Respiratory Tract Virus Metagenomic/Transcriptomic Analysis

Project: National Science and Technology CouncilNational Science and Technology Council Academic Grants

Project Details


Forty-two cytopathic effect (CPE)-positive isolates were collected from 2008 to 2012. All were tested negative though routine laboratory check. They were pooled into 8 groups each consisting of 5~6 isolates for reducing the sequencing cost. Each group of mixed samples was sent for next-generation sequencing (NGS), and a data analysis pipeline was proposed to identify viral pathogens in these mixed samples. In total we predicted 47 viruses from these 8 mixed samples. PCR and/or ELISA tests were individually conducted for each of these 42 isolates based on the predicted viral types in each group. Two isolates remained negative after all these tests. NGS was additionally implemented on each of them and predicted HPeV in both. In short, viruses detected by our NGS pipeline from these 42 isolates were 29 human rhinoviruses (HRVs), 10 human parechoviruses (HPeVs), 1 echovirus, 1 human adenovirus (HAdV) and 1 Rotavirus. We then focused on the 10 found Taiwanese HPeVs due to the reported clinical significance over HRVs. Their genomes were assembled and genetic diversity were explored based on the mapped NGS reads. One novel 6-nucleotide deletion was found in one HPeV-1 virus. In terms of nucleotide heterogeneity, 65 genetic variants were detected from these HPeVs. Most importantly, not only our HPeV-3 but also the other HPeV-3 strains in the same clade of phylogenetic tree was found recombinant from known HPeV-4 strains in the database. These demonstrated the proposed NGS data analysis pipeline useful to identify unknown viruses from mixed clinical samples, reveal their genetic identity and variants, as well as characterize their genetic features in terms of viral evolution.

Project IDs

Project ID:PB10308-4278
External Project ID:MOST103-2221-E182-022
Effective start/end date01/08/1431/07/15


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