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Related Experiment Video

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Environmental Sampling of Photosynthetic Microbes and Their Viruses: From Field to Lab
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Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.

Anne Gleizes1, Florian Laubscher2,3, Nicolas Guex4

  • 1Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.

Viruses
|November 3, 2020
PubMed
Summary

Virosaurus is a new, automated database for clinical metagenomics, offering a non-biased reference dataset to improve viral disease diagnosis. It aids in identifying diverse viral pathogens using high-throughput sequencing technologies.

Keywords:
HTSbioinformaticscomplete genomedatabasediagnosticssequencingviral infectionsviruses

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Area of Science:

  • Virology
  • Bioinformatics
  • Genomics

Background:

  • Viral genetic diversity poses challenges for diagnosing emerging and rare viral diseases.
  • High-throughput sequencing enables exploration of the global virome without prior pathogen assumptions.
  • Accurate clinical metagenomics requires a robust and comprehensive reference dataset.

Purpose of the Study:

  • To design and develop Virosaurus, a non-biased, automated, and annotated database for clinical metagenomics.
  • To provide a reliable reference dataset for accurate viral disease diagnosis.
  • To facilitate the analysis of clinically relevant viruses.

Main Methods:

  • Extraction and cleaning of raw viral sequences from GenBank.
  • Identification of complete viral sequences across diverse eukaryotic hosts.
  • Annotation of viral sequences with names, genotypes, and genomic features.
  • Clustering of sequences at 90% or 98% identity to remove redundancy.
  • Inclusion of genes instead of complete genomes for under-represented herpesviruses and poxviruses.

Main Results:

  • Virosaurus provides a comprehensive, non-biased, and annotated viral sequence database.
  • The database includes complete sequences for genera infecting vertebrates, plants, and other eukaryotes.
  • Sequence clustering analysis offers insights into the current state of viral genetic landscape knowledge.
  • Specific strategies were employed for under-represented viral families like herpesviruses and poxviruses.

Conclusions:

  • Virosaurus serves as a valuable resource for clinical metagenomics and viral diagnostics.
  • The database enhances the accuracy and efficiency of identifying viral pathogens.
  • The curated dataset aids in understanding viral genetic diversity and landscape knowledge.