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. 2024 Dec;43(12):2269-2276.
doi: 10.1007/s10096-024-04942-4. Epub 2024 Sep 19.

Detection of community-acquired respiratory viruses during COVID-19 pandemic in subtropical region in Japan

Wakaki Kami  1 , Takeshi Kinjo  2 , Hiroe Hashioka  1 , Wakako Arakaki  1 , Ami Takahashi  3 , Shohei Yogi  3   4 , Kohei Uechi  3 , Shiro Maeda  3 , Kazuko Yamamoto  1 , Jiro Fujita  1
Affiliations

Detection of community-acquired respiratory viruses during COVID-19 pandemic in subtropical region in Japan

Wakaki Kami et al. Eur J Clin Microbiol Infect Dis. 2024 Dec.

Abstract

Purpose: Coronavirus disease 2019 (COVID-19) pandemic changed the dynamics of other community-acquired respiratory viruses (CARVs), however, information regarding the frequency of CARV detection during COVID-19 pandemic in subtropical regions is limited. Additionally, studies comparing the diagnostic accuracy between multiplex and monoplex PCR for the diagnosis of COVID-19 are scarce.

Methods: We evaluated samples collected from patients suspected of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Okinawa, a subtropical climate in Japan, from March 2020 to March 2021. For SARS-CoV-2, results obtained from monoplex (NIID method) and multiplex (Allplex™ SARS-CoV-2 Assay) PCR were compared.

Results: In total, 744 samples were collected and 238 viruses were detected in 205 specimens, of which 22 showed viral co-infection. Viral co-infection was more common in patients aged 10 and under than in older patients (p = 0.0054). For CARV, 142 viruses were detected in 127 specimens (17.1%), and human rhinovirus (HRV) was most common. Overall concordance rate for two SARS-CoV-2 assays was 94.1%; 7 and 37 specimens were detected only by NIID and Allplex™ SARS-CoV-2 Assay, respectively. The median cycling threshold values of the 44 samples that were only positive for either the NIID or Allplex™ SARS-CoV-2 Assay were 37.91 for E gene, 38.13 for RdRp/S gene, 38.21 for N gene and 39.16 for N2 gene.

Conclusion: HRV was continuously detected during COVID-19 pandemic in the subtropical region and viral co-infection was more common in younger patients. For the diagnosis of COVID-19, multiplex PCR was more reliable, especially in samples with low viral load.

Keywords: COVID-19; Co-infection; Community acquired respiratory viruses; Multiplex PCR; SARS-CoV-2.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: This study was approved by the Institutional Review Board of the Ryukyu University (approved No.1621). The need for informed consent from each patient for inclusion was waived because this study was retrospective in approach, however patients were given the opportunity for opt-out via websites of research cites. Consent for publication: Not applicable. Competing Interests: The authors declare no competing interests.

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