Evidence map›Paper›PMID 35172129›Full record

ArticleCell host & microbe2022

Development of a T cell-based immunodiagnostic system to effectively distinguish SARS-CoV-2 infection and COVID-19 vaccination status.

Esther Dawen Yu, Eric Wang, Emily Garrigan, Benjamin Goodwin, Aaron Sutherland, Alison Tarke, James Chang, Rosa Isela Gálvez, Jose Mateus, Sydney I Ramirez and 10 more

Open access · bronzeAbstract read
In one paragraph

Article in Cell host & microbe, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.

0numbers the graph read from it
0cells of the map it votes in
41citing papers in PubMed
4.8field-weighted citation impact, top 4% 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

41 citing papers in PubMed, 49 citations in OpenAlex.

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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

20 authors at 3 institutions in 2 countries.

Esther Dawen YuCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Eric WangCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Emily GarriganCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Benjamin GoodwinCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Aaron SutherlandCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Alison TarkeCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa 16132, Italy.
James ChangCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Rosa Isela GálvezCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Jose MateusCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Sydney I RamirezCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA.
Stephen A RawlingsDepartment of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA.
Davey M SmithDepartment of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA.
Gilberto FilaciDepartment of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa 16132, Italy; Bioterapy Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy.
April FrazierCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Daniela WeiskopfCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Jennifer M DanCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA.
Shane CrottyCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA.
Alba GrifoniCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Alessandro SetteCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA UC92037, USA. Electronic address: alex@lji.org.
Ricardo da Silva AntunesCenter for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA. Electronic address: rantunes@lji.org.
La Jolla Institute for Immunology · USUniversity of California, San Diego · USUniversity of Genoa · IT

Funding

T follicular helper (Tfh) CD4+ T cell, germinal center, and antibody response dysfunction in human recurrent tonsillitisU19AI142742 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI Alessandro Sette · 2019 to 2026
$32.8M
RESEARCH IN INFECTIOUS DISEASEST32AI007036 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NIZET, VICTOR · 1985 to 2025
$9.2M
Large Scale T Cell Epitope Discovery:Global identification of epitopes derived from Zika (ZIKV), Chikungunya (CHIKV) viruses following natural infection and vaccination75N93019C00065 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI MITCHELL, MAYA · 2019 to 2023
$7.3M
UC San Diego RAPID Faculty Development Program in Infectious DiseasesR25AI147376 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ADRIANA H TREMOULET, Joann Trejo · 2020 to 2026
$2.5M
CD4 T cell, germinal center, and antibody response defects in recurrent tonsillitisR01AI135193 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI CROTTY, SHANE P · 2018 to 2022
$2.3M
NIAID NIH HHS 75N93019C00065NIAID NIH HHS R01 AI135193NIAID NIH HHS R25 AI147376NIAID NIH HHS T32 AI007036NIAID NIH HHS U19 AI142742
6 · The paper itself

Abstract

Both SARS-CoV-2 infections and COVID-19 vaccines elicit memory T cell responses. Here, we report the development of 2 pools of experimentally defined SARS-CoV-2 T cell epitopes that, in combination with spike, were used to discriminate 4 groups of subjects with different SARS-CoV-2 infection and COVID-19 vaccine status. The overall T cell-based classification accuracy was 89.2% and 88.5% in the experimental and validation cohorts. This scheme was applicable to different mRNA vaccines and different lengths of time post infection/post vaccination and yielded increased accuracy when compared to serological readouts. T cell responses from breakthrough infections were also studied and effectively segregated from vaccine responses, with a combined performance of 86.6% across all 239 subjects from the 5 groups. We anticipate that a T cell-based immunodiagnostic scheme to classify subjects based on their vaccination and natural infection history will be an important tool for longitudinal monitoring of vaccinations and for establishing SARS-CoV-2 correlates of protection.

Indexed as

COVID-19COVID-19 VaccinesAntibodies, ViralEpitopes, T-LymphocyteHumansSARS-CoV-2Spike Glycoprotein, CoronavirusVaccinationAntibodies, ViralCOVID-19 VaccinesEpitopes, T-LymphocyteSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2breakthrough infectionCOVID-19epitopeimmunodiagnostic toolSARS-CoV-2T cellsvaccinationviruses

Identifiers

PMID35172129
PMCPMC8824221
OpenAlexW4210844585

What OpenQuestion holds

Textmetadata
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.