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Yamashita A, Sakamoto T, Sekizuka T, et al. DGV: Dengue Genographic Viewer. Front Microbiol. 2016;7:875doi: 10.3389/fmicb.2016.00875.
Yamashita, A., Sakamoto, T., Sekizuka, T., Kato, K., Takasaki, T., & Kuroda, M. (2016). DGV: Dengue Genographic Viewer. Frontiers in microbiology, 7875. https://doi.org/10.3389/fmicb.2016.00875
Yamashita, Akifumi, et al. "DGV: Dengue Genographic Viewer." Frontiers in microbiology vol. 7 (2016): 875. doi: https://doi.org/10.3389/fmicb.2016.00875
Yamashita A, Sakamoto T, Sekizuka T, Kato K, Takasaki T, Kuroda M. DGV: Dengue Genographic Viewer. Front Microbiol. 2016 Jun 07;7:875. doi: 10.3389/fmicb.2016.00875. eCollection 2016. PMID: 27375595; PMCID: PMC4894901.
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Front Microbiol. 2016 Jun 07;7:875. doi: 10.3389/fmicb.2016.00875. eCollection 2016.

DGV: Dengue Genographic Viewer.

Frontiers in microbiology

Akifumi Yamashita, Tetsuya Sakamoto, Tsuyoshi Sekizuka, Kengo Kato, Tomohiko Takasaki, Makoto Kuroda

Affiliations

  1. Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan.
  2. Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan; Remote Operations Services Department, CTC System Management CorporationTokyo, Japan.
  3. Department of Virology I, National Institute of Infectious Diseases Tokyo, Japan.

PMID: 27375595 PMCID: PMC4894901 DOI: 10.3389/fmicb.2016.00875

Abstract

Dengue viruses (DENVs) and their vectors are widely distributed throughout the tropical and subtropical regions of the world. An autochthonous case of DENV was reported in Tokyo, Japan, in 2014, for the first time in 70 years. A comprehensive database of DENV sequences containing both serotype and genotype data and epidemiological data is crucial to trace DENV outbreak isolates and promptly respond to outbreaks. We constructed a DENV database containing the serotype, genotype, year and country/region of collection by collecting all publically available DENV sequence information from the National Center for Biotechnology Information (NCBI) and assigning genotype information. We also implemented the web service Dengue Genographic Viewer (DGV), which shows the geographical distribution of each DENV genotype in a user-specified time span. DGV also assigns the serotype and genotype to a user-specified sequence by performing a homology search against the curated DENV database, and shows its homologous sequences with the geographical position and year of collection. DGV also shows the distribution of DENV-infected entrants to Japan by plotting epidemiological data from the Infectious Agents Surveillance Report (IASR), Japan. This overview of the DENV genotype distribution may aid in planning for the control of DENV infections. DGV is freely available online at: (https://gph.niid.go.jp/geograph/dengue/content/genomemap).

Keywords: NGS; dengue virus; genograph; genotyping; web service

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