Evidence map›Paper›PMID 35988543›Full record

ArticleCell host & microbe2022

Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein.

Kamyab Javanmardi, Thomas H Segall-Shapiro, Chia-Wei Chou, Daniel R Boutz, Randall J Olsen, Xuping Xie, Hongjie Xia, Pei-Yong Shi, Charlie D Johnson, Ankur Annapareddy and 5 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
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 26 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
26citing papers in PubMed, 1 pooled it
4.0field-weighted citation impact, top 5% 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

26 citing papers in PubMed, 1 synthesis or guideline pooled it, 40 citations in OpenAlex.

  1. Pooled it
  2. Review
  3. Article
  4. Review
  5. AnnCovDB: a manually curated annotation database for mutations in SARS-CoV-2 spike protein.Database : the journal of biological databases and curation · 2025
    Article
  6. Article
  7. Review
  8. Article
  9. Mammalian Antigen Display for Pandemic Countermeasures.Methods in molecular biology (Clifton, N.J.) · 2024
    Article
  10. Review
  11. Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Mapping SARS-CoV-2 antigenic relationships and serological responses.bioRxiv : the preprint server for biology · 2023
    Article
  17. Review
  18. Observational
  19. Article
  20. Review
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

15 authors at 5 institutions in 1 country.

Kamyab JavanmardiDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. Electronic address: kjavanmardi@utexas.edu.
Thomas H Segall-ShapiroLaboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA.
Chia-Wei ChouDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
Daniel R BoutzDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA.
Randall J OlsenLaboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA; Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, HMRI and Department of Pathology and Genomic Medicine, HMH, Houston, TX, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA.
Xuping XieDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
Hongjie XiaDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
Pei-Yong ShiDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
Charlie D JohnsonDepartment of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
Ankur AnnapareddyDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
Scott WeaverUniversity of Texas Medical Branch, World Reference Center for Emerging Viruses and Arboviruses, Galveston, TX, USA.
James M MusserLaboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, HMRI and Department of Pathology and Genomic Medicine, HMH, Houston, TX, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA.
Andrew D EllingtonDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
Ilya J FinkelsteinDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA. Electronic address: ilya@finkelsteinlab.org.
Jimmy D GolliharDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA. Electronic address: jgollihar2@houstonmethodist.org.
The University of Texas at Austin · USThe University of Texas Medical Branch at Galveston · USCornell University · USHouston Methodist · USMethodist Hospital · US

Funding

Problem-to-Product Team Entrepreneurship and Active Mentoring (P2P-TEAM) Graduate Training ProgramT32GM139796 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI BRODBELT, JENNIFER S. · 2021 to 2025
$781k
NIGMS NIH HHS T32 GM139796
6 · The paper itself

Abstract

The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the repeated emergence of variants of concern. For the Omicron variant, sub-lineages BA.1 and BA.2, respectively, contain 33 and 29 nonsynonymous and indel spike protein mutations. These amino acid substitutions and indels are implicated in increased transmissibility and enhanced immune evasion. By reverting individual spike mutations of BA.1 or BA.2, we characterize the molecular effects of the Omicron spike mutations on expression, ACE2 receptor affinity, and neutralizing antibody recognition. We identified key mutations enabling escape from neutralizing antibodies at a variety of epitopes. Stabilizing mutations in the N-terminal and S2 domains of the spike protein can compensate for destabilizing mutations in the receptor binding domain, enabling the record number of mutations in Omicron. Our results provide a comprehensive account of the mutational effects in the Omicron spike protein and illustrate previously uncharacterized mechanisms of host evasion.

Indexed as

COVID-19Spike Glycoprotein, CoronavirusAngiotensin-Converting Enzyme 2Antibodies, NeutralizingAntibodies, ViralEpitopesHumansMembrane GlycoproteinsMutationSARS-CoV-2Viral Envelope ProteinsAngiotensin-Converting Enzyme 2Antibodies, NeutralizingAntibodies, ViralEpitopesMembrane GlycoproteinsSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2Viral Envelope Proteinscell displayCOVID-19flow cytometryhigh throughputviral glycoproteinVOCs

Identifiers

PMID35988543
PMCPMC9350683
OpenAlexW4289767353

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.