期刊
JOURNAL OF VIROLOGICAL METHODS
卷 209, 期 -, 页码 15-24出版社
ELSEVIER
DOI: 10.1016/j.jviromet.2014.08.011
关键词
RNA viral metagenomics; Turkey; Gastrointestinal virome
资金
- University of Minnesota, College of Veterinary Medicine Emerging and Zoonotic Disease signature program
- Pomeroy Chair for Avian Health endowment
RNA viruses have been associated with enteritis in poultry and have been isolated from diseased birds. The same viral agents have also been detected in healthy flocks bringing into question their role in health and disease. In order to understand better eukaryotic viruses in the gut, this project focused on evaluating alternative methods to purify and concentrate viral particles, which do not involve the use of density gradients, for generating viral metagenome data. In this study, the sequence outcomes of three tissue processing methods have been evaluated and a data analysis pipeline has been established for RNA viruses from the gastrointestinal tract. In addition, with the use of the best method and increased sequencing depth, a glimpse of the RNA viral community in the gastrointestinal tract of a clinically normal 5-week old turkey is presented. The viruses from the Reoviridae and Astroviridae families together accounted for 76.3% of total viruses identified. The rarefaction curve at the species level further indicated that majority of the species diversity was included with the increased sequencing depth, implying that viruses from other viral families were present in very low abundance. (C) 2014 Elsevier B.V. All rights reserved.
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