Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo

  1. Hangping Yao
  2. Xiangyun Lu
  3. Qiong Chen
  4. Kaijin Xu
  5. Yu Chen
  6. Minghui Cheng
  7. Keda Chen
  8. Linfang Cheng
  9. Tianhao Weng
  10. Danrong Shi
  11. Fumin Liu
  12. Zhigang Wu
  13. Mingjie Xie
  14. Haibo Wu
  15. Changzhong Jin
  16. Min Zheng
  17. Nanping Wu
  18. Chao Jiang
  19. Lanjuan Li

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Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally with more than 33 million patients diagnosed, taking more than a million lives. Abundant mutations were observed but the functional consequences of these mutations are largely unknown. We report the mutation spectrum, replication dynamics, and infectivity of 11 patient-derived viral isolates in diverse cell lines, including the human lung cancer cell line Calu-3. We observed 46 mutations, including 9 different mutations in the spike gene. Importantly, these viral isolates show significant and consistent variations in replication dynamics and infectivity in tested cell lines, up to a 1500-fold difference in viral titers at 24 h after infecting Calu-3 cells. Moreover, we show that the variations in viral titers among viral isolates are positively correlated with blood clotting function but inversely correlated with the amount of red blood cell and hemoglobin in patients. Therefore, we provide direct evidence that naturally occurring mutations in SARS-CoV-2 can substantially change its replication dynamics and infectivity in diverse human cell lines, with clinical implications in vivo.

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  1. Version published to 10.1038/s41421-020-00226-1
  2. ScreenIT

    SciScore for 10.1101/2020.04.14.20060160: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Sample collection, Viral isolation, cell infection, and electron microscopy: All samples, sources including sputum, nasopharyngeal swab, and stool, were collected from patients with COVID-19 with consent from all patients.
    IRB: The study was approved by the Clinical Research Ethics Committee of The First Affiliated Hospital, School of Medicine, Zhejiang University (Approval notice 2020-29) for emerging infectious diseases.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    The cells were again washed three times in ice-cold PBS, and then stained with the Alexa Fluor488®-conjugated Goat Anti-rabbit IgG secondary antibody (Abcam, Cat No. ab150077) for 1 hour at room temperature in the dark.
    Anti-rabbit IgG
    suggested: (Abcam Cat# ab150077, RRID:AB_2630356)
    Experimental Models: Cell Lines
    SentencesResources
    Before infecting Vero-E6 cells, all collected supernatant was filtered using a 0.45 µm filter to remove cell debris etc.
    Vero-E6
    suggested: None

    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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 12. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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 10.1101/2020.04.14.20060160 on medRxiv