著者

Tsuyoshi Sekizuka Kentaro Itokawa Masumichi Saito Michitsugu Shimatani Shutoku Matsuyama Hideki Hasegawa Tomoya Saito Makoto Kuroda

出版者

National Institute of Infectious Diseases, Japanese Journal of Infectious Diseases Editorial Committee

雑誌

Japanese Journal of Infectious Diseases (ISSN:13446304)

巻号頁・発行日

pp.JJID.2021.844, (Released:2022-02-28)

参考文献数

12

被引用文献数

22

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Prominent genomic recombination has been observed between the Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated from clinical specimens in Japan. Interestingly, the recombination variant detected in this study carries a spike protein identical to the one in the domestic Delta variant, thereby suggesting that further risks would not be concerned with infectivity and immune escape. The recombinant has been classified as XC lineage in the PANGOLIN database. It is necessary to intensively study such marked genetic variations and characterize the emerging variants after careful verification of their lineage and clade assignment.

著者

Fumihiko Takeuchi Tsuyoshi Sekizuka Akifumi Yamashita Yumiko Ogasawara Katsumi Mizuta Makoto Kuroda

出版者

National Institute of Infectious Diseases, Japanese Journal of Infectious Diseases Editorial Committee

雑誌

Japanese Journal of Infectious Diseases (ISSN:13446304)

巻号頁・発行日

vol.67, no.1, pp.62-65, 2014 (Released:2014-01-22)

参考文献数

13

被引用文献数

21 38

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Next-generation DNA sequencing technologies have led to a new method of identifying the causative agents of infectious diseases. The analysis comprises three steps. First, DNA/RNA is extracted and extensively sequenced from a specimen that includes the pathogen, human tissue and commensal microorganisms. Second, the sequenced reads are matched with a database of known sequences, and the organisms from which the individual reads were derived are inferred. Last, the percentages of the organisms' genomic sequences in the specimen (i.e., the metagenome) are estimated, and the pathogen is identified. The first and last steps have become easy due to the development of benchtop sequencers and metagenomic software. To facilitate the middle step, which requires computational resources and skill, we developed a cloud-computing pipeline, MePIC: “Metagenomic Pathogen Identification for Clinical specimens.” In the pipeline, unnecessary bases are trimmed off the reads, and human reads are removed. For the remaining reads, similar sequences are searched in the database of known nucleotide sequences. The search is drastically sped up by using a cloud-computing system. The webpage interface can be used easily by clinicians and epidemiologists. We believe that the use of the MePIC pipeline will promote metagenomic pathogen identification and improve the understanding of infectious diseases.

著者

Hiroki Ozawa Shigeru Tajima Eri Nakayama Kengo Kato Akifumi Yamashita Tsuyoshi Sekizuka Makoto Kuroda Shuzo Usuku

出版者

National Institute of Infectious Diseases, Japanese Journal of Infectious Diseases Editorial Committee

雑誌

Japanese Journal of Infectious Diseases (ISSN:13446304)

巻号頁・発行日

pp.JJID.2017.256, (Released:2017-12-26)

参考文献数

14

被引用文献数

3

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Zika virus (ZIKV) infection has been documented within Central and South America, Asia, and Africa. Here we report the isolation of virus from a patient infected with ZIKV returning to Japan from the Dominican Republic. The ZIKV strain was imaged by electron microscopy and its complete genome sequence was analyzed. Phylogenetic analysis and molecular characterization revealed that the strain was of the Asian lineage, and carried two unique mutations in its NS5 region. These mutations are characteristic of strains that originated in the Dominican Republic and the USA in 2016.