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Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic

Jila YavarianVirology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IranAhmad NejatiVirology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IranVahid SalimiVirology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IranNazanin Zahra Shafiei JandaghiVirology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IranKaveh SadeghiVirology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IranAdel AbediMathematics Department, Shahid Beheshti University, Tehran, IranAli Sharifi‐ZarchiDepartment of Computer Engineering, Sharif University of Technology, Tehran, IranMohammad Mehdí GouyaTalat Mokhtari‐AzadVirology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran

2022en

ABI

Annotatsiya

PURPOSE: Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Iran. METHODS: After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq platform. The sequencing data were analyzed and compared with reference sequences. RESULTS: During the 1st wave, V and L clades were detected. The second wave was recognized by G, GH and GR clades. Circulating clades during the 3rd wave were GH and GR. In the fourth wave GRY (alpha variant), GK (delta variant) and one GH clade (beta variant) were detected. All viruses in the fifth wave were in clade GK (delta variant). There were different mutations in all parts of the genomes but Spike-D614G, NSP12-P323L, N-R203K and N-G204R were the most frequent mutants in these studied viruses. CONCLUSIONS: These findings display the significance of SARS-CoV2 monitoring to help on time detection of possible variants for pandemic control and vaccination plans.

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DOI: 10.1371/journal.pone.0267847

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