The study of mutations and phylogenetics of the SARS-CoV-۲ spike gene in population from Tehran province

In December ۲۰۱۹, an outbreak of pneumonia of unknown etiology was reported in Wuhan, China. The virus, known as SARS-CoV-۲, 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-۲ S gene, the present study was conducted to determine the sequence, mutation pattern, and phylogenetic evaluation of this gene. For this purpose, ۱۲۰ 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 ۱۶۱ 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. ۱۶۱ nonsynonymous variations were found along the complete coding S gene with a high frequency of A۲۶۲T, D۶۱۴G, and P۸۶۳H, which were embedded in HVR۱, HVR۲, and HVR۳, 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-۲ 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.

کلیدواژه ها:

SARS-CoV-۲ ، S gene ، mutation ، Phylogenetics analysis