Evidence map›Paper›PMID 36223774›Full record

ArticleCell reports2022

Reduced B cell antigenicity of Omicron lowers host serologic response.

Jérôme Tubiana, Yufei Xiang, Li Fan, Haim J Wolfson, Kong Chen, Dina Schneidman-Duhovny, Yi Shi

Abstract read
In one paragraph

Article in Cell reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Jérôme TubianaBlavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel.
Yufei XiangCenter for Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Li FanDivision of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Haim J WolfsonBlavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel.
Kong ChenDivision of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA. Electronic address: koc5@pitt.edu.
Dina Schneidman-DuhovnySchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel. Electronic address: dina.schneidman@mail.huji.ac.il.
Yi ShiCenter for Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: wally.yis@gmail.com.

Funding

Development of multivalent, ultrapotent nanobody cocktails for SARS-CoV-2 neutralizationR01AI163011 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI William Paul Duprex, Yi Shi · 2022 to 2026
$3.1M
Mapping the Dynamic Interactome of Ig-fold Membrane Proteins Using Nanobody-Based ToolsR35GM137905 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Yi Shi · 2020 to 2026
$2.8M
Epigenetic regulation of chemokines in lung inflammationR01HL137709 · NHLBI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI CHEN, KONG · 2018 to 2021
$1.6M
NHLBI NIH HHS R01 HL137709NIAID NIH HHS R01 AI163011NIGMS NIH HHS R35 GM137905
6 · The paper itself

Abstract

The SARS-CoV-2 Omicron variant evades most neutralizing vaccine-induced antibodies and is associated with lower antibody titers upon breakthrough infections than previous variants. However, the mechanism remains unclear. Here, we find using a geometric deep-learning model that Omicron's extensively mutated receptor binding site (RBS) features reduced antigenicity compared with previous variants. Mice immunization experiments with different recombinant receptor binding domain (RBD) variants confirm that the serological response to Omicron is drastically attenuated and less potent. Analyses of serum cross-reactivity and competitive ELISA reveal a reduction in antibody response across both variable and conserved RBD epitopes. Computational modeling confirms that the RBS has a potential for further antigenicity reduction while retaining efficient receptor binding. Finally, we find a similar trend of antigenicity reduction over decades for hCoV229E, a common cold coronavirus. Thus, our study explains the reduced antibody titers associated with Omicron infection and reveals a possible trajectory of future viral evolution.

Indexed as

COVID-19Viral VaccinesAnimalsAntibodies, NeutralizingAntibodies, ViralEpitopesMiceNeutralization TestsSARS-CoV-2Spike Glycoprotein, CoronavirusAntibodies, NeutralizingAntibodies, ViralEpitopesSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2Viral Vaccinesantigenicitycomputational structural biologyCP: ImmunologyCP: Microbiologydeep learningOmicron variant of concernSARS-CoV-2spike protein

Identifiers

PMID36223774
PMCPMC9515332

What OpenQuestion holds

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Registered trials

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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.