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Open AccessJournal ArticleDOI

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.

TLDR
Single-cell transcriptome and T cell receptor analysis of bronchoalveolar lavage fluid suggests enrichment of proinflammatory macrophages in patients with severe COVID-19 and the presence of clonally expanded CD8 + T cells in Patients with moderate CO VID-19.
Abstract
Respiratory immune characteristics associated with Coronavirus Disease 2019 (COVID-19) severity are currently unclear. We characterized bronchoalveolar lavage fluid immune cells from patients with varying severity of COVID-19 and from healthy people by using single-cell RNA sequencing. Proinflammatory monocyte-derived macrophages were abundant in the bronchoalveolar lavage fluid from patients with severe COVID-9. Moderate cases were characterized by the presence of highly clonally expanded CD8+ T cells. This atlas of the bronchoalveolar immune microenvironment suggests potential mechanisms underlying pathogenesis and recovery in COVID-19.

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Journal ArticleDOI

Innate immunological pathways in COVID-19 pathogenesis

TL;DR: The emerging understanding of how SARS-CoV-2 and host-derived molecules activate specific pattern recognition receptors to elicit protective interferon responses and pathological cytokine responses is discussed, with particular focus on acute infection of the lung and lung pathophysiology in critical COVID-19.
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Neurobiology of SARS-CoV-2 interactions with the peripheral nervous system: implications for COVID-19 and pain

TL;DR: In this paper, the authors discuss how COVID-19 may interact with the peripheral nervous system to cause pain in the early and late stages of the disease and the implications of this potential neurotropism.
Journal ArticleDOI

SARS-CoV-2 in children: spectrum of disease, transmission and immunopathological underpinnings.

TL;DR: Overall, children appear to be less frequently infected by, and affected by, SARS-CoV-2 virus and the clinical disease COVID-19, including the spectrum of disease in children, the role of children in virus transmission, and host-virus factors that underpin the unique aspects of Sars-Cov-2 pathogenicity in children.
Journal ArticleDOI

Re-analysis of Single Cell Transcriptome Reveals That the NR3C1-CXCL8-Neutrophil Axis Determines the Severity of COVID-19.

TL;DR: Re-analyzed published scRNA-seq data of COVID-19 patient bronchoalveolar lavage fluid to further classify and compare immunological features according to the patient’s disease severity and suggested that severe CO VID-19 symptoms may be determined by differential expression of glucocorticoid receptors and neutrophils.
References
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Journal ArticleDOI

STAR: ultrafast universal RNA-seq aligner

TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
Journal ArticleDOI

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

TL;DR: An R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters and can be easily extended to other species and ontologies is presented.
Journal ArticleDOI

Comprehensive Integration of Single-Cell Data.

TL;DR: A strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities.
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