Evidence map›Paper›PMID 35956778›Full record

ArticleMolecules (Basel, Switzerland)2022

In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins.

Nancy D'Arminio, Deborah Giordano, Bernardina Scafuri, Carmen Biancaniello, Mauro Petrillo, Angelo Facchiano, Anna Marabotti

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

Article in Molecules (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.3field-weighted citation impact, top 44% 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

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. 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

7 authors at 3 institutions in 1 country.

Nancy D'ArminioDepartment of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
Deborah GiordanoNational Research Council, Institute of Food Science, 83100 Avellino, Italy.ORCID 0000-0002-5838-1913
Bernardina ScafuriDepartment of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
Carmen BiancanielloDepartment of Electrical Engineering and Information Technology, University of Naples "Federico II", 80128 Naples, Italy.
Mauro PetrilloSeidor Italy SRL, 21029 Milan, Italy.ORCID 0000-0002-6782-4704
Angelo FacchianoNational Research Council, Institute of Food Science, 83100 Avellino, Italy.ORCID 0000-0002-7077-4912
Anna MarabottiDepartment of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.ORCID 0000-0002-9510-5205
University of Salerno · ITInstitute of Food Science · ITUniversity of Naples Federico II · IT

Funding

Bank of Italy Contributo liberaleMinistry of Education, Universities and Research FFABR2017Ministry of Education, Universities and Research PRIN2017483NH8University of Salerno ORSA199808, ORSA208455, ORSA219407
6 · The paper itself

Abstract

The SARS-CoV-2 variant Omicron is characterized, among others, by more than 30 amino acid changes occurring on the spike glycoprotein with respect to the original SARS-CoV-2 spike protein. We report a comprehensive analysis of the effects of the Omicron spike amino acid changes in the interaction with human antibodies, obtained by modeling them into selected publicly available resolved 3D structures of spike-antibody complexes and investigating the effects of these mutations at structural level. We predict that the interactions of Omicron spike with human antibodies can be either negatively or positively affected by amino acid changes, with a predicted total loss of interactions only in a few complexes. Moreover, our analysis applied also to the spike-ACE2 interaction predicts that these amino acid changes may increase Omicron transmissibility. Our approach can be used to better understand SARS-CoV-2 transmissibility, detectability, and epidemiology and represents a model to be adopted also in the case of other variants.

Indexed as

COVID-19SARS-CoV-2Amino AcidsAngiotensin-Converting Enzyme 2HumansMutationPeptidyl-Dipeptidase ASpike Glycoprotein, CoronavirusAmino AcidsAngiotensin-Converting Enzyme 2Peptidyl-Dipeptidase ASpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2antibodiesprotein–protein interactionsprotein variantsSARS-CoV-2spike

Identifiers

PMID35956778
PMCPMC9370001
OpenAlexW4288719422

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.