Pathogen-specific ripple effects of COVID-19 nonpharmaceutical interventions in reshaping endemic disease dynamics

Abstract

Nonpharmaceutical interventions (NPIs) implemented during COVID-19 disrupted the transmission of many endemic infectious diseases, but their broader, system-wide effects across multiple pathogens remain incompletely understood. Using nearly a decade of weekly surveillance data for 32 infectious diseases in Tokyo, we combined time-series analyses, mechanistic modelling, and epidemic-trajectory reconstruction to investigate pathogen-specific changes associated with NPIs. High-incidence respiratory and intestinal infections decline most sharply in 2020, with reductions closely aligned with NPI stringency. Post-NPI rebounds vary substantially: respiratory syncytial virus and group A streptococcus peak several times above historical baselines, whereas influenza, hand, foot, and mouth disease, and herpangina return to pre-NPI levels. Model-based simulations suggest that differences in rebound magnitude and timing may depend on pathogen-specific epidemiological parameters related to immunity duration and susceptible replenishment. Beyond short-term resurgences, we also identify longer-lasting shifts in reported incidence trajectories, including reduced tuberculosis incidence, increased syphilis incidence, and a biennial phase shift in hand, foot, and mouth disease. COVID-19 NPIs produce profound but highly pathogen-specific changes in other infectious disease dynamics. These effects extend beyond temporary suppression and rebound, with several pathogens exhibiting persistent deviations in reported incidence trajectories after the NPI period. These findings highlight how pathogen-specific epidemiological characteristics may contribute to heterogeneous post-NPI trajectories, which could inform tailored control strategies. Measures such as mask wearing, school closures, and reduced social contact were widely used during the COVID-19 pandemic to limit the spread of SARS-CoV-2. These nonpharmaceutical interventions also affected many other infectious diseases, but their broader consequences have not been fully understood. In this study, we analysed nearly 10 years of weekly surveillance data for 32 infectious diseases in Tokyo. We found that many respiratory and intestinal infections fell sharply during 2020, but their resurgence after restrictions were lifted differed greatly between diseases. Some infections, such as respiratory syncytial virus infection and group A streptococcus infection, rebounded to unusually high levels, whereas others returned to patterns closer to those seen before the pandemic. We also found longer-term changes, including fewer tuberculosis cases, more syphilis cases, and a shift in the two-year cycle of hand, foot, and mouth disease. These results show that different infections may respond differently to large-scale public health measures, which may help improve disease surveillance and future control planning. Chen et al., analyse nearly a decade of surveillance data for 32 infectious diseases in Tokyo to assess how COVID-19 nonpharmaceutical interventions alter pathogen transmission dynamics. Respiratory and intestinal infections decline sharply during interventions, but post-intervention trajectories vary substantially, with some pathogens showing large rebounds and others exhibiting persistent shifts in incidence patterns.

The authors' abstract, as published at the source. Communications Medicine, 2026 · DOI ↗