A novel approach to estimating R t through infection networks: understanding regional transmission dynamics of COVID-19.

Abstract

INTRODUCTION: The effective reproduction number ( R t ) is a key indicator for monitoring and controlling infectious diseases such as COVID-19, where transmission patterns can differ substantially across demographics, regions, and phases of the pandemic. In this study, we propose a novel, network-based approach to empirically estimate R t using detailed transmission data from South Korea. By reconstructing infector-infectee pairs, our method incorporates local factors like mobility and social distancing, offering a more precise perspective than traditional methods. METHODS: We acquired infector-infectee pair data from the Korea Disease Control and Prevention Agency (KDCA) for 2020-2021 and built infection networks to derive empirical R t . This framework allows us to examine regional differences and the effects of social distancing measures. We also compared our results with Cori's R t , which employs incidence data and serial interval distributions, to highlight the advantages of an infection network-based strategy. RESULTS: Our empirical R t uncovered three distinct patterns. Early in the outbreak, when case numbers were low, R t remained near 1, indicating limited transmission. During superspreading events, our estimates showed sharper peaks than Cori's method, demonstrating higher sensitivity to sudden changes. As the Delta variant emerged, our R t values converged with Cori's, underscoring the utility of network-based methods for capturing nuanced shifts during high-variability phases. DISCUSSION: Incorporating infection networks into R t estimation thus provides decision-makers with timely insights for targeted interventions. Empirically reconstructing infection networks and directly estimating R t reveal real-time transmission dynamics often overlooked by aggregated approaches. This method can significantly improve outbreak forecasts, inform more precise public health policies, and strengthen pandemic preparedness.