Quantifying Iran’s endemic transition in COVID-19 through Omicron reproduction number estimates

The emergence of the SARS-CoV-2 Omicron variant in early 2022 substantially altered COVID-19 transmission dynamics in Iran, accelerating the transition toward an endemic-like pattern. We estimated the time-varying effective reproduction number (Rt) in Iran from January 2022 to December 2023 using daily reported case data from the Our World in Data (OWID) repository. Four complementary estimation methods were employed: Exponential Growth (EG), Maximum Likelihood (ML), Sequential Bayesian (SB), and Time-Dependent (TD). To mitigate reporting artifacts, a seven-day rolling average was applied; missing observations were imputed via linear interpolation, and anomalous outliers were cross-checked against official epidemiological bulletins. Sensitivity analyses varied the mean generation time between 2.5 and 3.5 days. Variant-specific Rt estimates were derived for periods dominated by the BA.1 and BA.4/BA.5 Omicron subvariants using genomic surveillance data. Regional comparisons with neighboring countries (Iraq, Turkey, Armenia, Azerbaijan, Afghanistan, and Pakistan) contextualized Iran’s transmission trends. Results indicate that Rt remained persistently above the epidemic threshold of 1.0 throughout the study period, with mean values ranging from 1.27 to 1.47 across methods. The BA.1 and BA.4/BA.5 periods exhibited mean Rt values of 1.35 and 1.31, respectively, suggesting sustained community transmission despite transient short-term dips below unity. An open-source R-based toolkit is provided to support reproducible Rt estimation under real-world data constraints. These findings offer quantitative evidence of endemic-phase transmission and inform future surveillance and preparedness strategies.