Comparative Analysis and Identification of Spike Mutations in Iranian COVID-19 Samples from the First Three Waves of Disease

Parisa Shoaei; Mohammad M Ranjbar; Samaneh Tokhanbigli; Behrouz Ataei; Abbas Alibakhshi; Shaghayegh Haghjooy Javanmard; Shahrzad Ahangarzadeh

doi:10.4103/abr.abr_171_22

Comparative Analysis and Identification of Spike Mutations in Iranian COVID-19 Samples from the First Three Waves of Disease

Adv Biomed Res. 2023 Jun 28:12:153. doi: 10.4103/abr.abr_171_22. eCollection 2023.

Authors

Parisa Shoaei¹, Mohammad M Ranjbar², Samaneh Tokhanbigli³, Behrouz Ataei³, Abbas Alibakhshi⁴, Shaghayegh Haghjooy Javanmard⁵, Shahrzad Ahangarzadeh³

Affiliations

¹ Nosocomial Infection Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
² Razi Vaccine and Serum Research Institute, Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.
³ Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
⁴ Molecular Medicine Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
⁵ Department of Physiology, Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran.

Abstract

Background: The spike surface glycoprotein of SARS-CoV-2 is the essential protein in virus attachment to the target cell and cell entrance. As this protein contains immunodominant epitopes and is the main target for immune recognition, it is the critical target for vaccine and therapeutics development. In the current research, we analyzed the variability and mutations of the spike glycoprotein isolated from 72 COVID-19-positive patients from Iran's first three waves of disease.

Materials and methods: The RNA was extracted from nasopharyngeal samples of confirmed COVID-19 cases and served as a template for cDNA synthesis and reverse transcriptase polymerase chain reaction. The reverse transcriptase polymerase chain reaction products of each sample were assembled and sequenced.

Results: After analysis of 72 sequences, we obtained 46 single nucleotide polymorphisms, including 23 that produce amino acid changes. Our analysis showed that the most frequent mutation was the D614G (in the samples of the second and third waves).

Conclusions: Our findings suggest that developing effective vaccines requires identifying the predominant variants of SARS-CoV-2 in each community.

Keywords: Mutation; SARS-CoV-2; spike glycoprotein.