ArticleNature communications2020
Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers, 3 of them syntheses that pooled it.
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
110 citing papers in PubMed, 3 syntheses or guidelines pooled it, 168 citations in OpenAlex.
- Exploring COVID-19 Pandemic Disparities with Transcriptomic Meta-analysis from the Perspective of Personalized Medicine.Journal of microbiology (Seoul, Korea) · 2024Pooled it
- Identifying novel host-based diagnostic biomarker panels for COVID-19: a whole-blood/nasopharyngeal transcriptome meta-analysis.Molecular medicine (Cambridge, Mass.) · 2022Pooled it
- Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors.Scientific reports · 2021Pooled it
- Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.Nature medicine · 2025Trial
- Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults.Nature microbiology · 2022Trial
- Article
- Host-microbiome archetypes differentiate infection from pathogen carriage in the human lower airway.Nature communications · 2026Article
- SARS-CoV-2 infection during the first trimester leads to profound immune dysregulation at the maternal-fetal interface despite limited virus detection in placental tissues.Nature communications · 2026Article
- Nasal Gene Expression in ART-Naive Adults with HIV and Pulmonary Tuberculosis in Uganda.medRxiv : the preprint server for health sciences · 2026Article
- Interrelational Proteomic Sequence Features Enhance Predictive Modeling: Application to COVID-19 Severity.Biomedicines · 2026Article
- The soluble G protein of respiratory syncytial virus promotes viral dissemination via TLR2-mediated NLRP3 priming and pyroptosis.Npj viruses · 2026Article
- Article
- Limited nasal IFN production contributes to delayed respiratory virus clearance and suboptimal vaccine responses.JCI insight · 2025Article
- IFN alpha inducible protein 27 (IFI27) acts as a positive regulator of PACT-dependent PKR activation after RNA virus infections.PLoS pathogens · 2025Article
- Beyond immunosuppression: decoding systemic immune dysregulation in ICU-acquired pneumonia.The European respiratory journal · 2025Article
- Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data.BMC bioinformatics · 2025Article
- Host gene expression in the Nasopharynx can discriminate microbiologically confirmed viral and bacterial lower respiratory tract infection.Journal of clinical and translational science · 2025Article
- Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load.PloS one · 2025Article
- Differential Inflammatory and Immune Response to Viral Infection in the Upper-Airway and Peripheral Blood of Mild COVID-19 Cases.Journal of personalized medicine · 2024Article
- Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia.Nature communications · 2024Article
50 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
23 authors at 2 institutions in 1 country.
Funding
Abstract
SARS-CoV-2 infection is characterized by peak viral load in the upper airway prior to or at the time of symptom onset, an unusual feature that has enabled widespread transmission of the virus and precipitated a global pandemic. How SARS-CoV-2 is able to achieve high titer in the absence of symptoms remains unclear. Here, we examine the upper airway host transcriptional response in patients with COVID-19 (n = 93), other viral (n = 41) or non-viral (n = 100) acute respiratory illnesses (ARIs). Compared with other viral ARIs, COVID-19 is characterized by a pronounced interferon response but attenuated activation of other innate immune pathways, including toll-like receptor, interleukin and chemokine signaling. The IL-1 and NLRP3 inflammasome pathways are markedly less responsive to SARS-CoV-2, commensurate with a signature of diminished neutrophil and macrophage recruitment. This pattern resembles previously described distinctions between symptomatic and asymptomatic viral infections and may partly explain the propensity for pre-symptomatic transmission in COVID-19. We further use machine learning to build 27-, 10- and 3-gene classifiers that differentiate COVID-19 from other ARIs with AUROCs of 0.981, 0.954 and 0.885, respectively. Classifier performance is stable across a wide range of viral load, suggesting utility in mitigating false positive or false negative results of direct SARS-CoV-2 tests.
Indexed as
Identifiers
What OpenQuestion holds
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.