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SARS-CoV-2 Variant-Dependent Alterations in Nasopharyngeal Microbiota and Host Inflammatory Response

ABSTRACT: SARS-CoV-2 infection alters both the nasopharyngeal microbiota and host inflammatory environment. In this study, nasopharyngeal samples collected in Chile during different phases of the pandemic were analyzed using 16S rRNA gene sequencing (V3–V4) and RT-qPCR quantification of IL-2, TNF-α, IFN-γ and IL-1ra. Machine-learning models (Random Forest and K-Nearest Neighbors) were applied to integrate microbial community profiles, cytokine expression, and SARS-CoV-2 variants (Gamma, Lambda, Delta). The results show variant-dependent immunomicrobial signatures characterized by TNF-α-driven inflammation and the expansion of opportunistic bacterial genera such as Acinetobacter, Prevotella, and Staphylococcus. These findings provide a comprehensive overview of the interplay between viral infection, microbiome structure, and inflammatory responses and highlight the utility of combining microbiome and cytokine profiling with machine-learning approaches to discriminate infection outcomes across SARS-CoV-2 variants.

ORGANISM(S): human metagenome

PROVIDER: GSE311689 | GEO | 2026/01/30

REPOSITORIES: GEO

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