Metagenomics-based detection of swine viruses

Abstract:

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．［Conclusion］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．

Key words:Keywords: viral metagenomics，random PCR，unknown virus，DNA virus，RNA virus