ArticleScientific reports2025
Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing.
Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
2 citing papers in PubMed.
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- NK Cells: A Powerful Squad Versus SARS-CoV-2.International journal of molecular sciences · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
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 cases. Pneumonia severity was associated with advanced age (proportion of elderly patients: 61.1 vs 78.3%; p = 0.032) and comorbid conditions, particularly diabetes mellitus (OR 2.03, 95% CI 1.03-4.02, p = 0.041), but showed no correlation with SARS-CoV-2 sub-lineages or coinfecting pathogens. While mNGS enhances coinfection diagnosis, COVID-19 outcomes are predominantly driven by host factors rather than Omicron subvariant evolution. Prioritized monitoring of elderly and comorbid individuals remained critical for severe pneumonia management.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.