ArticlePloS one2022
An in-silico study of the mutation-associated effects on the spike protein of SARS-CoV-2, Omicron variant.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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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.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 29 citations in OpenAlex.
- The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review.Human vaccines & immunotherapeutics · 2023Pooled it
- Multimodal Structural Characterization of SARS-CoV-2 Spike Variants: Spectroscopic and Computational Insights.International journal of molecular sciences · 2025Article
- Molecular mechanisms of SARS-CoV-2 entry: implications for biomedical strategies.Microbiology and molecular biology reviews : MMBR · 2025Review
- An Italian Single-Center Genomic Surveillance Study: Two-Year Analysis of SARS-CoV-2 Spike Protein Mutations.International journal of molecular sciences · 2025Article
- Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia.Iranian journal of medical sciences · 2024Article
- Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2.The Journal of chemical physics · 2024Article
- Dynamics of water-mediated interaction effects on the stability and transmission of Omicron.Scientific reports · 2023Article
- Article
- Omicron Coronavirus: pH-Dependent Electrostatic Potential and Energy of Association of Spike Protein to ACE2 Receptor.Viruses · 2023Article
- Lack of Evidence for a Role of ACE-2 Polymorphisms as a Bedside Clinical Prognostic Marker of COVID-19.Viruses · 2023Article
- Mutational analysis of catalytic site domain of CCHFV L RNA segment.Journal of molecular modeling · 2023Article
- Update on the omicron sub-variants BA.4 and BA.5.Reviews in medical virology · 2023Review
- SARS-CoV-2 and its impact on the cardiovascular and digestive systems - The interplay between new virus variants and human cells.Computational and structural biotechnology journal · 2023Review
- Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS-CoV-2.Protein science : a publication of the Protein Society · 2022Article
- Missense mutations in spike protein of SARS-CoV-2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor.Immunity, inflammation and disease · 2022Article
- Comparative Dynamics of Delta and Omicron SARS-CoV-2 Variants across and between California and Mexico.Viruses · 2022Article
- Laboratory and field evaluation of the STANDARD Q and Panbio™ SARS-CoV-2 antigen rapid test in Namibia using nasopharyngeal samples.PloS one · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The emergence of Omicron (B.1.1.529), a new Variant of Concern in the COVID-19 pandemic, while accompanied by the ongoing Delta variant infection, has once again fueled fears of a new infection wave and global health concern. In the Omicron variant, the receptor-binding domain (RBD) of its spike glycoprotein is heavily mutated, a feature critical for the transmission rate of the virus by interacting with hACE2. In this study, we used a combination of conventional and advanced neural network-based in silico approaches to predict how these mutations would affect the spike protein. The results demonstrated a decrease in the electrostatic potentials of residues corresponding to receptor recognition sites, an increase in the alkalinity of the protein, a change in hydrophobicity, variations in functional residues, and an increase in the percentage of alpha-helix structure. Moreover, several mutations were found to modulate the immunologic properties of the potential epitopes predicted from the spike protein. Our next step was to predict the structural changes of the spike and their effect on its interaction with the hACE2. The results revealed that the RBD of the Omicron variant had a higher affinity than the reference. Moreover, all-atom molecular dynamics simulations concluded that the RBD of the Omicron variant exhibits a more dispersed interaction network since mutations resulted in an increased number of hydrophobic interactions and hydrogen bonds with hACE2.
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Registered trials
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.