mNGS characterization of the viral spectrum
Metagenomic next-generation sequencing (mNGS) is a powerful tool for characterizing the viral spectrum in clinical samples. This study aims to analyze the viral composition in the clinical lung (BALF) and peripheral blood samples from patients using mNGS. A total of 338 samples, including 240 BALF and 69 peripheral blood samples for DNA sequencing, as well as 18 BALF and 11 peripheral blood samples for RNA sequencing, were subjected to shotgun sequencing. After removing host sequences, high-quality non-human reads were aligned to the virus database for viral composition analysis. Alpha and beta diversity indices were used to assess differences in virome composition between different sample types.  The impact of disease type on the virome was evaluated using  Principal Coordinates Analysis (PCoA) and the Spearman correlation was employed to explore virus-bacteria relationships in lung samples.