JJID vol. 58 Supplement

Annual Report on Findings of Infectious Agents in Japan 2004

Infectious Disease Surveillance Center under National Institute of Infectious Diseases (NIID) serves as an information center where laboratory data on pathogens are collected, analyzed and distributed for public use. The infectious agents information is highly valued as a material in Japan and other countries. Since 1983, the Annual Report has been pubished.

Print version

This Report is distributed in hard copy at no charge. To receive this Report, send an e-mail message or by fax.

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Download the Report as PDF

To see a printable version of the Report in the Adobe file format, click its [PDF] link.

CONTENTS	PAGE	PDF LINK
Forward Surveillance System	p. 1-19	PDF
The Topics of the Month of IASR	p. 21-45	PDF
Tables I. Reports on Isolation of Bacteria (including Fungi, Spirochetes and Protozoa)	p. 47-101	PDF
Tables II. Reports on Isolation/Detection of Viruses (including Rickettsiae and Chlamydiae)	p. 103-136	PDF
Appendix	p. 137-143	PDF

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vol 76 no.4, July 2023

 

ORIGINAL ARTICLES

Evolution and phylodynamics of Hemagglutinin protein of Influenza A/(H1N1) pdm09 virus isolates from India during 2009 to 2020

Kiruba Ramesh, Kannapiran Ethiraj, Sivasubramanian Srinivasan, Kaveri Krishnasamy, Kumar Rajendran, Gracyfathima Selvaraj, and Padmapriya Padmanaban

 

Can exhaled nitric oxide (FeNO) serve as a clinical indicator for patients hospitalized with Crimean-Congo Hemorrhagic Fever?

Ferhan Kerget and Buğra Kerget

 

Role of viral load and host cytokines in determining the disease severity of Respiratory Syncytial Virus associated acute lower respiratory tract infections in children

Subhabrata Sarkar, Radha Kanta Ratho, Meenu Singh, Mini Pritam Singh, Amarjeet Singh, and Megha Sharma

 

The ubiquitination of RIPK2 is mediated by Peli3 and negatively regulates the onset of infectious osteomyelitis

Lixiang Le, Haojie Shan, Yiwei Lin, Wenyang Xia, Xin Ma, Chaolai Jiang, Zhongmin Shi, and Youjia Xu

 

SHORT COMMUNICATIONS

Prevalence of sapovirus and astrovirus in pediatric infectious gastroenteritis surveillance in Kobe City, Japan, during 2016-2019

Takeshi Hanafusa, Kentaro Arikawa, and Yoshihiko Tanimoto

 

A fatal case of disseminated infection caused by community-associated methicillin-resistant Staphylococcus aureus USA300 clone

Hiroyuki Ote, Hideyuki Ito, Taroh Akira, Motoyuki Sugai, Junzo Hisatsune, Yuki Uehara, and Yuichiro Oba

 

Distribution of Human Sapovirus Strain Genotypes over the last four Decades in Japan: a Global Perspective

Yen Hai Doan, Yasutaka Yamashita, Hiroto Shinomiya, Takumi Motoya, Naomi Sakon, Rieko Suzuki, Hideaki Shimizu, Naoki Shigemoto, Seiya Harada, Shunsuke Yahiro, Kyoko Tomioka, Akie Sakagami, Yo Ueki, Rika Komagome, Kyohei Saka, Reiko Okamoto-Nakagawa, Komei Shirabe, Fuminori Mizukoshi, Yono Arita, Kei Haga, Kazuhiko Katayama, Hirokazu Kimura, Masamichi Muramatsu, and Tomoichiro Oka

 

Genetic characteristics of the virus detected in the first Mpox imported case in Tokyo, Japan

Fumi Kasuya, Akane Negishi, Ryota Kumagai, Isao Yoshida, Kou Murakami, Takushi Fujiwara, Michiya Hasegawa, Sachiko Harada, Arisa Amano, Makoto Inada, Sho Saito, Shinichiro Morioka, Norio Ohmagari, Yoshiyuki Sugishita, Hirofumi Miyake, Mami Nagashima, Kenji Sadamasu, and Kazuhisa Yoshimura

 

EPIDEMIOLOGY COMMUNICATION

A nosocomial outbreak caused by human rhinovirus species A type 61 in a welfare facility in Gunma Prefecture, Japan

Ryo Shimada, Hiroyuki Tsukagoshi, Rina Kubota, Daisuke Shinoda, Yuri Shinohara, Akio Saito, Fumitaka Inoue, Tadaaki Endo, and Nobuhiro Saruki

 

Advance Publication

Accepted manuscripts will be accessible in the Advance Publication section of the journal’s website at <https://www.jstage.jst.go.jp/browse/yoken/advpub/0/_contents> prior to the printing of the publication. Advance Publication is as an author’s final manuscript that has been accepted for publication without any modifications and has not yet been copyedited. Each manuscript is assigned with a DOI.

 

 _{JJID " Instructions to Authors" is renewed on January 24, 2024.} 

 

To see a printable version of the Instructions in the Adobe file format, click this [PDF] link.

 

JAPANESE JOURNAL OF INFECTIOUS DISEASES (JJID) is an official bimonthly publication of the National Institute of Infectious Diseases, Japan.

JJID publishes basic research papers on infectious diseases in humans with respect to the fields of bacteriology, virology, mycology, parasitology, medical entomology, vaccinology, toxinology, epidemiology, surveillance, and public health, related to infectious diseases. Papers on pathology, immunology, biochemistry, and blood safety related to microbial pathogens, and those covering various aspects of quality control of biological products are also encouraged.

The following types of papers are included in JJID: (1) Original Articles, (2) Short Communications, (3) Epidemiology Communications, (4) Invited Reviews, and (5) Letters to the Editor. The journal also occasionally includes brief reports on relevant academic activities of the National Institute of Infectious Diseases.

JJID articles are published open access under a CC BY license (Creative Commons Attribution 4.0 International License).

Copyright: The copyright belongs to the authors.

Submission process: MANUSCRIPT should be submitted via the online system at <http://mc.manuscriptcentral.com/jjid> and adhere to the instructions posted on this website.

The corresponding author should indicate the following in a cover letter. JJID editors reserve the right to judge whether the statement is appropriate:

1.       The manuscript is being submitted for consideration for publication in JJID.
2.       All authors have read the manuscript and agreed to its submission for publication in JJID.
3.       All authors have contributed to the study and are responsible for its content.
4.  -a   The manuscript that substantially includes the same content has not been submitted or published elsewhere.

       -b If any parts of the manuscript have already been posted as preprint (see Preprint Policy< https://www.niid.go.jp/niid/images/jjid/preprint/JJID_Preprint_policy_20220114.pdf > ), please specify its server and the DOI.

 

Review process: Each manuscript will be reviewed by editor(s) and reviewer(s) selected by the editor in confidence throughout the entire review process to verify its acceptability in terms of scientific quality and originality.

Accepted Publication: The manuscripts accepted for publication in JJID are posted online through the journal’s website: <http://www.niid.go.jp/niid/jjid.html>

Advance Publication: Accepted manuscripts will be accessible in the Advance Publication section of the journal’s website at <https://www.niid.go.jp/niid/ja/jjid/294-jjid/5171-advance-publication.html> prior to the printing of the publication. Advance Publication is as an author’s final manuscript that has been accepted for publication without any modifications and has not yet been copyedited. Each manuscript is assigned with a DOI.

Pre-Advance Publication: Manuscripts accepted for publication on specific topics with urgent priority selected by the Editorial Board in advance will be made open access immediately on the website of the National Institute of Infectious Diseases without any modifications or copyediting. Each manuscript is not assigned with a DOI.

Submission fee: There are no submission fees for JJID.

Page charge: There are no page charges for JJID.

Color charge: The cost for printing of color figures must be borne by the authors.

Reprint orders: Reprints can be ordered in advance by indicating the number desired (minimum of 50 copies). The cost of reprints will be sent to the corresponding author with an accompanying receipt.

ABOUT THE MANUSCRIPT

< IN GENERAL >

All documents should be double-spaced throughout, include line numbers, and each page must be numbered sequentially. A minimum 12-point font size should be used.

Basically, a standard MANUSCRIPT should be presented with the following structure:

Title Page, Abstract, Text, Acknowledgments, Conflict of interest, References, Figure legends, Tables and Figures.

Please note that the files of tables and figures should be uploaded separately from a main text file through the JJID submission portal site.

Abbreviations and symbols: JJID follows the American Society for Microbiology (ASM) Journal guidelines for abbreviations and symbols. Abbreviations of biological terms (e.g., culture media, reagents, or laboratory methods) should not be used unless they are well-known or helpful to the readers. Such abbreviations should be defined on their first appearance in the text.

Biological nomenclature: Scientific names of animals, plants, and microorganisms should be given in accordance with International Codes. Scientific names in the manuscript should be in italics or underlined. Generic names must be written in full in the title, on its first appearance in the text, and in the Abstract section. Elsewhere, if it is unlikely to cause confusion, the initial letter of the generic name may be used.

Chemical nomenclature: The nomenclature of chemical compounds should agree with the indexes of Chemical Abstracts.

Nucleotide and amino acid sequences: Prior to submission, nucleotide and/or amino acid sequence data should be deposited with GenBank/EMBL/DDBJ and an accession number should be included in the manuscript.

Ethical considerations: (i) When reporting research involving human subjects or the use of biological materials of human origin, authors must obtain prior authorization from an institutional ethical committee. Furthermore, authors must include a statement in an appropriate section declaring that all experiments were carried out in compliance with relevant laws and guidelines, and with the ethical standards of the Declaration of Helsinki. (ii) When patients are reported in the manuscript, any information that could reveal the patient’s identity should be excluded (iii) Research using recombinant DNA implies that the physical and biological containment conformed to the guidelines of a corresponding agency in the authors’ country. (iv) Animal experiments must also be performed under institutional authorization and in compliance with relevant laws and guidelines in the authors’ country. (v) Research using unique materials implies that the authors will make them available to qualified researchers for noncommercial use. JJID does not request informed consent from the patients or their guardians for publication. Please note that the descriptions on ethical considerations should be included in the Material and Methods section when necessary.

Supplemental materials: JJID does not accept any supplemental materials (e.g., Supplemental Tables, Supplemental Figures).

< STRUCTURE >

Title page: The following items should be included in the title page:

・Title of the manuscript

・Running title (Running head)

・Keywords (maximum of 5)

・Full names of the authors

----No change in author(s) is permitted after acceptance for publication.

・Name of the department and institution of the authors

・Telephone number, postal address, and e-mail address of the corresponding author. Only a maximum of two authors may be designated as corresponding authors.

ABSTRACT: A brief one-paragraph abstract of no more than 200 words. This paragraph should adequately summarize the essential findings of the study.

Text: The main text should include neither tables nor figures

(for Original Articles)

Original Articles should include the following sections in Text:

Introduction, Materials and Methods, Results, and Discussion.

  -INTRODUCTION: The introduction should outline the purpose, scope, and methods of the investigation and its relation to other work in the same field.

  -MATERIALS AND METHODS: This section should describe the equipment and materials utilized and the manners in which the work was conducted. Sufficient information should be provided to enable peers to accurately replicate the work. Detailed experimental methods must be included in this section, and not just as a figure legend. Standard laboratory procedures need not be described in detail, but reference citation is necessary. Ethical considerations should be described in this section when necessary.

  -RESULTS: The results obtained should be presented in this section, in the text or in tables or figures. The unnecessary duplication of information found in tables and figure legends in the main text should be avoided as much as possible.

  -DISCUSSION: This section should not repeat the description from the Introduction and the Results sections, but rather provide an interpretation of the results. Authors should address controversial or unresolved points, results obtained by other researchers, and the evidence available for drawing conclusions.

(for Short Communications and Epidemiology Communications)

Short Communications and Epidemiology Communications should include the following sections in Text:

The main text, including the aim of the study, methods used, results, and discussion in a non-structured form (i.e., not consisting of structured Introduction, Materials and Methods, Results, and Discussion sections). 

Acknowledgments: Financial support, including grants, fellowships, and scholarships should appear in this section.

Conflict of interest: All authors must disclose any commercial or other association (e.g., pharmaceutical stock ownership, consultancy, advisory board membership, travel grants, relevant patents, or research funding) that might present a conflict of interest regarding the manuscript submitted. The corresponding author is responsible for obtaining the relevant information from all co-authors. Appropriate declarations or “None to declare” should appear at the end of the text under the subheading “Conflict of interest.” This applies to all papers.

REFERENCES: References in text should be cited by the reference number, which should be issued in the order of their appearance, in parentheses. They should be listed in numerical order at the end of the manuscript. List the first three author names, followed by “et al.”

The JJID reference format should be followed precisely when preparing the manuscript for submission. If the reference format used does not match that of JJID, the manuscript may not be received for further review process.

----References to journals and books should follow the styles shown in the following examples:

1.   Journal

      1. Shirato K, Nao N, Katano H, et al. Development of genetic diagnostic methods for novel coronavirus 2019 (nCoV-2019) in Japan. Jpn J Infect Dis. 2020;73:304-307.

      2. Vizcaino MI, Crawford JM. The colibactin warhead crosslinks DNA. Nat Chem. 2015;7:411-417.

      3. Martinez AN, Talhali C, Moraes MO, et al. PCR-based techniques for leprosy diagnosis: from the laboratory to the clinic. PLoS Negl Trop Dis. 2014; 8: e2655.

      4. Fan C, Li K, Ding Y, et al. ACE2 expression in kidney and testis may cause kidney and testis damage after 2019-nCoV infection. MedRxiv. 2020;  doi: https://doi.org/10.1101/2020.02.12.20022418. Preprint.

 

2.   Book

     1. Jacobs WR Jr. Gene transfer in Mycobacterium tuberculosis: shuttle phasmids to enlightenment. In: Hatfull GF, Jacobs WR Jr, editors. Molecular Genetics of Mycobacteria. 2nd ed. Hoboken,

         NJ: John Wiley & Sons, Inc.; 2014. p.3-25 

 

3.   Language

     1. Wei ZY, Qian HY. Myocardial injury in patients with COVID-19 pneumonia. Zhonghua Xin Xue Guan Bing Za Zhi. 2020;48: E006. Chinese.

     2. Sato K, Takano A, Gaowa et al. Epidemics of tick-borne infectious diseases in Japan. Med Entomol Zool. 2019;70:3-14. Japanese.

 

4.   Web

      World Health Organization (WHO). Diarrhoeal Disease. Available at <https://www.who.int/news-room/fact-sheets/detail/diarrhoeal-disease>. Accessed May 2, 2017.

----Unpublished data or personal communications should not be included in the reference list, but may be cited in the text, with permission for personal communications.

Tables and Figures:

Tables: Tables should be prepared separately from the main text with a software Microsoft Word or Microsoft Excel. Tables should come with headings and footnotes. Headings should be concise and clearly present the subject matter. All tabular materials should be intelligible on their own.

･Distinct tables are numbered as Table 1, Table 2, Table 3, etc., not as Table 1A, Table 1B, Table 1C, etc.

･No vertical lines are allowed, horizontal lines (entire length) are restricted to three.

･Tables should be in black and white; rows and columns should not be shaded.

･Usage of bold and italic font within a table is not permitted. In case of using the special font, a reason of the usage must be described in footnote.

･Footnotes should be listed with superscript lowercase numbers, as 1), 2), 3), etc.

Figures: Graphs, diagrams, flow charts, drawings, and photographs are considered as figures. Please ensure that all figures are submitted in the highest print quality. All illustrations can either be in black and white line art or in color. Microsoft PowerPoint, Adobe Illustrator, Adobe Photoshop, TIFF, EPS, JPEG, or PDF files are all acceptable.

Figure legends: Prepare figure legends on a separate page. The legends should be concise and comprehensive, and should include enough information to make the figures understandable without frequent reference to the main text.

Tables and Figures should be numbered with Arabic numerals in the order of their appearance in the text. They should be cited in the text as, for example, “Table 3” or “Fig. 3.”

 

Table sample

 

< TYPES >

 Original Articles

Original research papers providing the full account of an investigation can be submitted.

Form: Title Page, Abstract, Text [Introduction, Materials and Methods, Results, Discussion], Acknowledgments, Conflict of interest, References, Figure legends, Tables, and Figures.

Table and Figure files should each be prepared separately from the main text.

Limitation: Maximum of 3000 words (Text only), 40 references, and 6 figures and tables (combined).

Short Communications

Brief research papers will be published as Short Communications, with the understanding that this does not mean that it will be published immediately. Although the maximum word count is limited, the manuscript should contain all the relevant, sufficient, and appropriate methods and results, including the aim of the study and discussion. Patient reports should also be submitted as a form of Short Communications. Simple case reports are not accepted unless they are of particular significance to public health.

Form: Title Page, Abstract, Text, Acknowledgments, Conflict of interest, References, Figure legends, Tables, and Figures.

Text should be prepared in a non-structured format. Tables and figures should be prepared as separate files.

Limitation: Maximum of 1200 words (Text only), 15 references, and 3 figures and tables (combined).

Epidemiology Communications

Reports on infectious disease outbreaks and other emerging or re-emerging infectious disease-related topics are accepted. Epidemiology communications on infectious diseases in Japan are particularly welcome.

Form: Title Page, Abstract, Text, Acknowledgements, Conflict of interest, References, Figure legends, Tables, and Figures.

Tables and figures should be prepared as separate files.

Limitation: Maximum of 1200 words (Text only), 15 references, and 3 Figures and Tables (combined).

Invited Reviews

Only reviews invited for submission to JJID by the JJID Editorial Committee are acceptable. This is intended for review articles concerning both current and historical progress made in research and policymaking regarding infectious diseases. Reviews submitted to JJID will be published upon evaluation during the review process.

Form: Applies to JJID Office rules

Letters to the Editor

Letters to the Editor offer opinions concerning the articles published in JJID. The authors of the original papers will be invited to respond to the letters and comment on their manuscripts. The cover letter should state the title of the article as well as the journal volume and number in which the article was published.

Form: Text should not be divided into sections.

References (maximum of 5) may be included.

January 24, 2024

　　　　　　　　　　　　　　　　　　　　　　　Editorial Office

Japanese Journal of Infectious Diseases

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