ArticleCell2021
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19.
Open access · hybridAbstract read
In one paragraph
Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 248 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
248citing papers in PubMed, 1 pooled it
18.1field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
248 citing papers in PubMed, 1 synthesis or guideline pooled it, 343 citations in OpenAlex.
- CCL5 Levels, Disease Progression, and Mortality in Respiratory Viral Infections: A Systematic Review and Meta-Analysis.JAMA network open · 2026Pooled it
- Pharmacokinetic-based failure of a detergent virucidal for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) nasal infections: A preclinical study and randomized controlled trial.International forum of allergy & rhinology · 2022Trial
- Autoantibodies neutralizing type I interferons in COVID-19 patients from southern Brazil.Journal of human immunity · 2026Article
- High prevalence of autoantibodies neutralizing type I IFNs in Japanese patients with hepatitis C.Journal of human immunity · 2026Article
- Review
- COVID-19 triggers pulmonary tumor outgrowth through hypoxia- and inflammation-induced VEGF-dependent angiogenesis.Signal transduction and targeted therapy · 2026Article
- Utility of Nasopharyngeal Aspirate Over Other Upper Airway Sampling Approaches for Cellular Immunology During Respiratory Viral Infection.The Journal of infectious diseases · 2026Article
- Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade.eLife · 2026Article
- Deconformer: efficient cell-type composition profiling of cfRNA across diverse cell types.Briefings in bioinformatics · 2026Article
- SARS-CoV-2 defective viral genomes from distinct genomic regions drive divergent interferon responses.PLoS pathogens · 2026Article
- Article
- Residential Greenness and Incident Chronic Rhinosinusitis After SARS-CoV-2 Infection in South Korea: A Nationwide Cohort Study.Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology · 2026Article
- Pre-existing antibodies predict protection while mucosal inflammation correlates with symptomaticmedRxiv : the preprint server for health sciences · 2026Article
- Association between clinical symptoms and time to pharyngeal PCR negativity among mild omicron COVID-19 patients: a retrospective study.BMC infectious diseases · 2026Article
- Annotation-free phenotype prediction using knowledge-augmented clustering from single-cell RNA sequencing data.Briefings in bioinformatics · 2026Article
- Interferon-Inducible Gene Upregulation Correlates With Successful Viral Clearance in Patients With BK Polyomavirus-Associated Nephropathy.Kidney international reports · 2026Article
- Coordinated immune-epithelial dynamics in the nasal epithelium protect against respiratory virus infection.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking the prediction of responding cells to perturbations affecting both gene expression and cellular abundance using scRNA sequencing.Scientific reports · 2026Article
- Redundant and distinct mechanisms suppress innate immune activation during SARS-CoV-2 infection.PLoS biology · 2026Article
- Unique nasal cell states induced by common pediatric respiratory viruses.bioRxiv : the preprint server for biology · 2026Article
188 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
25 authors at 4 institutions in 1 country.
Carly G K ZieglerProgram in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Vincent N MiaoProgram in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Anna H OwingsDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Andrew W NaviaRagon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Ying TangDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA.
Joshua D BromleyRagon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Microbiology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Peter LotfyBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA.
Meredith SloanDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Hannah LairdDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Haley B WilliamsDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Micayla GeorgeRagon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Riley S DrakeRagon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Taylor ChristianDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Adam ParkerDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Campbell B SindelDivision of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Molly W BurgerObstetrics and Gynecology, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Yilianys PrideDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Mohammad HasanDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA.
George E AbrahamDivision of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Michal SenitkoDivision of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Tanya O RobinsonDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Alex K ShalekProgram in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address: shalek@mit.edu.
Sarah C GloverDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA. Electronic address: scglover@umc.edu.
Bruce H HorwitzDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Division of Emergency Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: bruce.horwitz@childrens.harvard.edu.
Jose Ordovas-MontanesBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address: jose.ordovas-montanes@childrens.harvard.edu.
Broad Institute · USJackson Memorial Hospital · USUniversity of Mississippi Medical Center · USBoston Children's Hospital · US
Funding
Medical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0MTraining in the Molecular Biology of Neurodegeneration and Alzheimer's DiseaseT32AG000222 · NIA · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI Bruce A YANKNER · 1992 to 2026
$18.5MIdentifying Immune and Epithelial Network Signatures in Very Early Onset Inflammatory Bowel DiseaseRC2DK122532 · NIDDK · BOSTON CHILDREN'S HOSPITAL · PI KLEIN, CHRISTOPH, MUISE, ALEIXO M · 2020 to 2024
$9.1MAn integrated multiplexed genomic assay for low input clinical samples1U24AI118672 · NIAID · BROAD INSTITUTE, INC. · PI SHALEK, ALEX K · 2015 to 2019
$2.0MNIAID NIH HHS U24 AI118672NIA NIH HHS T32 AG000222NIDDK NIH HHS RC2 DK122532NIGMS NIH HHS T32 GM007753
Abstract
SARS-CoV-2 infection can cause severe respiratory COVID-19. However, many individuals present with isolated upper respiratory symptoms, suggesting potential to constrain viral pathology to the nasopharynx. Which cells SARS-CoV-2 primarily targets and how infection influences the respiratory epithelium remains incompletely understood. We performed scRNA-seq on nasopharyngeal swabs from 58 healthy and COVID-19 participants. During COVID-19, we observe expansion of secretory, loss of ciliated, and epithelial cell repopulation via deuterosomal cell expansion. In mild and moderate COVID-19, epithelial cells express anti-viral/interferon-responsive genes, while cells in severe COVID-19 have muted anti-viral responses despite equivalent viral loads. SARS-CoV-2 RNA
Indexed as
ImmunitySeverity of Illness IndexAdultAgedBystander EffectCohort StudiesCOVID-19FemaleHumansMaleMiddle AgedNasopharynxRespiratory MucosaRNA, ViralSARS-CoV-2Transcription, GeneticRNA, Viralanti-viralcorrelates of immunityCOVID-19epithelial immunityhumaninterferonnasal mucosaSARS-CoV-2scRNA-seq
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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.