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Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan

BACKGROUND: Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human respiratory cells causing COVID-19 disease. AIM: Here, we aimed to predict the three-dimensional...

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Autores principales: Al-Zyoud, Walid, Haddad, Hazem
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815659/
https://www.ncbi.nlm.nih.gov/pubmed/33506114
http://dx.doi.org/10.1016/j.bbrep.2020.100896
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author Al-Zyoud, Walid
Haddad, Hazem
author_facet Al-Zyoud, Walid
Haddad, Hazem
author_sort Al-Zyoud, Walid
collection PubMed
description BACKGROUND: Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human respiratory cells causing COVID-19 disease. AIM: Here, we aimed to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 from 20 Jordanian nasopharyngeal samples and to determine the percentage of single amino acid variants (SAV) in the spike protein of SARS-CoV-2. METHODS: The output of the Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) found four single amino acid variants in the spike gene. RESULTS: The first variant represented by 5% of samples that showed tyrosine deletion at Y144 located in the N terminal domain. The second and the dominant variant, represented by 62%, showed aspartate a coil amino acid substitution to glycine an extracellular amino acid at D614G located in the spike recognition binding site. The third variant, represented by 5%, showed aspartate substitution to tyrosine at D1139Y, and the fourth variant, represented by 5% glycine substitution to serine at G1167S. CONCLUSION: Our results have shown low mutational sensitivity in all variants except to D614G the one with the most likely neutral mutational sensitivity that all variants might not explicitly affect the function of spike glycoprotein. However, D614G might change the viral conformational plasticity and hence a potential viral fitness gain but one must be cautious about drawing any concrete conclusions about the severity of symptoms and viral transmission from genomic data only. GENERAL SIGNIFICANCE: Studying mutations such as D614G in deep is essential to control the pandemic in terms of immune systems, antibodies, or even vaccines.
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spelling pubmed-78156592021-01-26 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan Al-Zyoud, Walid Haddad, Hazem Biochem Biophys Rep Research Article BACKGROUND: Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human respiratory cells causing COVID-19 disease. AIM: Here, we aimed to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 from 20 Jordanian nasopharyngeal samples and to determine the percentage of single amino acid variants (SAV) in the spike protein of SARS-CoV-2. METHODS: The output of the Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) found four single amino acid variants in the spike gene. RESULTS: The first variant represented by 5% of samples that showed tyrosine deletion at Y144 located in the N terminal domain. The second and the dominant variant, represented by 62%, showed aspartate a coil amino acid substitution to glycine an extracellular amino acid at D614G located in the spike recognition binding site. The third variant, represented by 5%, showed aspartate substitution to tyrosine at D1139Y, and the fourth variant, represented by 5% glycine substitution to serine at G1167S. CONCLUSION: Our results have shown low mutational sensitivity in all variants except to D614G the one with the most likely neutral mutational sensitivity that all variants might not explicitly affect the function of spike glycoprotein. However, D614G might change the viral conformational plasticity and hence a potential viral fitness gain but one must be cautious about drawing any concrete conclusions about the severity of symptoms and viral transmission from genomic data only. GENERAL SIGNIFICANCE: Studying mutations such as D614G in deep is essential to control the pandemic in terms of immune systems, antibodies, or even vaccines. Elsevier 2020-12-29 /pmc/articles/PMC7815659/ /pubmed/33506114 http://dx.doi.org/10.1016/j.bbrep.2020.100896 Text en © 2020 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Al-Zyoud, Walid
Haddad, Hazem
Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan
title Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan
title_full Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan
title_fullStr Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan
title_full_unstemmed Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan
title_short Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan
title_sort mutational sensitivity of d614g in spike protein of sars-cov-2 in jordan
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815659/
https://www.ncbi.nlm.nih.gov/pubmed/33506114
http://dx.doi.org/10.1016/j.bbrep.2020.100896
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