Non-pharmaceutical interventions during the COVID-19 epidemic changed detection rates of other circulating respiratory pathogens in Japan

PLoS One. 2022 Jan 21;17(1):e0262874. doi: 10.1371/journal.pone.0262874. eCollection 2022.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has circulated worldwide and causes coronavirus disease 2019 (COVID-19). At the onset of the COVID-19 pandemic, infection control measures were taken, such as hand washing, mask wearing, and behavioral restrictions. However, it is not fully clear how the effects of these non-pharmaceutical interventions changed the prevalence of other pathogens associated with respiratory infections. In this study, we collected 3,508 nasopharyngeal swab samples from 3,249 patients who visited the Yamanashi Central Hospital in Japan from March 1, 2020 to February 28, 2021. We performed multiplex polymerase chain reaction (PCR) using the FilmArray Respiratory Panel and singleplex quantitative reverse transcription PCR targeting SARS-CoV-2 to detect respiratory disease-associated pathogens. At least one pathogen was detected in 246 (7.0%) of the 3,508 samples. Eleven types of pathogens were detected in the samples collected from March-May 2020, during which non-pharmaceutical interventions were not well implemented. In contrast, after non-pharmaceutical interventions were thoroughly implemented, only five types of pathogens were detected, and the majority were SARS-CoV-2, adenoviruses, or human rhinoviruses / enteroviruses. The 0-9 year age group had a higher prevalence of infection with adenoviruses and human rhinoviruses / enteroviruses compared with those 10 years and older, while those 10 years and older had a higher prevalence of infection with SARS-CoV-2 and other pathogens. These results indicated that non-pharmaceutical interventions likely reduced the diversity of circulating pathogens. Moreover, differences in the prevalence of pathogens were observed among the different age groups.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenoviruses, Human / classification
  • Adenoviruses, Human / genetics*
  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • COVID-19 / diagnosis
  • COVID-19 / epidemiology*
  • COVID-19 / prevention & control
  • COVID-19 / virology
  • Child
  • Child, Preschool
  • Enterovirus / classification
  • Enterovirus / genetics*
  • Female
  • Hand Disinfection / methods
  • Humans
  • Infant
  • Infant, Newborn
  • Japan / epidemiology
  • Male
  • Masks / supply & distribution
  • Middle Aged
  • Multiplex Polymerase Chain Reaction
  • Nasopharynx / virology
  • Prevalence
  • Quarantine / organization & administration
  • Respiratory Tract Infections / diagnosis
  • Respiratory Tract Infections / epidemiology*
  • Respiratory Tract Infections / prevention & control
  • Respiratory Tract Infections / virology
  • Rhinovirus / classification
  • Rhinovirus / genetics*
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / pathogenicity

Grants and funding

This study was supported by a Grant-in-Aid for the Genome Research Project from Yamanashi Prefecture (to Y.H. and M.O.), Grant-in-Aid for Early-Career Scientists 18K16292 (to Y.H.) and Grant-in-Aid for Scientific Research (B) 20H03668 (to Y.H.) from the Japan Society for the Promotion of Science (JSPS) KAKENHI, a Research Grant for Young Scholars (to Y.H.) from Satoshi Omura Foundation, the YASUDA Medical Foundation (to Y.H.), the Uehara Memorial Foundation (to Y.H.), and Medical Research Grants from the Takeda Science Foundation (to Y.H.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.