SARS-CoV-2 Omicron: Genotyping, Mutational Analysis, and Characterization of Subvariants in Iran

Background: Several SARS-CoV-2 variants with distinct characteristics have emerged, with Omicron sub-variants such as BA.1 to BA.5 being predominant since late 2021.Distinguishing sub-variants using phylogenetic and molecular analyzes provides a valuable approach in the context of epidemiological research. .Materials & Methods:Molecular epidemiology and sub-variants of SARS-CoV-2 omicron were investigated using 150 nasopharyngeal samples from COVID-19 patients in Tehran (Iran) from May 2022 to August 2023.Omicron lineages were differentiated using RT-PCR targeting Q493R, L452R, and 69-70 spike mutations.SARS-CoV-2 omicron sub-variants were determined by amplicon sequencing.Findings: The mean age of the study participants was 447 years, comprising 38.6% males and 61.4% females, which may have an effect on transmission and susceptibility of different ages.Also, 117 (78%) samples were positive for one of the three lineages, while 33 (22%) was none of the lineages, which were referred to as conclusive and inconclusive results, respectively.60.7% of the samples was the omicron lineage BA.4 or BA.5. Conclusion:Considering the prevalence of BA.4 and BA.5 in the study population and their differences with the parental SARS-CoV-2 variant, the primary vaccine seems to be not effective against the current omicron sub-variants.These results underscore the importance of vaccination as a critical strategy to prevent the spread of these variants.The suggested primer sets could be an easy way to screen sample variants and lineages and are useful for screening and sequencing samples in countries with limited resources.Continuous monitoring of omicron sub-variants is recommended for preventing the resurgence of COVID-19.