Molecular Study of SARS-CoV-2 Variants in Iranian Patients: A Multi-Center Study

 Since the beginning of the recent pandemic in December 2019, the growing waves of SARS-CoV-2 infection have been a major concern. Also, SARS-CoV-2 itself is increasingly developing during the pandemic. The development of a virus leads to emergent mutations and might change the virus-host interaction.

 The current study was conducted to investigate the prevalence of the circulating lineage of SARS-CoV-2 in Iranian COVID-19 patients.

In a cross-sectional study, nasopharyngeal samples of 83 SARS-CoV-2 positive patients, collected between December 2020 to May 2021 from multiple geographical locations in Iran, were studied. The nasopharyngeal samples were used for RNA extraction, and the extracted RNA was used for one-step RT-PCR analysis. Also, a specific primer pair for the spike was used for the amplification and sequencing via Sanger sequencing.

 Our findings revealed a high prevalence of the B 1.1.7 lineage of the SARS-CoV-2 variant after February 2020 in Iranian COVID-19 patients. The results showed some rare mutations, including M177I, I100C, I100T, L452R, N679K, Q173H, Y145H, A222V, and H49Y in evaluated samples.

 As a preliminary multicenter study in Iran, our study indicated the dominancy of the B 1.1.7 lineage in Iranian COVID-19 patients after February 2020 in all the evaluated provinces. Furthermore, 11 isolates represented deletion mutations in positions 209-211 of the Spike protein, similar to the Omicron (21K) variant (211 del only reported in the Omicron 21K clade). Follow-up studies are recommended for more comprehensive results.