Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

Global absence and targeting of protective immune states in severe COVID-19

(2021) Alexis J. Combes et al.   NATURE

A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection

(2021) Cornelia Blume et al.   NATURE GENETICS

Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys

(2021) Emily Speranza et al.   Science Translational Medicine

Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells

(2021) Anthony Kusnadi et al.   Science Immunology

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19

(2021) Can Liu et al.   CELL

Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity

(2021) Daisy A. Hoagland et al.   IMMUNITY

Characterizing T cell subsets in the nasal mucosa of children with acute respiratory symptoms

(2021) Peter R. Cosgrove et al.   PEDIATRIC RESEARCH

Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation

(2021) Daniel F. Dwyer et al.   Science Immunology

Tissue-specific immunity for a changing world

(2021) Stuart P. Weisberg et al.   CELL

Preexisting autoantibodies to type I IFNs underlie critical COVID-19 pneumonia in patients with APS-1

(2021) Paul Bastard et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Diverse Functional Autoantibodies in Patients with COVID-19

(2021) Eric Y. Wang et al.   NATURE

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

(2021) Toni M. Delorey et al.   NATURE

Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes

(2021) Neal G. Ravindra et al.   PLOS BIOLOGY

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

Viral load of SARS-CoV-2 in clinical samples

(2020) Yang Pan et al.   LANCET INFECTIOUS DISEASES

Clinical Characteristics of Coronavirus Disease 2019 in China

(2020) Wei-jie Guan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2

(2020) Renhong Yan et al.   SCIENCE

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

(2020) Qihui Wang et al.   CELL

SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract

(2020) Yixuan J. Hou et al.   CELL

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

(2020) Daniel Blanco-Melo et al.   CELL

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

(2020) Carly G.K. Ziegler et al.   CELL

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

Clinical Outcomes in 55 Patients With Severe Acute Respiratory Syndrome Coronavirus 2 Who Were Asymptomatic at Hospital Admission in Shenzhen, China

(2020) Yanrong Wang et al.   JOURNAL OF INFECTIOUS DISEASES

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

(2020) Waradon Sungnak et al.   NATURE MEDICINE

Antibody responses to SARS-CoV-2 in patients with COVID-19

(2020) Quan-Xin Long et al.   NATURE MEDICINE

Pulmonary Vascular Endothelialitis, Thrombosis, and Angiogenesis in Covid-19

(2020) Maximilian Ackermann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility

(2020) Melissa M. Arons et al.   NEW ENGLAND JOURNAL OF MEDICINE

SARS-CoV-2 infection protects against rechallenge in rhesus macaques

(2020) Abishek Chandrashekar et al.   SCIENCE

A Single-cell Atlas of the Human Healthy Airways

(2020) Marie Deprez et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

(2020) Jonas Schulte-Schrepping et al.   CELL

Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19

(2020) Aymeric Silvin et al.   CELL

Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients

(2020) Nan Wang et al.   Cell Host & Microbe

Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling

(2020) Benjamin Israelow et al.   JOURNAL OF EXPERIMENTAL MEDICINE

In situ detection of SARS-CoV-2 in lungs and airways of patients with COVID-19

(2020) Inga-Marie Schaefer et al.   MODERN PATHOLOGY

Longitudinal analyses reveal immunological misfiring in severe COVID-19

(2020) Carolina Lucas et al.   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

(2020) Robert Lorenz Chua et al.   NATURE BIOTECHNOLOGY

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

(2020) Aaron J. Wilk et al.   NATURE MEDICINE

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

(2020) Bo Li et al.   NATURE METHODS

Natural History of Asymptomatic SARS-CoV-2 Infection

(2020) Aki Sakurai et al.   NEW ENGLAND JOURNAL OF MEDICINE

Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications

(2020) Divij Mathew et al.   SCIENCE

Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients

(2020) Jérôme Hadjadj et al.   SCIENCE

Morphogenesis and cytopathic effect of SARS-CoV-2 infection in human airway epithelial cells

(2020) Na Zhu et al.   Nature Communications

A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis

(2020) Eric J. Snijder et al.   PLOS BIOLOGY

Transmission of SARS-CoV-2: A Review of Viral, Host, and Environmental Factors

(2020) Eric A. Meyerowitz et al.   ANNALS OF INTERNAL MEDICINE

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses

(2020) Abhik K. Banerjee et al.   CELL

Identification of required host factors for SARS-CoV-2 infection in human cells

(2020) Zharko Daniloski et al.   CELL

Genome-wide CRISPR screens reveal host factors critical for SARS-CoV-2 infection

(2020) Jin Wei et al.   CELL

COVID-19 pulmonary pathology: a multi-institutional autopsy cohort from Italy and New York City

(2020) Alain C. Borczuk et al.   MODERN PATHOLOGY

Animal models for COVID-19

(2020) César Muñoz-Fontela et al.   NATURE

Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option

(2020) Kevin W. Ng et al.   NATURE GENETICS

Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor

(2020) Olusegun O. Onabajo et al.   NATURE GENETICS

Characteristics of SARS-CoV-2 and COVID-19

(2020) Ben Hu et al.   NATURE REVIEWS MICROBIOLOGY

MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses

(2020) Anna Bruchez et al.   SCIENCE

Inborn errors of type I IFN immunity in patients with life-threatening COVID-19

(2020) Qian Zhang et al.   SCIENCE

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

(2020) Paul Bastard et al.   SCIENCE

Mechanisms of SARS-CoV-2 transmission and pathogenesis

(2020) Andrew G. Harrison et al.   TRENDS IN IMMUNOLOGY

SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant

(2020) Yoriyuki Konno et al.   Cell Reports

Flow Cytometric Analysis and Purification of Airway Epithelial Cell Subsets

(2020) Luke R Bonser et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Compromised Humoral Functional Evolution Tracks with SARS-CoV-2 Mortality

(2020) Tomer Zohar et al.   CELL

COVID-19-neutralizing antibodies predict disease severity and survival

(2020) Wilfredo F. Garcia-Beltran et al.   CELL

Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses

(2020) Ruofan Wang et al.   CELL

Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

(2020) William M. Schneider et al.   CELL

Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19

(2020) Yapeng Su et al.   CELL

Untuned antiviral immunity in COVID-19 revealed by temporal type I/III interferon patterns and flu comparison

(2020) Ioanna-Evdokia Galani et al.   NATURE IMMUNOLOGY

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

(2020) Jacob E. Lemieux et al.   SCIENCE

Safety and efficacy of inhaled nebulised interferon beta-1a (SNG001) for treatment of SARS-CoV-2 infection: a randomised, double-blind, placebo-controlled, phase 2 trial

(2020) Phillip D Monk et al.   Lancet Respiratory Medicine

Human Coronavirus: Host-Pathogen Interaction

(2019) To Sing Fung et al.   Annual Review of Microbiology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures

(2019) Sandra Ruiz García et al.   DEVELOPMENT

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

Allergic inflammatory memory in human respiratory epithelial progenitor cells

(2018) Jose Ordovas-Montanes et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

CDC20B is required for deuterosome-mediated centriole production in multiciliated cells

(2018) Diego R. Revinski et al.   Nature Communications

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Middle East Respiratory Syndrome Coronavirus nsp1 Inhibits Host Gene Expression by Selectively Targeting mRNAs Transcribed in the Nucleus while Sparing mRNAs of Cytoplasmic Origin

(2015) Kumari G. Lokugamage et al.   JOURNAL OF VIROLOGY

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Interferon induction of IFITM proteins promotes infection by human coronavirus OC43

(2014) X. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses

(2014) V. D. Menachery et al.   mBio

Dedifferentiation of committed epithelial cells into stem cells in vivo

(2013) Purushothama Rao Tata et al.   NATURE

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A two-pronged strategy to suppress host protein synthesis by SARS coronavirus Nsp1 protein

(2009) Wataru Kamitani et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Basal cells as stem cells of the mouse trachea and human airway epithelium

(2009) J. R. Rock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Severe Acute Respiratory Syndrome Coronavirus Triggers Apoptosis via Protein Kinase R but Is Resistant to Its Antiviral Activity

(2008) V. Krahling et al.   JOURNAL OF VIROLOGY

Mechanisms of Severe Acute Respiratory Syndrome Pathogenesis and Innate Immunomodulation

(2008) M. Frieman et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum

(2008) Kèvin Knoops et al.   PLOS BIOLOGY