Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion
BackgroundThe fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an in-silico study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion.MethodsThe analysis was based on...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Public Health |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpubh.2022.1052241/full |
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| author | Jose A. Jimenez Ruiz Cecilia Lopez Ramirez Cecilia Lopez Ramirez Jose Luis Lopez-Campos Jose Luis Lopez-Campos |
| author_facet | Jose A. Jimenez Ruiz Cecilia Lopez Ramirez Cecilia Lopez Ramirez Jose Luis Lopez-Campos Jose Luis Lopez-Campos |
| author_sort | Jose A. Jimenez Ruiz |
| collection | DOAJ |
| description | BackgroundThe fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an in-silico study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion.MethodsThe analysis was based on the structure of the spike protein from two SARS-CoV-2 variants, the original Wuhan and the Botswana (Omicron). The full-length genome sequences and protein sequences were obtained from databanks. The interaction of the spike proteins with the human Angiotensin Converting Enzyme 2 (ACE2) receptor was evaluated through the open-source software. The Immune Epitope Database was used to analyze the potential immune evasion of the viruses.ResultsOur data show that the Omicron spike protein resulted in 37 amino acid changes. The physicochemical properties of the spike had changed, and the electrostatic potentials differed between both variants. This resulted in a decrease in protein interactions, which does not establish a greater interaction with the ACE2 receptor. These changes compromise key receptor-binding motif residues in the SARS-CoV-2 spike protein that interact with neutralizing antibodies and ACE2.ConclusionsThese mutations appear to confer enhanced properties of infectivity. The Omicron variant appears to be more effective at evading immune responses. |
| first_indexed | 2024-04-13T13:47:56Z |
| format | Article |
| id | doaj.art-86dd8b284add44e2bfd9fc7f96f01a95 |
| institution | Directory Open Access Journal |
| issn | 2296-2565 |
| language | English |
| last_indexed | 2024-04-13T13:47:56Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Public Health |
| spelling | doaj.art-86dd8b284add44e2bfd9fc7f96f01a952022-12-22T02:44:26ZengFrontiers Media S.A.Frontiers in Public Health2296-25652022-11-011010.3389/fpubh.2022.10522411052241Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasionJose A. Jimenez Ruiz0Cecilia Lopez Ramirez1Cecilia Lopez Ramirez2Jose Luis Lopez-Campos3Jose Luis Lopez-Campos4Research Group on Electronic Technology and Industrial Computing (TIC-150) at the University of Seville, Seville, SpainUnidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, SpainCentro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, SpainUnidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, SpainCentro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, SpainBackgroundThe fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an in-silico study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion.MethodsThe analysis was based on the structure of the spike protein from two SARS-CoV-2 variants, the original Wuhan and the Botswana (Omicron). The full-length genome sequences and protein sequences were obtained from databanks. The interaction of the spike proteins with the human Angiotensin Converting Enzyme 2 (ACE2) receptor was evaluated through the open-source software. The Immune Epitope Database was used to analyze the potential immune evasion of the viruses.ResultsOur data show that the Omicron spike protein resulted in 37 amino acid changes. The physicochemical properties of the spike had changed, and the electrostatic potentials differed between both variants. This resulted in a decrease in protein interactions, which does not establish a greater interaction with the ACE2 receptor. These changes compromise key receptor-binding motif residues in the SARS-CoV-2 spike protein that interact with neutralizing antibodies and ACE2.ConclusionsThese mutations appear to confer enhanced properties of infectivity. The Omicron variant appears to be more effective at evading immune responses.https://www.frontiersin.org/articles/10.3389/fpubh.2022.1052241/fullSARS-CoV-2COVID-19immune evasionin-silicocoronavirus |
| spellingShingle | Jose A. Jimenez Ruiz Cecilia Lopez Ramirez Cecilia Lopez Ramirez Jose Luis Lopez-Campos Jose Luis Lopez-Campos Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion Frontiers in Public Health SARS-CoV-2 COVID-19 immune evasion in-silico coronavirus |
| title | Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion |
| title_full | Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion |
| title_fullStr | Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion |
| title_full_unstemmed | Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion |
| title_short | Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion |
| title_sort | spike protein of sars cov 2 omicron variant an in silico study evaluating spike interactions and immune evasion |
| topic | SARS-CoV-2 COVID-19 immune evasion in-silico coronavirus |
| url | https://www.frontiersin.org/articles/10.3389/fpubh.2022.1052241/full |
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