title: A survey of overlooked viral infections in biological experiment systems.
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.
authors.affiliation: 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.
authors.forename: Yajing
authors.initials: Y
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.affiliation: Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China.
authors.forename: Kunhan
authors.initials: K
authors.lastname: Xu
authors.affiliation: BGI-Tianjin, Airport Economic Area, Tianjin, China.
authors.forename: Peixiang
authors.initials: P
authors.lastname: Ni
authors.affiliation: 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.
authors.forename: Huan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Beijing Genome Institute (BGI), Yantian District, Shenzhen, China.
authors.forename: Jinmin
authors.initials: J
authors.lastname: Ma
authors.affiliation: 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.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Feng
authors.initials: F
authors.lastname: Xu
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D016679:Genome, Viral; D054884:Host-Pathogen Interactions; D006801:Humans; D010944:Plants; D034622:RNA Interference; D034741:RNA, Small Interfering; D012367:RNA, Viral; D014777:Virus Diseases / Q000453:epidemiology / Q000821:virology*; D014780:Viruses / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering; D012367:RNA, Viral