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

Yuki Nagakubo,Toshiharu Tsutsui,Masao Omata,Yoshihiro Miyashita,Kazuhiro Hosaka,Yumiko Kakizaki,Makoto Maejima,Kenji Amemiya,Hitomi Sueki,Masahiro Shibusawa,Hitoshi Mochizuki,Yosuke Hirotsu,Miyoko Hayakawa,Etsuro Ito

doi:10.1371/journal.pone.0262874

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.

Highlights

On March 11, 2020, the World Health Organization declared a worldwide pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1]
Coronaviruses belong to the Coronaviridae family and the ones known to infect humans belong to two genera, α-coronaviruses (HCoV-229E, human coronaviruses (HCoVs)-NL63) and β-coronaviruses
All samples were subjected to multiplex polymerase chain reaction (PCR) testing (FilmArray respiratory panel (RP) v1.7 or v2.1) to identify the presence of respiratory pathogens [20]

Summary

Introduction

On March 11, 2020, the World Health Organization declared a worldwide pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1]. As of October 2021, more than 230 million people have been infected with this virus, and 4.8 million have died as a result [2]. To suppress the spread of the virus, infection prevention measures have been implemented in many countries. The “common cold” refers to mild upper respiratory illness characterized by symptoms such as nasal congestion and discharge, sneezing, sore throat, and cough [3]. Several types of viruses are associated with the common cold [3, 4]. Rhinoviruses are responsible for approximately 30%–50% of all colds, human coronaviruses (HCoVs) are responsible for approximately 10%–15%, and influenza viruses are responsible for approximately 5%–15%. Coronaviruses belong to the Coronaviridae family and the ones known to infect humans belong to two genera, α-coronaviruses (HCoV-229E, HCoV-NL63) and β-coronaviruses (linage A, HCoV-OC43, HCoV-HKU1; linage B, SARS-CoV-1, SARS-CoV-2, MERS-CoV)

Methods

Results

Conclusion