Longitudinal characterization of COVID-19 across a surveillance transition in Japan: thirteen epidemic waves, 2020–2025

Long-term comparison of COVID-19 epidemic waves is challenging because surveillance systems and reporting practices change over time. In Japan, official reporting shifted repeatedly between January 2020 and December 2025, from comprehensive nationwide notification to restricted reporting and sentinel-based surveillance. Using publicly available national data on reported cases and deaths, we characterized 13 epidemic waves while explicitly accounting for reporting transitions. We described weekly incidence and mortality rates per 100,000 population using population-based indicators to enable comparison across heterogeneous surveillance frameworks. Early waves showed very high observed case fatality ratios. Observed case fatality ratios declined markedly in subsequent waves, although estimates varied with reporting criteria and adjustments for reporting limitations, including periods when mild cases were excluded. Death counts were available only through week 18 of 2023, precluding evaluation of population-based mortality and observed case fatality ratios after the transition to sentinel-based surveillance. This transparent bridging framework enables longitudinal, comparability-oriented description of 13 epidemic waves in Japan across the 2023 surveillance transition. These findings should be interpreted as descriptive patterns observed under evolving surveillance contexts, and causal attribution is beyond the scope of this study.