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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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The Genome-Based Virus Taxonomy with ICTV Database Extension.

Shinduck Kang1, Young-Chang Kim1

  • 1Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea.

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|January 3, 2019
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Summary

The International Committee on Taxonomy of Viruses (ICTV) classification system is being updated using next-generation sequencing (NGS) and bioinformatics. A new web system enhances viral taxonomy to strain and isolation levels, linking to NCBI and EMBL databases.

Keywords:
ICTV DB extensionVirus HistoryVirus taxonomy searching Web

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Area of Science:

  • Virology
  • Bioinformatics
  • Taxonomy

Background:

  • The International Committee on Taxonomy of Viruses (ICTV) has historically classified viruses based on phenotypic characteristics and in vivo/in vitro studies.
  • The 10th edition of the ICTV taxonomy has been published, but traditional methods face limitations with advancements in genomic data.
  • Next-generation sequencing (NGS) and bioinformatics analysis pipelines necessitate a reevaluation of viral classification systems.

Purpose of the Study:

  • To reconstruct viral taxonomy based on genotypic and in silico bioinformatics analysis, moving beyond traditional phenotypic methods.
  • To develop a web-based system and extend a database to support the proposed reconstruction of viral taxonomy.
  • To enhance the ICTV taxonomy to include strain and isolation levels for more granular classification.

Main Methods:

  • Construction of a web-based system for viral taxonomy.
  • Extension of an associated database, integrating ICTV taxonomy.
  • Connection to the NCBI database for viral gene searching and EMBL RESTful API for journal access.

Main Results:

  • A functional web system has been developed to extend viral taxonomy.
  • The system facilitates searching for specific viral genes via NCBI integration.
  • Enhanced accessibility to academic resources through EMBL API links.

Conclusions:

  • The developed web system and database provide a robust platform for reconstructing viral taxonomy using genotypic and bioinformatics approaches.
  • This approach allows for a more detailed classification of viruses, down to strain and isolation levels.
  • The integration with external databases and APIs improves data accessibility and utility for the scientific community.