Characterization and phylogenetic analysis of Iranian SARS‐CoV‐2 genomes: A phylogenomic study

Abstract Background and Aim Characterization of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) based on analyzing the evolution and mutations of viruses is crucial for tracking viral infections, potential mutants, and other pathogens. The purpose was to study the complete sequences of SARS‐CoV‐2 to reveal genetic distance and mutation rate among different provinces of Iran. Methods As of March 2020–April 2021, a total of 131 SARS‐CoV‐2 whole genome sequences submitted from Tehran and 133 SARS‐CoV‐2 full‐length sequences from 24 cities with high coverage submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild‐type variant Wuhan‐Hu‐1. Results The results of variant annotation were revealed 11,204 and 9468 distinct genomes were identified among the samples from different cities and Tehran, respectively. The phylogenetic analysis of genomic sequences showed the presence of eight GISAID clades, namely GH, GR, O, GRY, G, GK, L, and GV, and six Nextstrain clades; that is, 19A, 20A, 20B, 20I (alpha, V1), 20H (Beta, V2), and 21I (Delta) in Iran. The GH (GISAID clade), 20A (Nextstrain clade), and B.1 (Pango lineage) were predominant in Iran. Notably, analysis of the spike protein revealed D614G mutation (S_D614G) in 56% of the sequences. Also, the delta variant of the coronavirus, the super‐infectious strain that was first identified among the sequences submitted from the southern cities of the country such as Zahedan, Yazd and Bushehr, and most likely from these places to other cities of Iran as well has expanded. Conclusions Our results indicate that most of the circulated viruses in Iran in the early time of the pandemic had collected in eight GISAID clades. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS‐CoV‐2 in Iran