1. Microbiology and Infectious Disease
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Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation

  1. Mart M Lamers
  2. Anna Z Mykytyn
  3. Tim I Breugem
  4. Yiquan Wang
  5. Douglas C Wu
  6. Samra Riesebosch
  7. Petra B van den Doel
  8. Debby Schipper
  9. Theo Bestebroer
  10. Nicholas C Wu
  11. Bart L Haagmans  Is a corresponding author
  1. Erasmus MC, Netherlands
  2. University of Illinois at Urbana-Champaign, United States
  3. Invitae Corporation, United States
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Cite this article as: eLife 2021;10:e66815 doi: 10.7554/eLife.66815
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Abstract

Virus propagation methods generally use transformed cell lines to grow viruses from clinical specimens, which may force viruses to rapidly adapt to cell culture conditions, a process facilitated by high viral mutation rates. Upon propagation in VeroE6 cells, SARS-CoV-2 may mutate or delete the multibasic cleavage site (MBCS) in the spike protein. Previously, we showed that the MBCS facilitates serine protease-mediated entry into human airway cells (Mykytyn et al., 2021). Here, we report that propagating SARS-CoV-2 on the human airway cell line Calu-3 - that expresses serine proteases - prevents cell culture adaptations in the MBCS and directly adjacent to the MBCS (S686G). Similar results were obtained using a human airway organoid-based culture system for SARS-CoV-2 propagation. Thus, in-depth knowledge on the biology of a virus can be used to establish methods to prevent cell culture adaptation.

Data availability

All scripts used for data processing are deposited in GitHub: https://github.com/wchnicholas/SARS_CoV2_mutation. Raw sequencing data are available at the NIH Short Read Archive under accession number: BioProject PRJNA694097.

The following data sets were generated

Article and author information

Author details

  1. Mart M Lamers

    Viroscience, Erasmus MC, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1431-4022
  2. Anna Z Mykytyn

    Viroscience, Erasmus MC, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7188-6871
  3. Tim I Breugem

    Viroscience, Erasmus MC, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5558-7043
  4. Yiquan Wang

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1954-9808
  5. Douglas C Wu

    Invitae Corporation, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6179-3110
  6. Samra Riesebosch

    Viroscience Department, Erasmus MC, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  7. Petra B van den Doel

    Viroscience, Erasmus MC, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  8. Debby Schipper

    Viroscience, Erasmus MC, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  9. Theo Bestebroer

    Viroscience Department, Erasmus MC, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  10. Nicholas C Wu

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Bart L Haagmans

    Viroscience Department, Erasmus MC, Rotterdam, Netherlands
    For correspondence
    b.haagmans@erasmusmc.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6221-2015

Funding

Netherlands Organization for Health Research and Development (10150062010008)

  • Bart L Haagmans

PPP allowance (LSHM19136)

  • Bart L Haagmans

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Mark Marsh, University College London, United Kingdom

Publication history

  1. Received: January 22, 2021
  2. Accepted: April 8, 2021
  3. Accepted Manuscript published: April 9, 2021 (version 1)

Copyright

© 2021, Lamers et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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