Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

PLoS Pathogens

David Wang¹  Eileen J. Klein²  Adam F. Allred²  Carl D. Kirkwood³  Stacy R. Finkbeiner⁴  Phillip I. Tarr⁴ 

[1] Department of Emergency Medicine, Children's Hospital and Regional Medical Center, Seattle, Washington, United States of America;Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America;Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America;Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America

关键词: RNA sequence analysis;    Astroviruses;    Phylogenetic analysis;    Diarrhea;    Amino acid sequence analysis;    Sequence databases;    Sequence alignment;    Sequence analysis;   

DOI  :  10.1371/journal.ppat.1000011

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

Worldwide, approximately 1.8 million children die from diarrhea annually, and millions more suffer multiple episodes of nonfatal diarrhea. On average, in up to 40% of cases, no etiologic agent can be identified. The advent of metagenomic sequencing has enabled systematic and unbiased characterization of microbial populations; thus, metagenomic approaches have the potential to define the spectrum of viruses, including novel viruses, present in stool during episodes of acute diarrhea. The detection of novel or unexpected viruses would then enable investigations to assess whether these agents play a causal role in human diarrhea. In this study, we characterized the eukaryotic viral communities present in diarrhea specimens from 12 children by employing a strategy of “micro-mass sequencing” that entails minimal starting sample quantity (<100 mg stool), minimal sample purification, and limited sequencing (384 reads per sample). Using this methodology we detected known enteric viruses as well as multiple sequences from putatively novel viruses with only limited sequence similarity to viruses in GenBank.

【 授权许可】

CC BY