Respiratory Virus Infections during the COVID-19 Pandemic Revealed by Multiplex PCR Testing in Japan

Abstract

Under the strict quarantine policy imposed to combat the COVID-19 (coronavirus disease 2019) pandemic in Japan, the prevalence of respiratory infections by viruses other than SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has been largely unknown. However, such information on viral circulation is important in order to develop better management policies that are based on scientific data. Here, we retrospectively investigated respiratory virus infections in individuals who visited a community hospital with respiratory symptoms between June of 2020 and September of 2021 with the use of the BioFire FilmArray Respiratory Panel 2.1. Virus was detected in 65 out of a total of 328 subjects, with SARS-CoV-2 (67.7%), rhino/enterovirus (18.5%), and parainfluenza virus 3 (7.7%) accounting for most of the infections. No influenza virus or respiratory syncytial virus (RSV) infections were detected. The monthly cases of rhino/enterovirus infection were highest from winter to spring, with this temporal pattern differing from that of SARS-CoV-2. SARS-CoV-2 was detected more frequently (P < 0.001) in subjects with cough (31/104 cases, 29.8%) than in those without cough (13/224 cases, 5.8%), suggesting that cough might contribute to the prediction of COVID-19. Our findings also suggest that testing for rhino/enterovirus and parainfluenza virus 3, in addition to SARS-CoV-2, may be important for the rigorous diagnosis of respiratory virus infections. IMPORTANCE Influenza virus, RSV, adenovirus, and rhino/enterovirus were the major respiratory viruses before COVID-19 pandemic. Circulating respiratory viruses may have been affected by our strong quarantine policy during the COVID-19 pandemic. We checked the circulating respiratory viruses from our outpatients by using a multiplex PCR kit that had recently been released. SARS-CoV-2 was the most frequently detected virus, and it was followed by rhino/enterovirus and parainfluenza virus 3. No influenza virus or RSV infections were detected during our study period, suggesting that influenza virus and RSV became almost extinct. COVID-19 cases frequently experienced cough, and this frequency was statistically significantly higher than that observed in the cases without SARS-CoV-2 detection. The cough can be an indicator of COVID-19.

Keywords: COVID-19; FilmArray; SARS-CoV-2; coronavirus; multiplex PCR; respiratory virus.

FIG 1

Overview of PCR test results. (A) A total of 328 subjects were tested for respiratory virus pathogens via multiplex PCR analysis, yielding 65 (19.8%) positive results. (B) Among the 65 positive cases, SARS-CoV-2 was responsible for most of the infections, followed by rhino/enterovirus, coronaviruses other than SARS-CoV-2, and parainfluenza virus 3 (PIV3).

FIG 2

Monthly respiratory viral pathogen detection during the study period. The monthly totals of all of the PCR tests and the tests that were positive for SARS-CoV-2 or rhino/enterovirus during the study period are shown. The periods corresponding to the second through fifth national waves of SARS-CoV-2 infections that were caused by the wild-type, alpha, and delta strains are also indicated.

FIG 3

Viral test positivity, according to subject age. The overall PCR positivity rate for each age group was determined. *, P < 0.0125; NS, not significant (chi-square test with Bonferroni’s correction).