of poor English or lack of conformity to the standards set forth in these Instructions.

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

Title, running title, and byline. Each manuscript should present the results of an independent, cohesive study; thus, numbered series titles are not allowed. Avoid the main title/subtitle arrangement, complete sentences, and unnecessary articles. On the title page, include the title, running title (not to exceed 54 characters and spaces), name of each author, address(es) of the institution(s) at which the work was performed, each author's affiliation, and a footnote indicating the present address of any author no longer at the institution where the work was performed. Place an asterisk after the name of the author to whom inquiries regarding the paper should be addressed (see “Correspondent footnote” below).

Also include on the title page the word count for the abstract and the word count for the text (excluding the references, table footnotes, and figure legends).

Study group in byline. 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 may be given in a footnote keyed to the study group name in the byline or as a separate paragraph in Acknowledgments.

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.

Correspondent footnote. The complete mailing address, a single telephone number, a single fax number, and a single e-mail address for the corresponding author should be included on the title page of the manuscript. This information will be published in the article as a footnote to facilitate communication, and the e-mail address will be used to notify the corresponding author of availability of proofs and, later, of the PDF file of the published article.

Abstract. Limit the abstract to 250 words or fewer and concisely summarize the basic content of the paper without presenting extensive experimental details. Avoid abbreviations and references, and do not include diagrams. When it is essential to include a reference, use the same format as shown for the References section but omit the article title. Because the abstract will be published separately by abstracting services, it must be complete and understandable without reference to the text.

Introduction. The introduction should supply sufficient background information to allow the reader to understand and evaluate the results of the present study without referring to previous publications on the topic. The introduction should also provide the hypothesis that was addressed or the rationale for the present study. Choose references carefully to provide the most salient background rather than an exhaustive review of the topic.

Materials and Methods. The Materials and Methods section should include sufficient technical information to allow the experiments to be repeated. When centrifugation conditions are critical, give enough information to enable another investigator to repeat the procedure: make of centrifuge, model of rotor, temperature, time at maximum speed, and centrifugal force (× g rather than revolutions per minute). For commonly used materials and methods (e.g., media and protein concentration determinations), a simple reference is sufficient. If several alternative methods are commonly used, it is helpful to identify the method briefly as well as to cite the reference. For example, it is preferable to state “cells were broken by ultrasonic treatment as previously described (9)” rather than to state “cells were broken as previously described (9).” The reader should be allowed to assess the method without constant reference to previous publications. Describe new methods completely and give sources of unusual chemicals, equipment, or microbial strains. When large numbers of microbial strains or mutants are used in a study, include tables identifying the immediate sources (i.e., sources from whom the strains were obtained) and properties of the strains, mutants, bacteriophages, plasmids, etc.

A method, strain, etc., used in only one of several experiments reported in the paper may be described in the Results section or very briefly (one or two sentences) in a table footnote or figure legend. It is expected that the sources from whom the strains were obtained will be identified.

Results. In the Results section, include the rationale or design of the experiments as well as the results; reserve extensive interpretation of the results for the Discussion section. Present the results as concisely as possible in one of the following: text, table(s), or figure(s). Data in tables (e.g., cpm of radioactivity) should not contain more significant figures than the precision of the measurement allows. Illustrations (particularly photomicrographs and electron micrographs) should be limited to those that are absolutely necessary to show the experimental findings. Number figures and tables in the order in which they are cited in the text, and be sure to cite all figures and tables.

Discussion. The Discussion should provide an interpretation of the results in relation to previously published work and to the experimental system at hand and should not contain extensive repetition of the Results section or reiteration of the introduction. In short papers, the Results and Discussion sections may be combined.

Acknowledgments. The source of any financial support received for the work being published must be indicated in the Acknowledgments section. (It will be assumed that the absence of such an acknowledgment is a statement by the authors that no support was received.) The usual format is as follows: “This work was supported by Public Health Service grant CA-01234 from the National Cancer Institute.”

Recognition of personal assistance should be given as a separate paragraph, as should any statements disclaiming endorsement or approval of the views reflected in the paper or of a product mentioned therein.

Appendixes. Appendixes, which contain additional material to aid the reader, are permitted. Titles, authors, and References sections that are distinct from those of the primary article are not allowed. If it is not feasible to list the author(s) of the appendix in the byline or the Acknowledgments section of the primary article, rewrite the appendix so that it can be considered for publication as an independent article, either full-length or Note style. Equations, tables, and figures should be labeled with the letter “A” preceding the numeral to distinguish them from those cited in the main body of the text.

References. (i) Works listed in References. The References section must include all journal articles (both print and online), books and book chapters (both print and online), patents, theses and dissertations, and published conference proceedings (not abstracts; see below), as well as in-press journal articles, book chapters, and books (publication title must be given). Arrange the citations in alphabetical order (letter by letter, ignoring spaces and punctuation) by first author and number consecutively. Provide the names of all the authors for each reference. All listed references must be cited by number parenthetically in the text. Since title and byline information that is downloaded from PubMed does not show accents, italics, or special characters, authors should refer to the PDF files or hard-copy versions of the articles and incorporate the necessary corrections in the submitted manuscript. Abbreviate journal names according to BIOSIS Serial Sources (BIOSIS, Philadelphia, Pa., 2005).

Follow the styles shown in the examples below.

Print references:

• Arendsen, A. F., M. Q. Solimar, and S. W. Ragsdale. 1999. Nitrate-dependent regulation of acetate biosynthesis and nitrate respiration by Clostridium thermoaceticum. J. Bacteriol. 181:1489-1495.
• Cox, C. S., B. R. Brown, and J. C. Smith. J. Gen. Genet., in press.* {Article title is optional; journal title is mandatory.}
• da Costa, M. S., M. F. Nobre, and F. A. Rainey. 2001. Genus I. Thermus Brock and Freeze 1969, 295,^AL emend. Nobre, Trüper and da Costa 1996b, 605, p. 404-414. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. Springer, New York, N.Y.
• Elder, B. L., and S. E. Sharp. 2003. Cumitech 39, Competency assessment in the clinical laboratory. Coordinating ed., S. E. Sharp. ASM Press, Washington, D.C.
• Fitzgerald, G., and D. Shaw. In A. E. Waters (ed.), Clinical microbiology, in press. EFH Publishing Co., Boston, Mass.* {Chapter title is optional.}
• Forman, M. S., and A. Valsamakis. 2003. Specimen collection, transport, and processing: virology, p. 1227-1241. In P. R. Murray, E. J. Baron, M. A. Pfaller, J. H. Jorgensen, and R. H. Yolken (ed.), Manual of clinical microbiology, 8th ed. ASM Press, Washington, D.C.
• Green, P. N., D. Hood, and C. S. Dow. 1984. Taxonomic status of some methylotrophic bacteria, p. 251-254. In R. L. Crawford and R. S. Hanson (ed.), Microbial growth on C₁ compounds. Proceedings of the 4th International Symposium. American Society for Microbiology, Washington, D.C.
• Odell, J. C. 1970. Process for batch culturing. U.S. patent 484,363,770. {Include the name of the patented item/process if possible.}
• O'Malley, D. R. 1998. Ph.D. thesis. University of California, Los Angeles. {Title is optional.}

*A reference to an in-press ASM publication should state the control number (e.g., JVI00577-06) if it is a journal article or the name of the publication if it is a book.

Online references:

• Charlier, D., and N. Glansdorff. September 2004, posting date. Biosynthesis of arginine and polyamines. In R. Curtiss III et al. (ed.), EcoSal-Escherichia coli and Salmonella: cellular and molecular biology, chapter 3.6.1.10. [Online.] http://www.ecosal.org. ASM Press, Washington, D.C. {For online-only books or continually updated Web resources [for the latter, posting or accession date is required, but publisher's name and location are optional].}
• Dimick, J. B., H. G. Welch, and J. D. Birkmeyer. 18 August 2004, posting {or revision} date. Surgical mortality as an indicator of hospital quality. JAMA 292. [Online.] http://jama.ama-assn.org/cgi/content/short/292/7/847. {For online journals; page numbers may not be available.}
• Sullivan, C. J. (ed.). 1999-2001. Fungi: an evolving electronic resource for the microbiological community. ASM Press. [Online.] http://link.asmusa.de/link/service/books/91090. Accessed 7 September 2001. {For online-only books.}
• Zellnitz, F., and P. M. Foley. 2 October 1998, posting {or revision} date. History of virology. Am. Virol. J. 1:30-50. [Online.] http://wwwavj.html. {For online-only journals; page numbers may not be available.}
• Zheng, Z., and J. Zou. 5 September 2001. The initial step of the glycerolipid pathway: identification of glycerol-3-phosphate/dihydroxyacetonephosphate dual substrate acyltransferases in Saccharomyces cerevisiae. J. Biol. Chem. doi:10.1074/jbc.M104749200. {For papers published online in manuscript form.}

NOTE: A URL or DOI is necessary for each online-only reference; a posting or accession date is required for any online reference that is periodically updated or changed.

(ii) Items cited in the text. References to unpublished data, articles submitted for publication, meeting abstracts (including those published in journal supplements), personal communications, letters (irrespective of type) and authors' replies to letters, company publications, patent applications and patents pending, computer software, databases, and websites should be made parenthetically in the text as follows.

…similar results (R. B. Layton and C. C. Weathers, unpublished data).

…system was used (J. L. McInerney, A. F. Holden, and P.N. Brighton, submitted for publication).

…in mitochondria (S. De Wit, C. Thioux, and N. Clumeck, Abstr. 34th Intersci. Conf. Antimicrob. Agents Chemother., abstr. 114, 1994).

…for other bacteria (A. X. Jones, personal communication).

…discussed previously (L. B. Jensen, A. M. Hammerum, R. L. Poulsen, and H. Westh, Letter, Antimicrob. Agents Chemother. 43:724-725, 1999).

…discussed previously (S. L. W. On and P. A. R. Vandamme, Authors' Reply to Letter, J. Clin. Microbiol. 39:2751-2752, 2001).

…the manufacturer (Sigma manual, Sigma Chemical Co., St. Louis, Mo.).

…this process (V. R. Smoll, 20 June 1999, Australian Patent Office). {For non-U.S. patent applications, give the date of publication of the application.}

…information found at the XYZ website (http://cbx_iou.pgr).

…the ABC program (version 2.2; Department of Microbiology, State University [http://www.stu.micro]).

URLs for companies that produce any of the products mentioned in your study or for products being sold may NOT be included in the article. However, company URLs that permit access to scientific data related to the study or to shareware used in the study are permitted.

Notes. The 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 1,200 words; 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.

Minireviews. Minireviews are brief (limit of 6 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.

Minireviews do not have abstracts. In the Abstract section of the submission form, put “Not applicable.” The body of the Minireview may either have section headings or be set up like a Note (see above).

Guest Commentaries. Guest Commentaries are invited communications written in response to invitations issued by the editors and concern topics of interest to the broad readership of the journal that are not necessarily covered by Minireviews. They should raise issues of interest to the community of virologists, initiate or focus discussion, or propose position or consensus statements for leadership groups in research. Review 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 2 printed pages, and the format is like that of a Minireview (see above). Commentaries should be submitted via Rapid Review.

Letters to the Editor. Two types of Letters to the Editor may be submitted. The first type (Comment Letter) is intended for comments on articles published previously in the journal 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 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 edi- tor 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.

Errata. The 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. Send Errata directly to the ASM Journals Department (1752 N St., N.W., Washington, DC 20036-2904, USA), both on disk and in hard copy (only one hard copy is necessary). Please see a recent issue for correct formatting.

Authors' Corrections. The 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.

For omission of an author's name, the authors of the article and the author whose name was inadvertently omitted must agree, in writing, to publication of the Correction. For other 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. Copies of the agreement letters must accompany the Correction and be sent directly to the Journals Department. Send the Correction both on disk and in hard copy (only one hard copy is necessary). Please see a recent issue for correct formatting.

Corrections of a scientific nature (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 portion [noncritical] of the study) must be sent, both on disk and in hard copy, directly to the editor who handled the article and must be accompanied by signed letters of agreement from all of the authors of the article. If the editor believes that publication is warranted, he will send the Correction to the Journals Department for publication. Note that the addition of new data is not permitted.

Retractions. Retractions 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. Send a Retraction and an accompanying explanatory letter signed by all of the authors directly to the editor in chief of the journal. 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.

Digital files that are acceptable for production (see below) must be provided for all illustrations on return of the modified manuscript. (On initial submission, the entire paper may be submitted in PDF format.)

Table u1 Macintosh

Table u2 Windows

We strongly recommend that before returning their modified manuscripts, authors check the acceptability of their digital images for production by running their files through Rapid Inspector, a tool provided at the following URL: http://rapidinspector.cadmus.com/mw/. Rapid Inspector is an easy-to-use Web-based application that identifies file characteristics that may render the image unusable for production.

Illustrations may be continuous-tone images, line drawings, or composites. Color graphics may be submitted, but the cost of printing in color must be borne by the author. Suggestions about how to reduce costs and ensure accurate color reproduction are given below.

The preferred format for tables is MS Word; however, WordPerfect and Acrobat PDF are also acceptable (see the section on Tables below).

Since the contents of computer-generated images can be manipulated for better clarity, the Publications Board at its May 1992 meeting mandated that a description of the software/hardware used should be put in the figure legend(s).

Illustrations.

File types and formats. As mentioned above, illustrations may be supplied as PDF files for reviewing purposes only on initial submission; in fact, we recommend this option to minimize file upload time. At the modification stage, production quality digital files must be submitted: TIFF or EPS files from supported applications or PowerPoint files (black and white only). Except for figures produced in PowerPoint, all graphics submitted with modified manuscripts must be bitmap, grayscale, or CMYK (not RGB). Acceptable file types and formats for production are given in the charts above. More-detailed instructions for preparing illustrations are available on the World Wide Web at http://cjs.cadmus.com/da. Please review this information before preparing your files. If you require additional information, please send an e-mail inquiry to digitalart/at/cadmus.com.

Minimum resolution. It is extremely important that a high enough resolution is used. Any imported images must be at the correct resolution before they are placed. Note, however, that the higher the resolution, the larger the file and the longer the upload time. Publication quality will not be improved by using a resolution higher than the minimum. Minimum resolutions are as follows:

• 300 dpi for grayscale and color
• 600 dpi for lettering
• 1,200 dpi for line art
• 600 dpi for combination art (lettering and images)

Size. All graphics MUST be submitted at their intended publication size; that is, the image uploaded should be 100% of its print dimensions so that no reduction or enlargement is necessary. Resolution must be at the required level at the submitted size. Include only the significant portion of an illustration. White space must be cropped from the image, and excess space between panel labels and the image must be eliminated.

• Maximum width for a 1-column figure: 3 inches (ca. 8.4 cm)
• Maximum width for a 2-column figure: 6⅞ inches (ca. 17.4 cm)
• Minimum width for a 2-column figure: 4¼ inches (10.8 cm)
• Maximum height: 9 inches (23.0 cm)

Contrast. Illustrations must contain sufficient contrast to withstand the inevitable loss of contrast and detail inherent in the printing process. See also the section on color illustrations below.

Labeling and assembly. All final lettering, labeling, tooling, etc., MUST be incorporated into the figures. It cannot be added at a later date. If a figure number is included, it must appear well outside the boundaries of the image itself. (Numbering may need to be changed at the copyediting stage.) Each figure must be uploaded as a separate file, and any multipanel figures must be assembled into one file; i.e., rather than uploading a separate file for each panel in a figure, assemble all panels in one piece and supply them as one file.

Fonts. To avoid font problems, set all type in one of the following fonts: Helvetica, Times Roman, European PI, Mathematical PI, or Symbol. All fonts other than these five must be converted to paths (or outlines) in the application with which they were created. For font use in PowerPoint images, refer to the Cadmus digital art website, http://cjs.cadmus.com/da.

Compression. Images created with Macintosh applications may be compressed with Stuffit. Images created with Windows applications may be compressed with WINZIP or PKZIP.

Color illustrations. Because the process of placing ink on paper by using printing presses is different from that used to produce a photo print or a laser print and the color rendition on images viewed on a monitor depends to some extent on monitor resolution, some differences in color and contrast between the image you submit and the image printed in the journal or published online will be evident. (Figures showing red or green fluorescence and those with a significant range of colors may be difficult or impossible to reproduce exactly.) Color illustrations must be saved as either TIFF or EPS files, according to the application used (see charts above). The mode of the TIFF or EPS file must be CMYK, not RGB. Graphics in the RGB color space are intended for display on a monitor only and will not separate correctly for printing.

The cost of printing in color must be borne by the author. The current color costs may be accessed from the submission form in Rapid Review and, for accepted manuscripts, will be included in the acceptance letter sent out by ASM. Adherence to the following guidelines, in addition to the general ones above, will help to minimize costs and to ensure color reproduction that is as accurate as possible.

Include only the significant portions of illustrations so that the number of printed pages containing color figures is minimized. The individual panels of a single figure must be assembled in a single file, including any necessary labels. Optimal color reproduction will be obtained if the composites comprise panels containing similar colors of similar lightness or darkness. If necessary, make unlike panels into separate figures/files; this will increase the cost, but the color rendition will be more accurate since the two panels will be “scanned” separately.

Drawings. Submit graphs, charts, complicated chemical or mathematical formulas, diagrams, and other drawings as finished products not requiring additional artwork or typesetting. No part of the graph or drawing may be handwritten. 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:

• All art MUST be submitted at its intended publication size. For acceptable dimensions, see the Size section above.
• 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,
  • Generate the image at line screens of 85 lines per inch or lower.
  • When applying multiple shades of gray, differentiate the gray levels by at least 20%.
  • Never use levels of gray below 20% or above 70% as they will fade out or become totally black upon scanning and reduction.
• Use thick, solid lines that are no finer than 1 point in thickness.
• No type should be smaller than 6 points at the final publication size.
• Avoid layering type directly over shaded or textured areas.
• Avoid the use of reversed type (white lettering on a black background).
• Avoid heavy letters, which tend to close up, and unusual symbols, which the printer may not be able to reproduce in the legend.
• 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, M for 10⁶, etc.). A complete listing of SI symbols can be found in the International Union of Pure and Applied Chemistry (IUPAC) “Manual of Symbols and Terminology for Physicochemical Quantities and Units” (Pure Appl. Chem. 21:3-44, 1970). 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 Sequences. Nucleic acid sequences of limited length which are the primary subject of a study may be presented freestyle in the most effective format. Longer 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 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, 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, 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 Legends. Legends 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.

Tables. Tables 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 (p. 16) 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.

TABLE 1 Distribution of protein and ATPase in fractions of dialyzed membranesa

Cover Photographs and Drawings. JVI publishes photographs and drawings on the front cover. 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 Nomenclature. The recognized authority for the names of chemical compounds is Chemical Abstracts (CAS, Columbus, Ohio) and its indexes. The Merck Index, 13th ed. (Merck & Co., Inc., Whitehouse Station, N.J., 2001), is also an excellent source. For biochemical terminology, including abbreviations and symbols, consult Biochemical Nomenclature and Related Documents (1978; reprinted for The Biochemical Society, London, England) 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, N.Y., 1992) 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 Mice. For 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 Viruses. Names used for viruses should be those approved by the International Committee on Taxonomy of Viruses (ICTV) and published in Virus Taxonomy: Classification and Nomenclature of Viruses, Seventh Report of the Inter- national Committee on Taxonomy of Viruses (M. H. V. van Regenmortel et al., ed., Academic Press, San Diego, Calif., 2000). 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 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 Bacteria. Binary 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 Nomenclature. To 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, TolIII, etc., or a series of nucleic acid polymerase mutants might be designated Pol1, Pol2, 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 which 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).

“Mutant” versus “mutation.”. Authors are reminded of the distinction between a mutation (an alteration of the primary sequence of the genetic material) and a mutant (a strain carrying one or more mutations). One may speak about the mapping of a mutation, but one cannot map a mutant. Likewise, a mutant has no genetic locus, only a phenotype.

“Homology” versus “similarity.”. For use of terms that describe relationships between genes, consult the articles by Theissen (Nature 415:741, 2002) and Fitch (Trends Genet. 16:227-231, 2000).

“Homology” implies a relationship between genes that share a common evolutionary origin; partial homology is not recognized. When sequence comparisons are discussed, it is more appropriate to use the term “percent sequence similarity” or “percent sequence identity,” as appropriate.

Verb Tense. ASM 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. 207-209 in How To Write and Publish a Scientific Paper, 5th ed.

Abbreviations.

General. Abbreviations should be used as an aid to the reader, rather than as a convenience to the author, and therefore their use should be limited. Abbreviations other than those recommended by the IUPAC-IUB (Biochemical Nomenclature and Related Documents, 1978) should be used only when a case can be made for necessity, such as in tables and figures.

It is often possible to use pronouns or to paraphrase a long word after its first use (e.g., “the drug” or “the substrate”). Standard chemical symbols and trivial names or their symbols (folate, Ala, Leu, etc.) may also be used.

It is strongly recommended that all abbreviations except those listed below be introduced in the first paragraph in Materials and Methods. Alternatively, define each abbreviation and introduce it in parentheses the first time it is used; e.g., “cultures were grown in Eagle minimal essential medium (MEM).” Generally, eliminate abbreviations that are not used at least three times in the text (including tables and figure legends).

Not requiring introduction. In addition to abbreviations for Système International d'Unités (SI) units of measurement, other common units (e.g., bp, kb, and Da), and chemical symbols for the elements, the following should be used without definition in the title, abstract, text, figure legends, and tables: DNA (deoxyribonucleic acid); cDNA (complementary DNA); RNA (ribonucleic acid); cRNA (complementary RNA); RNase (ribonuclease); DNase (deoxyribonuclease); rRNA (ribosomal RNA); mRNA (messenger RNA); tRNA (transfer RNA); AMP, ADP, ATP, dAMP, ddATP, GTP, etc. (for the respective 5′ phosphates of adenosine and other nucleosides) (add 2′-, 3′-, or 5′- when needed for contrast); ATPase, dGTPase, etc. (adenosine triphosphatase, deoxyguanosine triphosphatase, etc.); NAD (nicotinamide adenine dinucleotide); NAD⁺ (nicotinamide adenine dinucleotide, oxidized); NADH (nicotinamide adenine dinucleotide, reduced); NADP (nicotinamide adenine dinucleotide phosphate); NADPH (nicotinamide adenine dinucleotide phosphate, reduced); NADP⁺ (nicotinamide adenine dinucleotide phosphate, oxidized); poly(A), poly(dT), etc. (polyadenylic acid, polydeoxythymidylic acid, etc.); oligo(dT), etc. (oligodeoxythymidylic acid, etc.); UV (ultraviolet); PFU (plaque-forming units); CFU (colony-forming units); MIC (minimal inhibitory concentration); Tris [tris(hydroxymethyl)aminomethane]; DEAE (diethylaminoethyl); EDTA (ethylenediaminetetraacetic acid); EGTA [ethylene glycol-bis(β-aminoethyl ether)-N,N,N′,N′-tetraacetic acid]; HEPES (N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid); PCR (polymerase chain reaction); and AIDS (acquired immunodeficiency syndrome). Abbreviations for cell lines (e.g., HeLa) also need not be defined.

The following abbreviations should be used without definition in tables:

• amt (amount)
• approx (approximately)
• avg (average)
• concn (concentration)
• diam (diameter)
• expt (experiment)
• exptl (experimental)
• ht (height)
• mo (month)
• mol wt (molecular weight)
• no. (number)
• prepn (preparation)
• SD (standard deviation)
• SE (standard error)
• SEM (standard error of the mean)
• sp act (specific activity)
• sp gr (specific gravity)
• temp (temperature)
• tr (trace)
• vol (volume)
• vs (versus)
• wk (week)
• wt (weight)
• yr (year)

Reporting Numerical Data. Standard 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 Compounds. For 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).