Next-generation sequencing of Omicron SARS-CoV-2 variants in Hormozgan Province, Iran, and evaluation of the effects of mutations on RBD and ORF9b protein function

The emergence of the Omicron variant in November 2021 marked a significant turning point in the COVID-19 pandemic due to its unprecedented number of mutations compared to previous variants. To better understand its clinical impact and evolutionary trajectory, we conducted a comprehensive genomic epidemiology study analyzing 528 SARS-CoV-2 samples collected in Iran between March 2021 and March 2023. Using nanopore sequencing with ≥96 % genome coverage and advanced bioinformatics tools including the Nextclade platform, we systematically characterized the mutational profiles of circulating variants with particular focus on the receptor-binding domain (RBD) and ORF9b proteins. Our analysis revealed BA.5.2 as the dominant strain (32.4 % prevalence), followed by XBB.1.9.1 (14.2 %), with only 17.6 % of cases occurring in vaccinated individuals. Through molecular docking and dynamics simulations, we demonstrated that key variants including BA.5.2, XBB.1.5, and XBB.1.9 exhibit enhanced binding affinity to host receptors, with RBD showing stronger interactions with ACE2 and ORF9b variants displaying improved binding to TOM70. Notably, our findings suggest similar pathogenic potential between the XBB.1.5/XBB.1.9 and BA.5 lineages, while highlighting the utility of whole genome entropy analysis for predicting viral evolution patterns. These results provide valuable insights for guiding vaccine development, therapeutic design, and public health strategies against evolving SARS-CoV-2 variants.