SARS-CoV-2: A Retrospective Study from a Reference Laboratory in North Jakarta and Reflection on Provincial-to-National COVID-19 Fluctuation Using 30 Months of Data

Understanding COVID-19 transitions towards endemicity is vital by examining center-specific data within provincial and national contexts. This retrospective study aimed to enhance public health management and understanding of COVID-19 dynamics using data from Atma Jaya Catholic University of Indonesia (AJCUI) and open-source databases from Jakarta and Indonesia’s official websites from July 2020 to December 2022. Trends across data sources were compared, and correlations between positivity rates at AJCUI and Jakarta/Indonesia were assessed using linear regression. A total of 8,354,809 positive samples were analyzed nationally, showing similar trends and peaks of positivity rates across databases, with positive correlations between AJCUI–Jakarta (β = 1.154; p < 0.001; 95% CI = 0.86–1.45) alongside AJCUI–Indonesia (β = 1.262; p < 0.001; 95% CI = 0.74–1.79). Mobility restriction policies substantially reduced the positivity rate within the study period. Further analysis of AJCUI showed that higher proportions of low Ct value (≤30) were associated with increased contemporaneous positivity at AJCUI (β = 0.442; p < 0.001) and Jakarta (β = 0.319; p < 0.001), although inadequately reflected in Indonesia (β = 0.039; p = 0.589). This study highlights the potential of incorporating Ct value distributions as epidemiological indicators within surveillance systems. These findings support the importance of comprehensive laboratory data recording to better characterize COVID-19 transmission patterns across different surveillance levels, alerting policymakers to establish efficient policies.