A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach.

ABSTRACT: Metagenomic approaches to detect viral genomes and variants in clinical samples have various challenges, including low viral titers and bacterial and human genome contamination. To address these limitations, we examined a next-generation sequencing (NGS) and iterative mapping approach for virus detection in clinical samples. We analyzed 40 clinical specimens from hospitalized children diagnosed with acute bronchiolitis, croup, or respiratory tract infections in which virus identification by viral culture or polymerase chain reaction (PCR) was unsuccessful. For our NGS data analysis pipeline, clinical samples were pooled into two NGS groups to reduce sequencing costs, and the depth and coverage of assembled contigs were effectively increased using an iterative mapping approach. PCR was indi

SUBMITTER: Gong YN 

PROVIDER: S-EPMC7087367 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature