{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T20:12:54Z","timestamp":1773432774297,"version":"3.50.1"},"reference-count":34,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,11,29]],"date-time":"2022-11-29T00:00:00Z","timestamp":1669680000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Public Health"],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>The fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an <jats:italic>in-silico<\/jats:italic> study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>The 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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Our 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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>These mutations appear to confer enhanced properties of infectivity. The Omicron variant appears to be more effective at evading immune responses.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fpubh.2022.1052241","type":"journal-article","created":{"date-parts":[[2022,11,29]],"date-time":"2022-11-29T08:43:31Z","timestamp":1669711411000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion"],"prefix":"10.3389","volume":"10","author":[{"given":"Jose A.","family":"Jimenez Ruiz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cecilia","family":"Lopez Ramirez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jose Luis","family":"Lopez-Campos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,11,29]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"2001","DOI":"10.1111\/1462-2920.15053","article-title":"SARS-CoV-2 variants: Relevance for symptom granularity, epidemiology, immunity (herd, vaccines), virus origin and containment?","volume":"22","author":"Danchin","year":"2020","journal-title":"Environ Microbiol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.arbres.2022.03.011","article-title":"Short and long-term impact of COVID-19 infection on previous respiratory diseases","volume":"58","author":"Chiner-Vives","year":"2022","journal-title":"Arch Bronconeumol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.arbres.2022.03.001","article-title":"The emergence of COVID-19 as a cause of death in 2020 and its effect on mortality by diseases of the respiratory system in Spain: trends and their determinants compared to 2019","volume":"58","author":"Soriano","year":"2022","journal-title":"Arch Bronconeumol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1016\/j.ijid.2021.11.040","article-title":"Emergence of new SARS-CoV-2 Variant of Concern Omicron (B. 11529) - highlights Africa's research capabilities, but exposes major knowledge gaps, inequities of vaccine distribution, inadequacies in global COVID-19 response and control efforts","volume":"114","author":"Petersen","year":"2022","journal-title":"Int J Infect Dis."},{"key":"B5","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/d41586-021-03552-w","article-title":"Heavily mutated Omicron variant puts scientists on alert","volume":"600","author":"Callaway","year":"2021","journal-title":"Nature."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.1101\/2021.12.02.470946","article-title":"Omicron and delta variant of SARS-CoV-2: a comparative computational study of spike protein","volume":"94","author":"Kumar","year":"2022","journal-title":"J Med Virol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"6977","DOI":"10.1038\/s41467-021-27325-1","article-title":"Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants","volume":"12","author":"Koehler","year":"2021","journal-title":"Nat Commun."},{"key":"B8","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1038\/d41586-021-03825-4","article-title":"Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift","volume":"602","author":"Cameroni","year":"2022","journal-title":"Nature."},{"key":"B9","doi-asserted-by":"publisher","first-page":"2021","DOI":"10.1101\/2021.12.12.472313","article-title":"Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces","author":"Lubin","year":"2021","journal-title":"bioRxiv [Preprint]."},{"key":"B10","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1101\/2021.12.14.21267755","article-title":"mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant","volume":"185","author":"Garcia-Beltran","year":"2022","journal-title":"Cell."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/22221751.2021.2022440","article-title":"Omicron variant showed lower neutralizing sensitivity than other SARS-CoV-2 variants to immune sera elicited by vaccines after boost","author":"Ai","year":"2021","journal-title":"Emerg Microbes Infect"},{"key":"B12","doi-asserted-by":"publisher","first-page":"W597","DOI":"10.1093\/nar\/gkt376","article-title":"Analysis Tool Web Services from the EMBL-EBI","volume":"41","author":"McWilliam","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B13","doi-asserted-by":"publisher","first-page":"3557","DOI":"10.1016\/S0021-9258(19)34176-6","article-title":"A one-letter notation for amino acid sequences. 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