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. To this end, 120 positive samples were included in the study to evaluate the complete S gene sequence by Reverse transcriptase-PCR.Subsequent to the sequencing process, the gene assembly, blasting, mutation analysis, and phylogenetic analysis 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. The majority of highly variable fragments have been identified in the loop secondary structure of protein. In the present study, the predominant variants (predominantly alpha variants) and mutations were observed to be in parallel with the evolution of the virus and its fitness. A comprehensive overview of the genetic mutation of the first three waves of SARS-CoV-2 in Iran was provided, which could be used to make significant decisions and take effective measures in future pandemics to develop vaccines, kits and effective therapeutics.