title: Using Small RNA Deep Sequencing Data to Detect Human Viruses.
abstract: Small RNA sequencing (sRNA-seq) can be used to detect viruses in infected hosts without the necessity to have any prior knowledge or specialized sample preparation. The sRNA-seq method was initially used for viral detection and identification in plants and then in invertebrates and fungi. However, it is still controversial to use sRNA-seq in the detection of mammalian or human viruses. In this study, we used 931 sRNA-seq runs of data from the NCBI SRA database to detect and identify viruses in human cells or tissues, particularly from some clinical samples. Six viruses including HPV-18, HBV, HCV, HIV-1, SMRV, and EBV were detected from 36 runs of data. Four viruses were consistent with the annotations from the previous studies. HIV-1 was found in clinical samples without the HIV-positive reports, and SMRV was found in Diffuse Large B-Cell Lymphoma cells for the first time. In conclusion, these results suggest the sRNA-seq can be used to detect viruses in mammals and humans.
authors.affiliation: Department of Gynaecology, The Second Hospital, Tianjin Medical University, Tianjin 300211, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Wang
authors.affiliation: College of Life Sciences, Nankai University, Tianjin 300071, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Sun
authors.affiliation: School of Mathematical Sciences, Nankai University, Tianjin 300071, China.
authors.forename: Jishou
authors.initials: J
authors.lastname: Ruan
authors.affiliation: Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.affiliation: College of Life Sciences, Nankai University, Tianjin 300071, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
authors.forename: Chengjie
authors.initials: C
authors.lastname: Chen
authors.affiliation: International Potato Center (CIP), Apartado 1558, Lima 12, Peru.
authors.forename: Jan F
authors.initials: JF
authors.lastname: Kreuze
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA.
authors.forename: ZhangJun
authors.initials: Z
authors.lastname: Fei
authors.affiliation: Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong 523808, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Zhu
authors.affiliation: College of Life Sciences, Nankai University, Tianjin 300071, China.
authors.forename: Shan
authors.identifier: 0000-0002-8919-1338
authors.initials: S
authors.lastname: Gao
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000821:virology; D006367:HeLa Cells; D006509:Hepatitis B / Q000821:virology; D006801:Humans; D008099:Liver / Q000821:virology; D008113:Liver Neoplasms / Q000821:virology; D012367:RNA, Viral / Q000032:analysis* / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014777:Virus Diseases / Q000821:virology; D014780:Viruses / Q000235:genetics*
chemical_list: D012367:RNA, Viral