The study of mutations and phylogenetics of the SARS-CoV-2 spike gene in population from Tehran province

Document Type : Original Articles

Authors

1 Razi vaccine and Sera institute

2 Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran

3 Applied Biotechnology Research Center, Baqiyatallah University of Medical Science, Tehran, Iran

4 Department of Electrical and Computer Engineering, Faculty of Engineering, University of Waterloo, Waterloo, ON N2L Canada

5 Department of Microbiology, Faculty of Sciences, Islamic Azad University, Karaj Branch, Karaj, Iran

6 Razi vaccine and sera research institute

10.32592/ARI.2025.80.1.185

Abstract

In December 2019, an outbreak of pneumonia of unknown etiology was reported in Wuhan, China. The virus, known as SARS-CoV-2, is contagious and infects the lower respiratory tract. Since various coherent research needs to be conducted in Iran to detect mutations in the SARS-CoV-2 S gene, the present study was conducted to determine the sequence, mutation pattern, and phylogenetic evaluation of this gene. For this purpose, 120 positive samples were included to evaluate the complete S gene sequence by Reverse transcriptase-PCR. After sequencing, the gene assembly, blasting, mutation analysis, and phylogenetic analyzes were performed using MEGA-X. A total of 161 mutations were observed in the S gene sequences of Iran. The results of the phylogenetic tree showed that all the S gene sequences of Iranian samples were divergent from the Wuhan strain and had the most similarity to it and also alpha variants. 161 nonsynonymous variations were found along the complete coding S gene with a high frequency of A262T, D614G, and P863H, which were embedded in HVR1, HVR2, and HVR3, respectively. Most of Highly variable fragments have been identified in loop secondary structure of protein.
In the current study, the predominant variants (mostly alpha variants) and mutations were in parallel with the evolution of the virus and its fitness. We provided a wide picture of the genetic mutation of first three waves of SARS-CoV-2 in Iran which could be used to make big decisions and take effective decisions in the next pandemics to develop vaccines and kits and effective therapeutics.

Keywords

Main Subjects

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Archives of Razi Institute
Volume 80, Issue 1
January and February 2025
Pages 185-192

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