Premium
Characterization of the nasopharyngeal viral microbiome from children with community‐acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection
Author(s) -
Xu Lili,
Zhu Yun,
Ren Lili,
Xu Baoping,
Liu Chunyan,
Xie Zhengde,
Shen Kunling
Publication year - 2017
Publication title -
journal of medical virology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.782
H-Index - 121
eISSN - 1096-9071
pISSN - 0146-6615
DOI - 10.1002/jmv.24895
Subject(s) - human virome , virology , biology , metagenomics , virus , respiratory tract infections , human bocavirus , multiplex , microbiology and biotechnology , pneumonia , respiratory system , medicine , gene , bioinformatics , genetics , anatomy
In the present study, 50 nasopharyngeal swabs from children with community‐acquired pneumonia (CAP) but negative for 18 common respiratory viruses, as measured by the Luminex xTAG Respiratory Viral Panel Assay, were subjected to multiplex metagenomic analyses using a next‐generation sequencing platform. Taxonomic analysis showed that all sequence reads could be assigned to a specific species. An average of 95.13% were assigned to the Bacteria kingdom, whereas, only 0.72% were potentially virus derived. This snapshot of the respiratory tract virome revealed most viral reads to be respiratory tract related, classified into four known virus families: Paramyxoviridae , Herpesviridae , Anelloviridae , and Polyomaviridae . Importantly, we detected a novel human parainfluenza virus 3 (HPIV 3) strain with a 32‐bp insertion in the haemagglutinin‐neuraminidase (HN) gene that produced a negative result in the Luminex assay, highlighting the strength of virome metagenomic analysis to identify not only novel viruses but also viruses likely to be missed by ordinary clinical tests. Thus, virome metagenomic analysis could become a viable clinical diagnostic method.