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A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients.
Gene. 2022 Mar 01; 813:146113.GENE

Abstract

Since late 2019, when SARS-CoV-2 was reported at Wuhan, several sequence analyses have been performed and SARS-CoV-2 genome sequences have been submitted in various databases. Moreover, the impact of these variants on infectivity and response to neutralizing antibodies has been assessed. In the present study, we retrieved a total number of 176 complete and high-quality S glycoprotein sequences of Iranian SARS-COV-2 in public database of the GISAID and GenBank from April 2020 up to May 2021. Then, we identified the number of variables, singleton and parsimony informative sites at both gene and protein levels and discussed the possible functional consequences of important mutations on the infectivity and response to neutralizing antibodies. Phylogenetic tree was constructed to represent the relationship between Iranian SARS-COV2 and variants of concern (VOC), variants of interest (VOI) and reference sequence. We found that the four current VOCs - Alpha, Beta, Gamma and Delta - are circulated in different regions in Iran. The Delta variant is notably more transmissible than other variants, and is expected to become a dominant variant. However, some of the Delta variants in Iran carry an additional mutation, namely E1202Q in the HR2 subdomain that might confer an advantage to viral/cell membrane fusion process. We also observed some more common mutations such as an N-terminal domain (NTD) deletion at position I210 and P863H in fusion peptide-heptad repeat 1 span region in Iranian SARS-COV-2. The reported mutations in the current project have practical significance in prediction of disease spread as well as design of vaccines and drugs.

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Authors+Show Affiliations

Eslami S
Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran; Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran.
Glassy MC
Translational Neuro-Oncology Laboratory, San Diego (UCSD) Moores Cancer Center, University of California, CA, United States.
Ghafouri-Fard S
Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran. Electronic address: s.ghafourifard@sbmu.ac.ir.

MeSH

Antibodies, NeutralizingAntibodies, ViralCOVID-19Databases, GeneticHumansIranMutationPhylogenyProtein BindingRNA, ViralSARS-CoV-2Sequence Analysis, DNASpike Glycoprotein, Coronavirus

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34896524

Citation

Eslami, Solat, et al. "A Comprehensive Overview of Identified Mutations in SARS CoV-2 Spike Glycoprotein Among Iranian Patients." Gene, vol. 813, 2022, p. 146113.
Eslami S, Glassy MC, Ghafouri-Fard S. A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Gene. 2022;813:146113.
Eslami, S., Glassy, M. C., & Ghafouri-Fard, S. (2022). A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Gene, 813, 146113. https://doi.org/10.1016/j.gene.2021.146113
Eslami S, Glassy MC, Ghafouri-Fard S. A Comprehensive Overview of Identified Mutations in SARS CoV-2 Spike Glycoprotein Among Iranian Patients. Gene. 2022 Mar 1;813:146113. PubMed PMID: 34896524.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. AU - Eslami,Solat, AU - Glassy,Mark C, AU - Ghafouri-Fard,Soudeh, Y1 - 2021/12/09/ PY - 2021/07/22/received PY - 2021/10/31/revised PY - 2021/12/06/accepted PY - 2021/12/14/pubmed PY - 2022/1/22/medline PY - 2021/12/13/entrez KW - Mutation KW - SARS CoV-2 KW - Spike protein KW - Variants of concern (VOC) KW - Variants of interest (VOI) SP - 146113 EP - 146113 JF - Gene JO - Gene VL - 813 N2 - Since late 2019, when SARS-CoV-2 was reported at Wuhan, several sequence analyses have been performed and SARS-CoV-2 genome sequences have been submitted in various databases. Moreover, the impact of these variants on infectivity and response to neutralizing antibodies has been assessed. In the present study, we retrieved a total number of 176 complete and high-quality S glycoprotein sequences of Iranian SARS-COV-2 in public database of the GISAID and GenBank from April 2020 up to May 2021. Then, we identified the number of variables, singleton and parsimony informative sites at both gene and protein levels and discussed the possible functional consequences of important mutations on the infectivity and response to neutralizing antibodies. Phylogenetic tree was constructed to represent the relationship between Iranian SARS-COV2 and variants of concern (VOC), variants of interest (VOI) and reference sequence. We found that the four current VOCs - Alpha, Beta, Gamma and Delta - are circulated in different regions in Iran. The Delta variant is notably more transmissible than other variants, and is expected to become a dominant variant. However, some of the Delta variants in Iran carry an additional mutation, namely E1202Q in the HR2 subdomain that might confer an advantage to viral/cell membrane fusion process. We also observed some more common mutations such as an N-terminal domain (NTD) deletion at position I210 and P863H in fusion peptide-heptad repeat 1 span region in Iranian SARS-COV-2. The reported mutations in the current project have practical significance in prediction of disease spread as well as design of vaccines and drugs. SN - 1879-0038 UR - https://www.unboundmedicine.com/medline/citation/34896524/A_comprehensive_overview_of_identified_mutations_in_SARS_CoV_2_spike_glycoprotein_among_Iranian_patients_ DB - PRIME DP - Unbound Medicine ER -