title: Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach.
abstract: Viral infectious diseases represent a major threat to public health and are among the greatest disease burdens worldwide. Rapid and accurate identification of viral agents is crucial for both outbreak control and estimating regional disease burdens. Recently developed metagenomic methods have proven to be powerful tools for simultaneous pathogen detection. Here, we performed a systematic study of the capability of the short-read-based metagenomic approach in the molecular detection of viral pathogens in nasopharyngeal aspirate samples from patients with acute lower respiratory tract infections (n = 16). Using the high-throughput capacity of ultradeep sequencing and a dedicated data interpretation method, we successfully identified seven species of known respiratory viral agents from 15 samples, a result that was consistent with results of conventional PCR assays. We also detected a coinfected case that was missed by regular PCR testing. Using the metagenomic data, 11 draft genomes of the abundantly detected viruses in the samples were reconstructed with 21.84% to 98.53% coverage. Our results show the power of the short-read-based metagenomic approach for accurate and parallel screening of viral pathogens. Although there are some inherent difficulties in applying this approach to clinical samples, including a lack of controls, limited specimen quantity, and high contamination rate, our work will facilitate further application of this unprecedented high-throughput method to clinical samples.
authors.affiliation: State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, 6 Rongjing Eastern Street, BDA, Beijing 100176, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Yang
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.forename: Lili
authors.initials: L
authors.lastname: Ren
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Xiong
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Wu
authors.forename: Jie
authors.initials: J
authors.lastname: Dong
authors.forename: Lilian
authors.initials: L
authors.lastname: Sun
authors.forename: Ting
authors.initials: T
authors.lastname: Zhang
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Hu
authors.forename: Jiang
authors.initials: J
authors.lastname: Du
authors.forename: Jianwei
authors.initials: J
authors.lastname: Wang
authors.forename: Qi
authors.initials: Q
authors.lastname: Jin
mesh_terms: D002648:Child; D002675:Child, Preschool; D019411:Clinical Laboratory Techniques / Q000379:methods*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D007223:Infant; D008297:Male; D056186:Metagenomics / Q000379:methods*; D009305:Nasopharynx / Q000821:virology; D012140:Respiratory Tract Diseases / Q000175:diagnosis* / Q000821:virology; D014773:Virology / Q000379:methods*; D014777:Virus Diseases / Q000175:diagnosis* / Q000821:virology; D014780:Viruses / Q000145:classification* / Q000302:isolation & purification*