Coinfections with Respiratory Pathogens among COVID-19 Patients in Korea

  1. Kyoung Ho Roh
  2. Yu Kyung Kim
  3. Shin-Woo Kim
  4. Eun-Rim Kang
  5. Yong-Jin Yang
  6. Sun-Kyung Jung
  7. Sun-Hwa Lee
  8. Nackmoon Sung

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Abstract

The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper and lower respiratory specimens and coinfection with other respiratory pathogens in patients with coronavirus disease 2019 (COVID-19) was investigated. Study subjects (N = 342) were retrospectively enrolled after being confirmed as SARS-CoV-2 positive, and their nasopharyngeal swab (NPS), oropharyngeal swab (OPS), and sputum specimens were restored for SARS-CoV-2 retesting and respiratory pathogen detection. The majority of the subjects (96.5%, N = 330) were confirmed as SARS-CoV-2 positive using NPS/OPS specimens. Among the COVID-19 patients (N = 342), 7.9% (N = 27) and 0.9% (N = 3) were coinfected with respiratory viruses and Mycoplasma pneumoniae, respectively, yielding an 8.8% (N = 30) overall respiratory pathogen coinfection rate. Of the respiratory virus coinfection cases (N = 27), 92.6% (N = 25) were coinfected with a single respiratory virus and 7.4% (N = 2) with two viruses (metapneumovirus/adenovirus and rhinovirus/bocavirus). No triple coinfections of other respiratory viruses or bacteria with SARS-CoV-2 were detected. Respiratory viruses coinfected in the patients with COVID-19 were as follows: rhinovirus (N = 7, 2.1%), respiratory syncytial virus A and B (N = 6, 1.8%), non-SARS-CoV-2 coronaviruses (229E, NL63, and OC43, N = 5, 1.5%), metapneumovirus (N = 4, 1.2%), influenza A (N = 3, 0.9%), adenovirus (N = 3, 0.9%), and bocavirus (N = 1, 0.3%). In conclusion, the diagnostic value of utilizing NPS/OPS specimens is excellent, and, as the first report in Korea, coinfection with respiratory pathogens was detected at a rate of 8.8% in patients with COVID-19.

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  1. Version published to 10.1155/2021/6651045
  2. ScreenIT

    SciScore for 10.1101/2020.12.18.20248449: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementConsent: Ethics statement: We retrospectively analyzed the request forms and RT-PCR assay results of the study subjects, which were exempted from informed consent.
    IRB: This study was approved by the Institutional Review Boards of Seegene Medical Foundation (SMF-IRB-2020-003) and Kyungpook National University Hospital (
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analysis was conducted using GraphPad Prism software (Version 5.0; GraphPad Software, Inc., La Jolla, CA, USA) and GraphPad InStat software (Version 3.0).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad InStat
    suggested: (GraphPad, RRID:SCR_000306)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    The current study has a few limitations. The effect of coinfection on the treatment outcomes of COVID-19 patients enrolled in this study is unavailable. The study subjects in this study were retrospectively enrolled during the process of screening COVID-19 in the region of the first outbreak in Korea. Thus, the scope of this study was to investigate the coinfection rates of respiratory pathogens among patients with COVID-19, not hospitalized, but diagnosed as positive during the screening process for SARS-CoV-2. Additionally, the results of the study cannot represent the coinfection rates for the winter when respiratory pathogens such as influenza are dominant. The study subjects were only enrolled in February; therefore, investigating the coinfection rates with respiratory pathogens would be interesting during the whole winter season, especially from November to March in Korea. In summary, the upper respiratory tract specimen (NPS/UPS) provided excellent detection of SARS-CoV-2 without lower respiratory specimens (sputum) in the RT-PCR assay. However, detection of coinfections with respiratory pathogens in COVID-19 required both upper and lower respiratory specimens. Coinfection rates in patients with COVID-19 (N = 258) with respiratory pathogens were 9.7% (N = 25) with mostly virus (8.5%, N = 22) and an atypical bacterium, M. pneumoniae (1.2%, N = 3). The most common respiratory virus detected as a coinfecting agent was HRV, followed by non-SARS-CoV-2 coronaviruses, HRV, MP...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

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  3. Version published to 10.1101/2020.12.18.20248449v1 on medRxiv