Epidemiology of respiratory tract infections using multiplex PCR in a Japanese acute care hospital during the COVID19 pandemic

Daisuke Kitagawa; Taito Kitano; Madoka Furumori; Soma Suzuki; Yui Shintani; Yuki Suzuki; Akiyo Nakano; Ryuichi Nakano; Atsuko Nishiyama; Sayaka Yoshida; Hisakazu Yano; Koichi Maeda; Fumihiko Nakamura

doi:10.1016/j.heliyon.2023.e14424

Epidemiology of respiratory tract infections using multiplex PCR in a Japanese acute care hospital during the COVID19 pandemic

Heliyon. 2023 Mar 11;9(3):e14424. doi: 10.1016/j.heliyon.2023.e14424. eCollection 2023 Mar.

Authors

Affiliations

¹ Department of Laboratory Medicine, Nara Prefecture General Medical Center, Japan.
² Department of Microbiology and Infectious Diseases, Nara Medical University, Japan.
³ Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
⁴ Department of Pediatrics, Nara Prefecture General Medical Center, Japan.
⁵ Department of Infectious Diseases, Nara Prefecture General Medical Center, Japan.

Abstract

Introduction: We aimed to investigate the epidemiology of respiratory infections by season and age during the COVID-19 pandemic in a Japanese acute care hospital using multiplex PCR testing.

Methods: We detected 21 pathogens in specimens from outpatients with respiratory symptoms at the Nara Prefecture General Medical Center using the multiplex PCR-based FilmArray Respiratory Panel 2.1 (bioMérieux).

Results: Of the 3177 cases, 1215 (38.2%) were infected with at least one causative virus, and 1641 viruses were detected. The most common viruses detected were human rhinovirus/enterovirus (n = 655) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (n = 264). Additionally, 321 (10.1%) of these cases were infected with two or more overlapping viruses. There were 23 cases of co-infection with SARS-CoV-2 and other viruses. In the winter months from December 2020 to March 2021, the number of detected viruses was relatively low, followed by the surge of human rhinovirus/enterovirus, respiratory syncytial virus (RSV), and parainfluenza type 3 in the spring and summer of 2021. While the number of human rhinovirus/entero-virus remained relatively high after the 2021 summer, the number of other viruses detected since September 2021 was low. After December 2021, the number of SARS-CoV-2 increased rapidly.

Conclusions: Continuous monitoring of the epidemiology of respiratory infection is important to understand the prolonged impact of the COVID-19 pandemic.

Keywords: COVID19; Epidemiology; FilmArray respiratory panel 2.1; Multiplex PCR; Respiratory infection virus; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).