Heatmap of respiratory infections in Tokyo 2016-2026
#19,356
We've a new report in Nature today which looks at the reported incidence of 32 different infectious diseases in Tokyo, Japan over a nearly 10-year span (2016-2025), that shows the changes that occurred during and after the height of the COVID/NPI era.
While some people still have doubts over the effectiveness of NPIs, the incidence of common respiratory infections (influenza, RSV, pertussis, even chickenpox) plummeted during 2020-2021 (see above graphic).
But after the NPI mandates ended, most of these viral scourges returned; some with seemingly even greater intensity than before the lockdown. We followed many similar increases around the world.
CDC HAN #0484: Increase in Pediatric Invasive Group A Streptococcal Infections
Denmark SSI Declares A Mycoplasma Pneumonia Epidemic
WHO Statement (DON) On Respiratory Illness Surge Reported In Northern China
Others, like influenza, eventually returned to near pre-pandemic levels, although the influenza B/Yamagata lineage is now considered missing-in-action, with its last sighting in March of 2020.
Notably, the incidence of tuberculosis reported in Tokyo dropped roughly 40% after the lockdown ended.
The chart on vector-borne and/or sexually transmitted diseases is equally fascinating, as syphilis and HIV/AIDS reporting suggested only a small reduction during lockdown, and the incidence of syphilis sharply increased after the lockdown ended.
In fairness, during the height of the pandemic, a lot of testing capacity was diverted to COVID, meaning rising or falling trends during that time period may not have been fully captured, which could account for some of the abrupt shifts seen after the lockdown ended.
Admittedly, some of these post-pandemic shifts may be incidental findings, and not directly related to the lockdown. The authors warn:
Our cross correlation analyses quantify the temporal alignment between changes in reported incidence and NPI-related indicators (Fig. 2b, c), although these associations should not be interpreted as evidence of the independent causal effect of individual NPIs.
I've only reproduced a small excerpt from the study. Follow the link to read it in its entirety. I'll have a brief postscript after the break.
Pathogen-specific ripple effects of COVID-19 nonpharmaceutical interventions in reshaping endemic disease dynamicsDaipeng Chen, Seyed M. Moghadas & Gergely Röst
Communications Medicine (2026) Cite this article
We’re sharing this article early to provide faster access to peer-reviewed, accepted research. It is citable and carries a permanent DOI. This version is subject to further edits and will be replaced automatically by the final Version of Record. All legal disclaimers apply.
Abstract
Background
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.
Methods
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.
Results
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.
Conclusions
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.
Plain language summary
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.
For logistical and political reasons, the world stopped reporting and counting COVID deaths quite early in the pandemic, but a 2022 Lancet report estimated 18.2 million excess deaths during the first 2 years.
How many have died since then is unknown, as is how many deaths were prevented by the COVID vaccines, social distancing, and NPIs. It is probably fair to say all are measured in the millions.
But every action (or inaction) has unintended consequences . . some good, some bad. Some we may be able to predict, others not so much.
Pandemics, like life, can only be understood by looking backwards.
But with enough honest introspection, we might better understand - and handle - the next one.
