SARS‐CoV‐2 show no infectivity at later stages in a prolonged COVID‐19 patient despite positivity in RNA testing

  1. Xiu‐Feng Wan
  2. Cynthia Y. Tang
  3. Detlef Ritter
  4. Yang Wang
  5. Tao Li
  6. Karen Segovia
  7. Martina Kosikova
  8. Marc Johnson
  9. Hyung J. Kwon
  10. Hang Xie
  11. Richard D. Hammer
  12. Jane A. McElroy
  13. Aws Hamid
  14. Natalie D. Collins
  15. Jun Hang
  16. Simone Camp

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Abstract

Inpatient coronavirus disease 2019 (COVID‐19) cases present enormous costs to patients and health systems in the United States. Many hospitalized patients may continue testing COVID‐19 positive even after the resolution of symptoms. Thus, a pressing concern for clinicians is the safety of discharging these asymptomatic patients if they have any remaining infectivity. This case report explores the viral viability in a patient with persistent COVID‐19 over the course of a 2‐month hospitalization. Positive nasopharyngeal swab samples were collected and isolated in the laboratory and analyzed by quantitative reverse‐transcription polymerase chain reactions (qRT‐PCR), and serology was tested for neutralizing antibodies throughout the hospitalization period. The patient experienced waning symptoms by hospital day 40 and had no viable virus growth by hospital day 41, suggesting no risk of infectivity, despite positive RT‐PCR results which prolonged his hospital stay. Notably, this case showed infectivity for at least 24 days after disease onset, which is longer than the discontinuation of transmission‐based precautions recommended by the Center for Disease Control and Prevention. Thus, our findings suggest that the timeline for discontinuing transmission‐based precautions may need to be extended for patients with severe and prolonged COVID‐19 disease. Additional large‐scale studies are needed to draw definitive conclusions on the appropriate clinical management for these patients.

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  1. Version published to 10.1002/jmv.27001
  2. ScreenIT

    SciScore for 10.1101/2021.03.18.21253228: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics statement: This study was approved by the University of Missouri-Columbia Institutional Review Board (#2023844) and at the Institutional Biosafety Committee Biosafety Level 3 (#20-14).
    IACUC: Ethics statement: This study was approved by the University of Missouri-Columbia Institutional Review Board (#2023844) and at the Institutional Biosafety Committee Biosafety Level 3 (#20-14).
    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
    Tissue culture infectious dose (TCID50): Viral samples were serially diluted from 1:101 to at most, 1:1012 in Opti-Minimal Essential Medium Reduced-Serum Medium. 200µL of the diluted virus was placed in four wells of Vero E6 cells that were seeded in 96-well plates for each dilution for 1 day and incubated at 37°C in 5% CO2 for 3 days.
    Vero E6
    suggested: None
    Software and Algorithms
    SentencesResources
    The quality of paired-end reads obtained from MiSeq sequencing were analyzed by using Qiagen CLC Genomics Workbench 20.0.4 and Qiagen “Analysis of SARS-CoV-2 using MinION sequences” Protocol with a quality threshold of 0.05, and a minimal coverage of 10× was used in genetic variant analyses.
    MinION
    suggested: (MinION, RRID:SCR_017985)
    Sequence identities were calculated using MEGA v10.1.8 with the function of p-distance, the proportion (p) of nucleotide sites (http://www.megasoftware.net/mega.php).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Phylogenetic analyses and molecular characterization: Nucleotide sequences were aligned using MUSCLE v3.8.31, and the mutations were analyzed using BioEdit v7.2.5.
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    BioEdit
    suggested: (BioEdit, RRID:SCR_007361)
    The maximum-likelihood (ML) phylogeny tree was constructed using BEAST 2.5 with Yule Model, and Strict Clock.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    Phylogenetic trees were then visualized by Figtree v1.4.4.
    Figtree
    suggested: (FigTree, RRID:SCR_008515)

    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 primary limitation of this study is that the available data encompasses a single patient. Confounding factors include the multiple clinical treatments that the patient received. Bacterial pneumonia was treated with broad spectrum antibiotics from D3-40. Antifungals were given to treat oral candidiasis D45-52, and methylprednisolone (steroid) was administered from D41-57 for eosinophilic bronchiolitis. In summary, the patient was on steroid medication and had just completed antifungal therapy when they retested positive for SARS-CoV-2 between D54-56. Additionally, previous studies indicate T-cell immune responses, which were not analyzed in this study, might play roles in clinical outcomes. A strength of this study is the use of three serological assays to monitor antibody development. Intriguingly, only S1-based IgA titers clearly increased via ELISA during the recurrent infection period, consistent with Nab titers using live virus (Table 1). Although the pseudotyped NI assay detected Nabs, potential discrepancies from live virus-based NI assay, as in this study, indicate that caution is needed when interpreting pseudotyped NI data. In summary, this report follows the clinical and serological timeline of a patient with severe and persistent COVID-19. This patient demonstrated viable virus growth at least 24 days after symptom onset. These findings suggest that separate discontinuation of transmission-based precaution guidelines for patients with persistent symptoms and ex...

    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.

  3. Version published to 10.1101/2021.03.18.21253228 on medRxiv