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SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study)
An essential step in SARS-CoV-2 infection is binding the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to the ACE2 receptor on the surface of host cells. Therefore, variation in this region can have crucial effects on clinical outcomes and the emergence of variants of concern (VOCs)...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Published by Elsevier Ltd.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9116045/ https://www.ncbi.nlm.nih.gov/pubmed/35597364 http://dx.doi.org/10.1016/j.micpath.2022.105595 |
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author | Hajizadeh, Faezeh Khanizadeh, Sayyad Khodadadi, Hamidreza Mokhayeri, Yaser Ajorloo, Mehdi Malekshahi, Asra Heydari, Ezatoallah |
author_facet | Hajizadeh, Faezeh Khanizadeh, Sayyad Khodadadi, Hamidreza Mokhayeri, Yaser Ajorloo, Mehdi Malekshahi, Asra Heydari, Ezatoallah |
author_sort | Hajizadeh, Faezeh |
collection | PubMed |
description | An essential step in SARS-CoV-2 infection is binding the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to the ACE2 receptor on the surface of host cells. Therefore, variation in this region can have crucial effects on clinical outcomes and the emergence of variants of concern (VOCs) and variants of interest (VOIs). In this cross-sectional descriptive study, 54 patients with SARS-COV-2 infection were enrolled. After collecting samples and identifying the virus using the One-Step Real-Time qRT-PCR technique and confirming the viral infection, the region containing the RBD region for detection of any mutations was amplified using the Nested-PCR method. Finally, to identify probable mutations, the Nested-PCR product was sequenced. Our data show that the most mutant strains in circulation in our population are the delta variant (90.74%), alpha variant (5.56%), and omicron variant (3.70%), respectively. Pangolin Lineages strains were B.1.1.7(Alpha variant), B.1.617.2(Delta variant) and B.1.1.529(Omicron variant). Also, the mutation profile of variants suggests that N501Y, T478K, and D614G amino acid substitutions, are the significant mutations in the alpha and delta variants that are common with the Omicron variant. The highest frequency of clinical signs in the patients were: lung involvement (42.59%); fever, chills (40.74%); body pain (15%), and other signs (1.67%). Our data revealed that SARS-COV-2 RBD region variation results in substituting essential amino acids and the emergence of the new variant. We can consider it as a predictor for monitoring the emergence of variants of concerns and viral outcomes. |
format | Online Article Text |
id | pubmed-9116045 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Published by Elsevier Ltd. |
record_format | MEDLINE/PubMed |
spelling | pubmed-91160452022-05-18 SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study) Hajizadeh, Faezeh Khanizadeh, Sayyad Khodadadi, Hamidreza Mokhayeri, Yaser Ajorloo, Mehdi Malekshahi, Asra Heydari, Ezatoallah Microb Pathog Article An essential step in SARS-CoV-2 infection is binding the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to the ACE2 receptor on the surface of host cells. Therefore, variation in this region can have crucial effects on clinical outcomes and the emergence of variants of concern (VOCs) and variants of interest (VOIs). In this cross-sectional descriptive study, 54 patients with SARS-COV-2 infection were enrolled. After collecting samples and identifying the virus using the One-Step Real-Time qRT-PCR technique and confirming the viral infection, the region containing the RBD region for detection of any mutations was amplified using the Nested-PCR method. Finally, to identify probable mutations, the Nested-PCR product was sequenced. Our data show that the most mutant strains in circulation in our population are the delta variant (90.74%), alpha variant (5.56%), and omicron variant (3.70%), respectively. Pangolin Lineages strains were B.1.1.7(Alpha variant), B.1.617.2(Delta variant) and B.1.1.529(Omicron variant). Also, the mutation profile of variants suggests that N501Y, T478K, and D614G amino acid substitutions, are the significant mutations in the alpha and delta variants that are common with the Omicron variant. The highest frequency of clinical signs in the patients were: lung involvement (42.59%); fever, chills (40.74%); body pain (15%), and other signs (1.67%). Our data revealed that SARS-COV-2 RBD region variation results in substituting essential amino acids and the emergence of the new variant. We can consider it as a predictor for monitoring the emergence of variants of concerns and viral outcomes. Published by Elsevier Ltd. 2022-07 2022-05-18 /pmc/articles/PMC9116045/ /pubmed/35597364 http://dx.doi.org/10.1016/j.micpath.2022.105595 Text en © 2022 Published by Elsevier Ltd. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Hajizadeh, Faezeh Khanizadeh, Sayyad Khodadadi, Hamidreza Mokhayeri, Yaser Ajorloo, Mehdi Malekshahi, Asra Heydari, Ezatoallah SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study) |
title | SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study) |
title_full | SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study) |
title_fullStr | SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study) |
title_full_unstemmed | SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study) |
title_short | SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study) |
title_sort | sars-cov-2 rbd (receptor binding domain) mutations and variants (a sectional-analytical study) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9116045/ https://www.ncbi.nlm.nih.gov/pubmed/35597364 http://dx.doi.org/10.1016/j.micpath.2022.105595 |
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