Evidence map›Paper›PMID 38117652›Full record

ArticleCell reports2024

The HLA-II immunopeptidome of SARS-CoV-2.

Shira Weingarten-Gabbay, Da-Yuan Chen, Siranush Sarkizova, Hannah B Taylor, Matteo Gentili, Gabrielle M Hernandez, Leah R Pearlman, Matthew R Bauer, Charles M Rice, Karl R Clauser and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
2.2field-weighted citation impact, top 12% of its field
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

15 citing papers in PubMed, 14 citations in OpenAlex.

  1. The diverse functions of viral microproteins.bioRxiv : the preprint server for biology · 2026
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  4. Frontiers in immunology · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors at 6 institutions in 1 country.

Shira Weingarten-GabbayBroad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA. Electronic address: shirawg@broadinstitute.org.
Da-Yuan ChenDepartment of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
Siranush SarkizovaBroad Institute of MIT and Harvard University, Cambridge, MA, USA.
Hannah B TaylorBroad Institute of MIT and Harvard University, Cambridge, MA, USA.
Matteo GentiliBroad Institute of MIT and Harvard University, Cambridge, MA, USA.
Gabrielle M HernandezBroad Institute of MIT and Harvard University, Cambridge, MA, USA.
Leah R PearlmanBroad Institute of MIT and Harvard University, Cambridge, MA, USA.
Matthew R BauerHarvard Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard University Medical School, Boston, MA, USA.
Charles M RiceLaboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
Karl R ClauserBroad Institute of MIT and Harvard University, Cambridge, MA, USA.
Nir HacohenBroad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
Steven A CarrBroad Institute of MIT and Harvard University, Cambridge, MA, USA.
Jennifer G AbelinBroad Institute of MIT and Harvard University, Cambridge, MA, USA.
Mohsan SaeedDepartment of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
Pardis C SabetiBroad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Broad Institute · USBoston University · USHarvard University · USConcord Consortium · USMassachusetts General Hospital · USRockefeller University · US

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI EARL, ASHLEE MIRIAM · 2014 to 2024
$66.5M
Center of Excellence for High Throughput Proteogenomic CharacterizationU24CA210986 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, GILLETTE, MICHAEL A · 2016 to 2020
$6.4M
Center of Excellence for High Throughput Proteogenomic CharacterizationU24CA270823 · NCI · BROAD INSTITUTE, INC. · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.3M
Integrated high throughput proteogenomic data analysis center for CPTACU24CA210979 · NCI · BROAD INSTITUTE, INC. · PI BIRGER, CHET, GETZ, GAD A · 2016 to 2020
$4.4M
Center for comprehensive proteogenomic data analysisU24CA271075 · NCI · BROAD INSTITUTE, INC. · PI GAD A GETZ, Denkanikota R Mani · 2022 to 2026
$3.9M
NCI NIH HHS U24 CA210979NCI NIH HHS U24 CA210986NCI NIH HHS U24 CA270823NCI NIH HHS U24 CA271075NIAID NIH HHS U19 AI110818
6 · The paper itself

Abstract

Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides that are naturally processed and loaded onto human leukocyte antigen-II (HLA-II) complexes in infected cells. We identify over 500 unique viral peptides from canonical proteins as well as from overlapping internal open reading frames. Most HLA-II peptides colocalize with known CD4

Indexed as

COVID-19SARS-CoV-2CD8-Positive T-LymphocytesEpitopes, T-LymphocyteHistocompatibility AntigensHistocompatibility Antigens Class IHLA AntigensHumansPeptidesEpitopes, T-LymphocyteHistocompatibility AntigensHistocompatibility Antigens Class IHLA AntigensPeptidesantigen processing and presentationCD4(+) T cellCP: ImmunologyCP: MicrobiologyHLA-IIimmunityimmunopeptidomenoncanonical proteinSARS-CoV-2viral antigen

Identifiers

PMID38117652
PMCPMC10860710
OpenAlexW4389977213

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.