Post-pandemic ecological reshaping of respiratory pathogen circulation: A six-year FilmArray(R)-based surveillance study in Tokyo, Japan (2020-2026)
- 1Department of Academic-Industrial Partnerships Promotion, Center for Clinical Sciences, Japan Institute for Health Security, 1-21-1 Toyama, Shinjuku-ku, Tokyo 1
Abstract
BackgroundThe COVID-19 pandemic substantially altered respiratory pathogen circulation worldwide. However, longitudinal analyses of changes in respiratory pathogen ecology across the pandemic and post-pandemic periods remain limited.
MethodsWe analyzed 19,968 respiratory samples tested with the BioFire(R) FilmArray(R) Respiratory Panel at a hospital in Tokyo, Japan, between January 2020 and March 2026. We evaluated temporal changes in pathogen circulation, age-specific epidemiology, co-detection patterns, pairwise pathogen associations, and clinical parameters.
ResultsAt least one respiratory pathogen was detected in 27.8% of tests. Respiratory pathogens resurged asynchronously following the relaxation of COVID-19-related public health measures. Influenza virus circulation remained markedly suppressed until late 2022 before re-emerging in successive large seasonal epidemics, whereas other pathogens, including RSV, human metapneumovirus, and Mycoplasma pneumoniae, exhibited distinct resurgence patterns. Pathogen distributions also varied by age. Human rhinovirus/enterovirus remained predominant among young children, whereas SARS-CoV-2 predominated among older adults. Co-detection occurred in 14.0% of positive specimens and was significantly more frequent in younger patients. Pairwise analysis identified both positive and negative pathogen associations; however, the patterns varied across age groups and study periods.
ConclusionsRespiratory pathogen circulation changed substantially during the transition from the COVID-19 pandemic to the post-pandemic period, with pathogen-specific, age- and period-dependent patterns. Continued surveillance is warranted to determine how respiratory pathogen circulation will evolve and to inform infection control strategies in the post-pandemic era.
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BibTeX
@misc{takeuchi2026postpandemic,
title = {{Post-pandemic ecological reshaping of respiratory pathogen circulation: A six-year FilmArray(R)-based surveillance study in Tokyo, Japan (2020-2026)}},
author = {J. S. Takeuchi and M. Kurokawa and K. Yamamoto and J. Yamanaka and E. Morino and S. Takayanagi-Nishisako and N. Ohmagari and W. Sugiura and M. Kimura},
howpublished = {medRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.28.26360747},
url = {https://www.medrxiv.org/content/10.64898/2026.08.28.26360747v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Post-pandemic ecological reshaping of respiratory pathogen circulation: A six-year FilmArray(R)-based surveillance study in Tokyo, Japan (2020-2026)
AU - J. S. Takeuchi
AU - M. Kurokawa
AU - K. Yamamoto
AU - J. Yamanaka
AU - E. Morino
AU - S. Takayanagi-Nishisako
AU - N. Ohmagari
AU - W. Sugiura
AU - M. Kimura
PY - 2026
DA - 2026/08/28
PB - medRxiv
DO - 10.64898/2026.08.28.26360747
UR - https://www.medrxiv.org/content/10.64898/2026.08.28.26360747v1
AB - BackgroundThe COVID-19 pandemic substantially altered respiratory pathogen circulation worldwide. However, longitudinal analyses of changes in respiratory pathogen ecology across the pandemic and post-pandemic periods remain limited. MethodsWe analyzed 19,968 respiratory samples tested with the BioFire(R) FilmArray(R) Respiratory Panel at a hospital in Tokyo, Japan, between January 2020 and March 2026. We evaluated temporal changes in pathogen circulation, age-specific epidemiology, co-detection patterns, pairwise pathogen associations, and clinical parameters. ResultsAt least one respiratory pathogen was detected in 27.8% of tests. Respiratory pathogens resurged asynchronously following the relaxation of COVID-19-related public health measures. Influenza virus circulation remained markedly suppressed until late 2022 before re-emerging in successive large seasonal epidemics, whereas other pathogens, including RSV, human metapneumovirus, and Mycoplasma pneumoniae, exhibited distinct resurgence patterns. Pathogen distributions also varied by age. Human rhinovirus/enterovirus remained predominant among young children, whereas SARS-CoV-2 predominated among older adults. Co-detection occurred in 14.0% of positive specimens and was significantly more frequent in younger patients. Pairwise analysis identified both positive and negative pathogen associations; however, the patterns varied across age groups and study periods. ConclusionsRespiratory pathogen circulation changed substantially during the transition from the COVID-19 pandemic to the post-pandemic period, with pathogen-specific, age- and period-dependent patterns. Continued surveillance is warranted to determine how respiratory pathogen circulation will evolve and to inform infection control strategies in the post-pandemic era.
ER -