Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing.

ABSTRACT: Metagenomic next-generation sequencing (mNGS) is widely used to diagnose complex infections in hospitalized patients, particularly those associated with COVID-19 which has garnered significant concern over the past five years. To investigate the molecular epidemic of the viral variant and the potential co-infection pathogens, we conducted retrospective mNGS analysis of 254 SARS-CoV-2-positive specimens collected from 200 hospitalized patients between March and September 2023. Phylogenetic analysis of the identified Omicron subvariants showed minimal evolutionary divergence, with no association between sub-lineages and pneumonia severity. Notably, mNGS demonstrated enhanced detection of polymicrobial coinfections, identifying bacterial, fungal, and viral co-pathogens in 92.5% (185/200) of c

SUBMITTER: Li X 

PROVIDER: S-EPMC12122725 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature