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PLoS One. 2014 Aug 21;9(8):e105348. doi: 10.1371/journal.pone.0105348. eCollection 2014.

A survey of overlooked viral infections in biological experiment systems.

Author information

1
College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China; College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China.
2
NERC/Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom; Beijing Genome Institute (BGI), Yantian District, Shenzhen, China; Department of Zoology, University of Oxford, Oxford, United Kingdom.
3
Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China.
4
BGI-Tianjin, Airport Economic Area, Tianjin, China.
5
College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China.
6
Beijing Genome Institute (BGI), Yantian District, Shenzhen, China.
7
Beijing Genome Institute (BGI), Yantian District, Shenzhen, China; Department of Zoology, University of Oxford, Oxford, United Kingdom; Prince Aljawhra Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia; James D. Watson Institute of Genome Science, Hangzhou, China.

Abstract

It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.

PMID:
25144530
PMCID:
PMC4140767
DOI:
10.1371/journal.pone.0105348
[Indexed for MEDLINE]
Free PMC Article

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