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Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection

ABSTRACT: The antiviral immune response to SARS-CoV-2 infection can limit viral spread and prevent development of pneumonic COVID-19. However, the protective immunological response associated with successful viral containment in the upper airways remain unclear. Here, we combine a multiomics approach with longitudinal sampling to reveal temporally resolved protective immune signatures in non-pneumonic and ambulatory SARS-CoV-2 infected patients and associate specific immune trajectories with upper airway viral containment. We see a distinct systemic rather than local immune state associated with viral containment, characterized by interferon stimulated gene (ISG) upregulation across circulating immune cell subsets in non-pneumonic SARS-CoV2 infection. We report reduced cytotoxic potential of Natural Killer (NK) and T cells, and an immune-modulatory monocyte phenotype with protective immunity in COVID-19. Together, we show protective immune trajectories in SARS-CoV2 infection, which have important implications for patient prognosis and the development of immunomodulatory therapies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE193708 | GEO | 2022/01/17

REPOSITORIES: GEO

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Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection

Project description:The antiviral immune response to SARS-CoV-2 infection can limit viral spread and prevent development of pneumonic COVID-19. However, the protective immunological response associated with successful viral containment in the upper airways remain unclear. Here, we combine a multiomics approach with longitudinal sampling to reveal temporally resolved protective immune signatures in non-pneumonic and ambulatory SARS-CoV-2 infected patients and associate specific immune trajectories with upper airway viral containment. We see a distinct systemic rather than local immune state associated with viral containment, characterized by interferon stimulated gene (ISG) upregulation across circulating immune cell subsets in non-pneumonic SARS-CoV2 infection. We report reduced cytotoxic potential of Natural Killer (NK) and T cells, and an immune-modulatory monocyte phenotype with protective immunity in COVID-19. Together, we show protective immune trajectories in SARS-CoV2 infection, which have important implications for patient prognosis and the development of immunomodulatory therapies.

2022-01-17 | PXD030785 | Pride

Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection

Project description:Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection

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Ad26.COV2.S Prevents SARS-CoV-2 Induced Pathways of Inflammation and Thrombosis in Hamsters

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2022-03-26 | GSE196893 | GEO

TCR profiling of COVID convalescent and healthy donor whole blood with nCounter

Project description:This study investigated the cellular immune response in people who had recovered from SARS-CoV2 infection(COVID-19).

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Whole Blood profiling of COVID convalescent and Healthy donors with nCounter

Project description:This study investigated the cellular immune response in people who had recovered from SARS-CoV2 infection (COVID-19).

2022-08-21 | GSE211378 | GEO

SARS-CoV-2 produces a microRNA, CoV2-miR-O8, in patients with COVID-19 infection

Project description:SARS-CoV-2 can generate viral microRNAs (v-miRNAs) that target host gene expression. This study used small RNAseq to identify the v-miRNAs present in COVID-19 patients' nasopharyngeal swabs. The study identified a specific conserved v-miRNA sequence (CoV2-miR-O8) unique to SARS-CoV-2 that is highly present in COVID-19 patients' samples, interacts with Argonaute, and has features consistent with Dicer and Drosha generation. CoV2-miR-O8 is predicted to target specific human genes and can be detected by RTPCR assays in patients.

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Evasion of antiviral innate immunity by SARS-CoV-2 NSP1 is exerted through H3K9 di-methylation

Project description:The pathogen causing the current COVID-19 pandemic, the severe acute respiratory syndrome coronavirus (SARS-CoV-2), evades the innate immune machinery through the independent action of several viral proteins, including the nonstructural protein 1 (NSP1). NSP1 has multiple functions, but the relative contribution of NSP1-mediated translational repression, ribosome-proximate degradation of host mRNA, or other molecular mechanisms to viral immune evasion remains unclear. Here we combined several genome wide approaches, including RNA-seq, ribosome footprinting, and ChIP-seq to find that NSP1 predominantly affects transcription of immune-related genes. NSP1 expression in A549 cells induced Histone 3 Lysine 9 (H3K9) methylation of antiviral gene loci, leading to specific suppression of type I and type III interferon pathways. Treatment with the G9a/GLP H3K9 methyltransferase inhibitor UNC0638 reverses this suppression of antiviral genes and blocks viral replication after SARS-CoV2 infection of A549 cells. Our results call attention to epigenetic reprogramming induced by SARS-CoV2 and highlight the importance to identify innate factors regulating histone modification of gene loci targeted by SARS-CoV-2, with possible relevance to the understanding and therapy of other immunomodulatory diseases.

2023-07-12 | GSE208116 | GEO

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Functional Assessment of US SARS-CoV-2 L452R Epsilon Variant

Project description:The multiple mutations comprising the epsilon variant demonstrates the independent convergent evolution of SARS-CoV-2 with its spike protein mutation L452R also present in the delta variant. Cells infected with live viral samples of the epsilon viral variant compared to non-epsilon variant displayed increased sensitivity to neutralization antibodies (NAb) suggesting an intact humoral response (P< 1.0 e-4). The ability for SARS-CoV2 to become more infectious but less virulent is supported mechanistically in the downregulation of viral processing pathways seen by multiomic analyses. Importantly, this paired transcriptomics and proteomic profiling of cellular response to live virus revealed an altered leukocyte response and metabolic mRNA processing in cells upon live viral infection of the epsilon variant. To ascertain host response to SARS-CoV-2 infection, primary COVID-19 positive nasopharyngeal samples were transcriptomically profiled a differential innate immune response (P<2.0 e-12) but, a relatively unaltered T cell response in the patients carrying the epsilon variant (P< 2.0 e-3). In fact, patients infected with SARS-CoV-2 and those vaccinated with the BNT162b2 vaccine have comparable CD4+/CD8+ T-cell immune responses to the B.1.429 variant (P<5 e-2). The epsilon variant alters viral processing response in infected cells, and the host innate immune response in COVID-19 positive nasopharyngeal swabs, but generates a protective host T cell response molecular signature in both vaccinated and unvaccinated patients.

2022-05-06 | PXD027995 | Pride

Analysis of blood and nasal epithelial transcriptomes to identify mechanisms associated with control of SARS-CoV-2 viral load in the upper respiratory tract

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2023-04-01 | E-MTAB-12791 | biostudies-arrayexpress

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