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The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures

The global scale of the COVID-19 pandemic has demonstrated the evolution of SARS-CoV-2 and the clues of adaptation. After two years and two months since the declaration of the pandemic, several variants have emerged and become fixed in the human population thanks to extrinsic selective pressures but...

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Autores principales: López-Cortés, Georgina I., Palacios-Pérez, Miryam, Veledíaz, Hannya F., Hernández-Aguilar, Margarita, López-Hernández, Gerardo R., Zamudio, Gabriel S., José, Marco V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9230601/
https://www.ncbi.nlm.nih.gov/pubmed/35746472
http://dx.doi.org/10.3390/vaccines10060864
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author López-Cortés, Georgina I.
Palacios-Pérez, Miryam
Veledíaz, Hannya F.
Hernández-Aguilar, Margarita
López-Hernández, Gerardo R.
Zamudio, Gabriel S.
José, Marco V.
author_facet López-Cortés, Georgina I.
Palacios-Pérez, Miryam
Veledíaz, Hannya F.
Hernández-Aguilar, Margarita
López-Hernández, Gerardo R.
Zamudio, Gabriel S.
José, Marco V.
author_sort López-Cortés, Georgina I.
collection PubMed
description The global scale of the COVID-19 pandemic has demonstrated the evolution of SARS-CoV-2 and the clues of adaptation. After two years and two months since the declaration of the pandemic, several variants have emerged and become fixed in the human population thanks to extrinsic selective pressures but also to the inherent mutational capacity of the virus. Here, we applied a neutral substitution evolution test to the spike (S) protein of Omicron’s protein and compared it to the others’ variant of concern (VOC) neutral evolution. We carried out comparisons among the interactions between the S proteins from the VOCs (Alpha, Beta, Gamma, Delta and Omicron) and the receptor ACE2. The shared amino acids among all the ACE2 binding S proteins remain constant, indicating that these amino acids are essential for the accurate binding to the receptor. The complexes of the RBD for every variant with the receptor were used to identify the amino acids involved in the protein—protein interaction (PPI). The RBD of Omicron establishes 82 contacts, compared to the 74 of the Wuhan original viral protein. Hence, the mean number of contacts per residue is higher, making the contact thermodynamically more stable. The RBDs of the VOCs are similar in sequence and structure; however, Omicron’s RBD presents the largest deviation from the structure by 1.11 Å RMSD, caused by a set of mutations near the glycosylation N343. The chemical properties and structure near the glycosylation N343 of the Omicron S protein are different from the original protein, which provoke reduced recognition by the neutralizing antibodies. Our results hint that selective pressures are induced by mass vaccination throughout the world and by the persistence of recurrent infections in immunosuppressed individuals, who did not eliminate the infection and ended up facilitating the selection of viruses whose characteristics are different from the previous VOCs, less pathogenic but with higher transmissibility.
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spelling pubmed-92306012022-06-25 The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures López-Cortés, Georgina I. Palacios-Pérez, Miryam Veledíaz, Hannya F. Hernández-Aguilar, Margarita López-Hernández, Gerardo R. Zamudio, Gabriel S. José, Marco V. Vaccines (Basel) Article The global scale of the COVID-19 pandemic has demonstrated the evolution of SARS-CoV-2 and the clues of adaptation. After two years and two months since the declaration of the pandemic, several variants have emerged and become fixed in the human population thanks to extrinsic selective pressures but also to the inherent mutational capacity of the virus. Here, we applied a neutral substitution evolution test to the spike (S) protein of Omicron’s protein and compared it to the others’ variant of concern (VOC) neutral evolution. We carried out comparisons among the interactions between the S proteins from the VOCs (Alpha, Beta, Gamma, Delta and Omicron) and the receptor ACE2. The shared amino acids among all the ACE2 binding S proteins remain constant, indicating that these amino acids are essential for the accurate binding to the receptor. The complexes of the RBD for every variant with the receptor were used to identify the amino acids involved in the protein—protein interaction (PPI). The RBD of Omicron establishes 82 contacts, compared to the 74 of the Wuhan original viral protein. Hence, the mean number of contacts per residue is higher, making the contact thermodynamically more stable. The RBDs of the VOCs are similar in sequence and structure; however, Omicron’s RBD presents the largest deviation from the structure by 1.11 Å RMSD, caused by a set of mutations near the glycosylation N343. The chemical properties and structure near the glycosylation N343 of the Omicron S protein are different from the original protein, which provoke reduced recognition by the neutralizing antibodies. Our results hint that selective pressures are induced by mass vaccination throughout the world and by the persistence of recurrent infections in immunosuppressed individuals, who did not eliminate the infection and ended up facilitating the selection of viruses whose characteristics are different from the previous VOCs, less pathogenic but with higher transmissibility. MDPI 2022-05-28 /pmc/articles/PMC9230601/ /pubmed/35746472 http://dx.doi.org/10.3390/vaccines10060864 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
López-Cortés, Georgina I.
Palacios-Pérez, Miryam
Veledíaz, Hannya F.
Hernández-Aguilar, Margarita
López-Hernández, Gerardo R.
Zamudio, Gabriel S.
José, Marco V.
The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures
title The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures
title_full The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures
title_fullStr The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures
title_full_unstemmed The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures
title_short The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures
title_sort spike protein of sars-cov-2 is adapting because of selective pressures
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9230601/
https://www.ncbi.nlm.nih.gov/pubmed/35746472
http://dx.doi.org/10.3390/vaccines10060864
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