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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: <jats:italic>Paramyxoviridae<\/jats:italic>, <jats:italic>Herpesviridae<\/jats:italic>, <jats:italic>Anelloviridae<\/jats:italic>, and <jats:italic>Polyomaviridae<\/jats:italic>. Importantly, we detected a novel human parainfluenza virus 3 (HPIV 3) strain with a 32\u2010bp insertion in the haemagglutinin\u2010neuraminidase (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. 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