ArticlePLoS biology2021
Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes.
Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
180 citing papers in PubMed, 2 syntheses or guidelines pooled it, 271 citations in OpenAlex.
- Single-cell RNA sequencing offers novel perspectives in viral infection research.Frontiers in cellular and infection microbiology · 2026Pooled it
- [Pulmonary innate immune response in Sars-cov-2 infection]Revista de la Facultad de Ciencias Medicas (Cordoba, Argentina) · 2022Pooled it
- SARS-CoV-2 defective viral genomes from distinct genomic regions drive divergent interferon responses.PLoS pathogens · 2026Article
- Cadherin 1 negatively regulates SARS-CoV-2 infection in the olfactory epithelium.EMBO reports · 2026Article
- Temporal Dynamics of Innate Immune Activation and Viral Interference During Sequential Co-Infection with Influenza A Virus and SARS-CoV-2: Molecular Mechanisms, Clinical Evidence, and Therapeutic Implications.International journal of molecular sciences · 2026Review
- Annotation-free phenotype prediction using knowledge-augmented clustering from single-cell RNA sequencing data.Briefings in bioinformatics · 2026Article
- Tonic and early interferons defend against respiratory viruses in primary human lung organoid-derived air-liquid interface cultures.Journal of virology · 2026Article
- Antibody Transcytosis and Neutralizing Activity in Respiratory Epithelial Cells.bioRxiv : the preprint server for biology · 2026Article
- Standardizing antiviral response metrics for mono- and combination therapies in acute, chronic and latent viral infections.Virology journal · 2026Review
- Temporal variation in markers of immune signaling and wound repair in primary human airway epithelial cells following acute versus repeated woodsmoke condensate exposure.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- MCL1 promotes porcine epidemic diarrhea virus replication by modulating arachidonic acid metabolic pathway.PLoS pathogens · 2026Article
- Genetic and chemical correction of cystic fibrosis reduces airway susceptibility to SARS-CoV-2.American journal of physiology. Lung cellular and molecular physiology · 2026Article
- scDEcrypter: Uncertainty-aware differential expression analysis for viral infection in scRNA-seq.bioRxiv : the preprint server for biology · 2026Article
- Intrinsic OASL expression governs heterogeneity in interferon induction during influenza A virus infection.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Host transcriptomic analysis reveals a defective intracellular environment that limits SARS-CoV-2 replication in CFTR-deficient airway epithelium.Frontiers in cellular and infection microbiology · 2026Article
- Immune Delay, Beyond Immune Evasion, as a Driver of Pathogen Propagation Competence Through Neutrophil Dysregulation, to be Mitigated by Low-Frequency Electromagnetic Fields (LF-EMF).International journal of molecular sciences · 2025Review
- Modelling the Variability in Immunity Build-Up and Waning Following RNA-Based Vaccination.Viruses · 2025Article
- Article
- Intestinal microbiota dynamics in piglets: the interplay with swine enteric coronavirus infections and implications for disease control.Animal microbiome · 2025Review
- 1'-Cyanocytidine-5'-isobutyryl is a potent SARS-CoV-2 inhibitor in culture and infected Syrian hamsters.Science advances · 2025Article
120 more citing papers are in PubMed but not listed here.
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Authors and funding
27 authors at 4 institutions in 2 countries.
Funding
Abstract
There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.
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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 OpenQuestion graph.