Evidence map›Paper›PMID 39833605›Full record

ArticleNature immunology2025

Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2.

Jaclyn M L Walsh, Vincent N Miao, Anna H Owings, Ying Tang, Joshua D Bromley, Samuel W Kazer, Kyle Kimler, Chelsea Asare, Carly G K Ziegler, Samira Ibrahim and 28 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature immunology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Review
  2. Article
  3. Unique nasal cell states induced by common pediatric respiratory viruses.bioRxiv : the preprint server for biology · 2026
    Article
  4. Review
  5. Article
  6. Article
  7. Enhanced Production of Lipid Mediators in Plasma and Activation of DNA Damage Pathways in PBMCs Are Correlated With the Severity of Ancestral SARS-CoV-2 Infection.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025
    Article
  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

38 authors.

Jaclyn M L Walsh *Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6292-1006
Vincent N Miao *Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Anna H Owings *Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.ORCID http://orcid.org/0000-0002-1139-8857
Ying Tang *Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-4357-2343
Joshua D Bromley *Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Samuel W KazerDivision of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
Kyle KimlerDivision of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-4735-9064
Chelsea AsareDivision of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
Carly G K ZieglerBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Samira IbrahimBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Tasneem JivanjeeBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Micayla GeorgeBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Andrew W NaviaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Riley S DrakeBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Adam ParkerDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA.
Benjamin C BillingsleyDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
Paul DotherowDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA.
Spurthi TaruguDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
Sai K KotaDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA.
Hannah LairdDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
T Grant WichmanDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
Yesenia T DavisDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA.
Neha S DhaliwalDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
Yilianys PrideDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA.
Yanglin GuoDivision of Pulmonary, Critical Care and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
Michal SenitkoDivision of Pulmonary, Critical Care and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
Jessie HarveyDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
John T BatesDepartment of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA.ORCID http://orcid.org/0000-0001-5545-6871
Gill DiamondDepartment of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA.ORCID http://orcid.org/0000-0002-3596-9773
Michael R GarrettDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
D Ashley RobinsonDepartment of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA.
I J FrameDepartment of Pathology, University of Mississippi Medical Center, Jackson, MS, USA.
Jonathan J LyonsDivision of Allergy and Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-2346-8189
Tanya O RobinsonDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA.
Alex K ShalekProgram in Immunology, Harvard Medical School, Boston, MA, USA.
Bruce H HorwitzDivision of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
Sarah C GloverDivision of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS, USA.
Jose Ordovas-MontanesDivision of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA. jose.ordovas-montanes@childrens.harvard.edu.ORCID http://orcid.org/0000-0001-5444-5601

Funding

STRUCTURE-FUNCTION RELATIONSHIPS IN THE ALIMENTARY TRACTP30DK034854 · NIDDK · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI JONATHAN C KAGAN · 1986 to 2026
$32.4M
Pilot Projects ProgramP30GM149404 · NIGMS · UNIVERSITY OF MISSISSIPPI MED CTR · PI John E Hall · 2023 to 2026
$6.3M
Initiation of immune responses to SARS COV2 in the oral cavity and upper airwayR01DE031928 · NIDCR · UNIVERSITY OF MISSISSIPPI MED CTR · PI GILL DIAMOND, SARAH C GLOVER · 2022 to 2026
$3.8M
Balancing epithelial cell resistance and resilience to respiratory viral infectionsR01HL162642 · NHLBI · BOSTON CHILDREN'S HOSPITAL · PI Jose Manuel Ordovas-Montanes · 2023 to 2026
$3.4M
NRSA Training CoreTL1TR002543 · NCATS · HARVARD MEDICAL SCHOOL · PI MICHEL, THOMAS · 2018 to 2022
$3.4M
TPSAB1-derived tryptases promote myeloproliferation and anaphylaxisR00AI138586 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jonathan Lyons · 2024 to 2026
$2.3M
An integrated multiplexed genomic assay for low input clinical samples1U24AI118672 · NIAID · BROAD INSTITUTE, INC. · PI SHALEK, ALEX K · 2015 to 2019
$2.0M
NCATS NIH HHS TL1 TR002543NHLBI NIH HHS R01 HL162642NIAID NIH HHS R00 AI138586NIAID NIH HHS SI2 AI138586NIAID NIH HHS U24 AI118672NIDCR NIH HHS R01 DE031928NIDDK NIH HHS P30 DK034854NIGMS NIH HHS P30 GM149404U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI) HL162642U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR) DE031928
6 · The paper itself

Abstract

Viral variant and host vaccination status impact infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet how these factors shift cellular responses in the human nasal mucosa remains uncharacterized. We performed single-cell RNA sequencing (scRNA-seq) on nasopharyngeal swabs from vaccinated and unvaccinated adults with acute Delta and Omicron SARS-CoV-2 infections and integrated with data from acute infections with ancestral SARS-CoV-2. Patients with Delta and Omicron exhibited greater similarity in nasal cell composition driven by myeloid, T cell and SARS-CoV-2

Indexed as

COVID-19COVID-19 VaccinesNasal MucosaSARS-CoV-2AdultAgedFemaleHumansMacrophagesMaleMiddle AgedNasopharynxRNA, ViralSingle-Cell AnalysisVaccinationCOVID-19 VaccinesRNA, Viral

Identifiers

PMID39833605
PMCPMC13052507

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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.