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Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
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The blood DNA virome in 8,000 humans
Ahmed Moustafa1, Chao Xie2, Ewen Kirkness1
1Human Longevity Inc., San Diego, California, United States of America.
Plos Pathogens
|March 23, 2017
Summary
The blood virome in 8,240 individuals revealed 94 viruses, including 19 human viruses in 42% of participants. Contamination from reagents and environment poses challenges for identifying novel pathogens.
Area of Science:
- Virology
- Genomics
- Infectious Diseases
Background:
- Characterizing the blood virome is crucial for transfusion safety and identifying novel pathogens.
- Whole-genome sequencing provides a comprehensive approach to studying viral presence in blood.
Purpose of the Study:
- To explore the non-human sequence data from whole-genome sequencing of blood to characterize the human blood virome.
- To identify viral sequences in a large cohort without prior infectious disease ascertainment.
Main Methods:
- Whole-genome sequencing of blood from 8,240 individuals.
- Extraction of viral sequences from reads not mapping to the human reference genome.
- Large-scale data analysis involving 1 Petabyte of data and 0.5 trillion similarity searches.
Main Results:
- Sequences from 94 different viruses were mapped, including 19 human DNA viruses, proviruses, and RNA viruses in 42% of participants.
- Specific viruses relevant to transfusion medicine, such as Merkel cell polyomavirus and Human Papillomavirus, were identified.
- Unexpected DNA sequences from RNA viruses (Hepatitis C virus, Influenza virus) were detected, attributed to integration and DNA vaccination, respectively.
Conclusions:
- The study identified a diverse blood virome, with significant contributions from contaminants.
- Age, sex, and ancestry influence viral prevalence in the blood.
- Distinguishing true human viral sequences from contaminants is a major challenge for future research and pathogen discovery.
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