Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID-19)

  1. Jeroen J. A. van Kampen
  2. David A. M. C. van de Vijver
  3. Pieter L. A. Fraaij
  4. Bart L. Haagmans
  5. Mart M. Lamers
  6. Nisreen Okba
  7. Johannes P. C. van den Akker
  8. Henrik Endeman
  9. Diederik A. M. P. J. Gommers
  10. Jan J. Cornelissen
  11. Rogier A. S. Hoek
  12. Menno M. van der Eerden
  13. Dennis A. Hesselink
  14. Herold J. Metselaar
  15. Annelies Verbon
  16. Jurriaan E. M. de Steenwinkel
  17. Georgina I. Aron
  18. Eric C. M. van Gorp
  19. Sander van Boheemen
  20. Jolanda C. Voermans
  21. Charles A. B. Boucher
  22. Richard Molenkamp
  23. Marion P. G. Koopmans
  24. Corine Geurtsvankessel
  25. Annemiek A. van der Eijk

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Abstract

Key questions in COVID-19 are the duration and determinants of infectious virus shedding. Here, we report that infectious virus shedding is detected by virus cultures in 23 of the 129 patients (17.8%) hospitalized with COVID-19. The median duration of shedding infectious virus is 8 days post onset of symptoms (IQR 5–11) and drops below 5% after 15.2 days post onset of symptoms (95% confidence interval (CI) 13.4–17.2). Multivariate analyses identify viral loads above 7 log 10 RNA copies/mL (odds ratio [OR] of 14.7 (CI 3.57-58.1; p  < 0.001) as independently associated with isolation of infectious SARS-CoV-2 from the respiratory tract. A serum neutralizing antibody titre of at least 1:20 (OR of 0.01 (CI 0.003-0.08; p  < 0.001) is independently associated with non-infectious SARS-CoV-2. We conclude that quantitative viral RNA load assays and serological assays could be used in test-based strategies to discontinue or de-escalate infection prevention and control precautions.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.08.20125310: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Our institutional review board approved the use of these data and samples (METC-2015-306) and written informed consent was waived.
    Consent: Our institutional review board approved the use of these data and samples (METC-2015-306) and written informed consent was waived.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    5 Vero cells, clone 118, were used for isolation of infectious SARS-CoV-2 from respiratory tract samples.
    Vero
    suggested: None
    Software and Algorithms
    SentencesResources
    All variables having a p-value <0.1 in univariate analysis were submitted into a multivariate general estimating equation to account for repeated measurements obtained from the same patient during hospitalization.21 For this analysis we used the geepack package and R version 4.0.0.21 Probit analyses were performed with MedCalc version 19.2.3 (MedCalc Software Ltd).
    MedCalc
    suggested: (MedCalc, RRID:SCR_015044)

    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:
    Our study has some limitations. Firstly, virological data was obtained from diagnostic samples only and samples were not prospectively collected at predefined timepoints. However, as many aspects of COVID-19 were still unclear, a sampling-rich diagnostic approach was applied in our institution with regular virological monitoring of confirmed COVID-19 patients. This approach resulted in a large high quality dataset from a considerable number of patients including patients with a immunocompromised status. The strikingly similar viral RNA load cut-off for a 5% probability of a positive virus culture found by us and by Wölfel and colleagues underpins the validity of the results.5 Secondly, we used in vitro cell cultures as a surrogate marker for infectious virus shedding. The success of SARS-CoV-2 isolation is dependent on which cell lines is used.29 Vero cells are currently regarded as the gold standard to detect infectious SAR-CoV-2, but the true limit of detection is unknown. Notwithstanding the above, experimental evidence from a COVID-19 hamster model showed that transmission of SARS-CoV-2 correlated well with detection of infectious SARS-CoV-2 from respiratory tract samples using in vitro Vero cell cultures while detection of viral RNA did not.13 More data from experimental models, and epidemiological and modeling studies on transmission which take viral RNA load and antibody response into account are needed for further validation of this approach. It should be noted that, ...

    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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1038/s41467-020-20568-4
  3. ScreenIT

    SciScore for 10.1101/2020.06.08.20125310: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementOur institutional review board approved the use of these data and samples ( METC-2015-306 ) and written informed consent was waived.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    5 Vero cells , clone 118 , were used for isolation of infectious SARS-CoV-2 from respiratory tract samples.
    Vero
    suggested: None
    Software and Algorithms
    SentencesResources
    Research in context Evidence before this study We searched PubMed, bioRxiv, and medRxiv for articles that reported on shedding of infectious virus in COVID-19 patients using the search terms (“coronavirus” OR “SARS” OR “SARS-CoV-2” OR “COVID-19”
    PubMed
    suggested: (PubMed, SCR_004846)
          <div style="margin-bottom:8px">
        <div><b>bioRxiv</b></div>
        <div>suggested: (bioRxiv, <a href="https://scicrunch.org/resources/Any/search?q=SCR_003933">SCR_003933</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All variables having a p-value <0.1 in univariate analysis were submitted into a multivariate general estimating equation to account for repeated measurements obtained from the same patient during hospitalization.21 For this analysis we used the geepack package and R version 4.0.0.21 Probit analyses were performed with MedCalc version 19.2.3 ( MedCalc Software Ltd) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>MedCalc</b></div>
        <div>suggested: (MedCalc, <a href="https://scicrunch.org/resources/Any/search?q=SCR_015044">SCR_015044</a>)</div>
      </div>
    </td></tr></table>

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

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.06.08.20125310v1 on medRxiv