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Viral detection by high-throughput sequencing.

Daisuke Motooka1, Shota Nakamura, Katsuro Hagiwara

  • 1Department of Infection Metagenomics, Research Institute for Microbial Disease, Osaka University, Osaka, Japan.

Methods in Molecular Biology (Clifton, N.J.)
|October 8, 2014
PubMed
Summary

High-throughput sequencing of cow fecal samples revealed diverse viral populations, including plant and insect viruses. This metagenomic approach offers a comprehensive view of animal gut and food source viromes.

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Area of Science:

  • Metagenomics
  • Virology
  • Animal Science

Background:

  • Understanding the viral communities within animal gastrointestinal tracts is crucial for animal health and food safety.
  • Previous studies often focused on specific viral targets, limiting comprehensive analysis of the entire virome.

Purpose of the Study:

  • To detect and characterize viral populations in fecal samples from adult cows using high-throughput sequencing.
  • To explore the potential of metagenomic analysis for a comprehensive understanding of animal intestinal and food source viromes.

Main Methods:

  • Application of the Ion PGM high-throughput sequencing platform for viral detection.
  • Random reverse transcription polymerase chain reaction (RT-PCR) amplification of RNA from fecal specimens (N=8).
  • Synthesis of complementary DNA (cDNA) and subsequent unbiased high-throughput sequencing using the 318 v2 semiconductor chip.

Main Results:

  • Viral genome sequences were successfully detected in all eight fecal specimens analyzed.
  • Sequencing yielded an average of 270,000 reads per sample.
  • Detected viral sequences included bacteriophages, mammal- and insect-derived viruses, as well as partial sequences of plant, algal, and protozoal viruses.

Conclusions:

  • Metagenomic analysis of cow fecal samples provides a comprehensive overview of the associated viral communities.
  • The study demonstrates the utility of high-throughput sequencing for broad viral detection in animal feces.
  • Findings suggest that the detected viruses may originate from the animal's intestine or its food sources.