title: [Metagenomics-based detection of swine viruses].
abstract: Extreme varieties of viruses exist in the environment and animals, some of which are unknown. However, many unknown viruses are barely detected by means of conventional virus isolation and PCR assay.
  
  
  OBJECTIVE
  To develop a technology platform for detecting unknown viruses.
  
  
  METHODS
  We established the technology based on viral metagenomics in combination with novel molecular diagnostics. The technology is consisted of removal of host nucleic acid, random PCR amplification, large-scale sequencing, and bioinformatics.
  
  
  RESULTS
  The technology was applied to detect classical swine fever virus (CSFV)-infected cells and a tissue sample of a pig infected with porcine circovirus type 2 (PCV2). We amplified 13.7% sequences of CSFV genome and 47.2% those of PCV2 genome, respectively. Moreover, we amplified 16.4% sequences of the simian parainfluenza virus type 5 genome from an unknown virus cell culture using the developed method. In addition, using the developed method combined with the high-throughput sequencing, we detected 1.1% virus sequences, including CSFV, PCV2, torque teno sus virus (TTSuV), porcine bocavirus (PBoV) and human adenovirus type 6 (Ad6) from 7 clinical swine samples of unknown causative agents.
  
  
  CONCLUSIONS
  The developed metagenomics-based method showed good sensitivity for detection of both DNA and RNA viruses from diverse swine samples, and has potential for universal detection of known and unknown viruses. It might facilitate the diagnosis of emerging viral diseases.
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China. wencai911@163.com
authors.forename: Wen
authors.initials: W
authors.lastname: Han
authors.forename: Yuzi
authors.initials: Y
authors.lastname: Luo
authors.forename: Bibo
authors.initials: B
authors.lastname: Zhao
authors.forename: Yuan
authors.initials: Y
authors.lastname: Sun
authors.forename: Su
authors.initials: S
authors.lastname: Li
authors.forename: Huaji
authors.initials: H
authors.lastname: Qiu
mesh_terms: D000818:Animals; D006692:Classical Swine Fever Virus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D056186:Metagenomics; D013552:Swine; D013553:Swine Diseases / Q000821:virology; D014777:Virus Diseases / Q000662:veterinary* / Q000821:virology; D014780:Viruses / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*