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Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel
Matthew Cotten1, Bas Oude Munnink2, Marta Canuti2
1Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
Plos One
|April 4, 2014
Summary
We developed a new method to detect and assemble full viral genomes from fecal samples. This tool aids in understanding viral infections like HIV-1 by analyzing the gut virome.
Area of Science:
- Virology
- Bioinformatics
- Genomics
Background:
- The gut virome plays a role in health and disease, but comprehensive analysis is challenging.
- Understanding viral populations in fecal material is crucial for infectious disease research.
Purpose of the Study:
- To develop and validate a novel method for full viral genome detection and assembly from fecal samples.
- To assess the fecal virome in individuals with Human Immunodeficiency Virus type 1 (HIV-1) infection.
Main Methods:
- Optimized nucleic acid preparation for fecal virus detection.
- Utilized Illumina MiSeq sequencing for viral genetic material.
- Developed a novel Python algorithm (SLIM) for virus identification and de novo assembly of full viral genomes.
Main Results:
- Successfully assembled 12 complete viral genomes from 6 virus families.
- Detected high levels of enteropathic viruses in HIV-1 infected patients.
- Quantified mammalian, plant, and bacterial virus content in fecal samples.
Conclusions:
- The developed method is sensitive and effective for comprehensive fecal virome analysis.
- This approach can reveal viral contributions to HIV-1 pathogenesis.
- Provides a powerful tool for virus detection and studying virome changes during HIV-1 progression.
