COVID-19 Reproduction Number and Endemic Transition in Iran: A Retrospective Analysis of the Omicron Era

Characterizing the transition of a pandemic to an endemic phase is a complex undertaking, defined by profound shifts in viral transmissibility and population-level immunity. The effective reproduction number (Rt) serves as an indispensable metric for monitoring this process. This study presents a detailed retrospective analysis of the COVID-19 reproduction number in Iran across 2022 and 2023, a critical period dominated by the Omicron variant and its sublineages. Our objective is to quantitatively delineate the transmission dynamics that accompanied the conclusion of the pandemic’s emergency phase within the region. Drawing upon daily smoothed case data from the Our World in Data repository for the period of January 1, 2022, to December 31, 2023, we employed a multi-method framework to estimate Rt, encompassing Exponential Growth (EG), Maximum Likelihood (ML), Sequential Bayesian (SB), and Time-Dependent (TD) models. A literature-derived gamma distribution was utilized to model the generation time for the Omicron variant. This primary analysis was fortified by a sensitivity analysis of the generation time, a comparative assessment of R during distinct Omicron subvariant waves, and a regional comparison with neighboring countries. Our findings reveal that despite a marked reduction in disease severity, the reproduction number in Iran consistently remained above the critical threshold of 1.0 throughout the 2022–2023 period, with estimates from all four methods converging in the range of 1.27 to 1.47. Although transient periods of control (Rt<1) were observed, rolling averages never sustained a sub-unity level, indicating persistent community transmission. Variant-specific analysis elucidated a high R-value for Omicron BA.1 (1.35), which slightly attenuated for BA.4/BA.5 (1.32). Regional analysis further substantiated that while Iran achieved momentary control early in 2022, this state was not maintained.