De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report

  1. Shiv Gandhi
  2. Jonathan Klein
  3. Alexander J. Robertson
  4. Mario A. Peña-Hernández
  5. Michelle J. Lin
  6. Pavitra Roychoudhury
  7. Peiwen Lu
  8. John Fournier
  9. David Ferguson
  10. Shah A. K. Mohamed Bakhash
  11. M. Catherine Muenker
  12. Ariktha Srivathsan
  13. Elsio A. Wunder
  14. Nicholas Kerantzas
  15. Wenshuai Wang
  16. Brett Lindenbach
  17. Anna Pyle
  18. Craig B. Wilen
  19. Onyema Ogbuagu
  20. Alexander L. Greninger
  21. Akiko Iwasaki
  22. Wade L. Schulz
  23. Albert I. Ko

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Abstract

SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but have not been reported in patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient with acquired B-cell deficiency who developed an indolent, protracted course of SARS-CoV-2 infection. Remdesivir therapy alleviated symptoms and produced a transient virologic response, but her course was complicated by recrudescence of high-grade viral shedding. Whole genome sequencing identified a mutation, E802D, in the nsp12 RNA-dependent RNA polymerase, which was not present in pre-treatment specimens. In vitro experiments demonstrated that the mutation conferred a ~6-fold increase in remdesivir IC 50 but resulted in a fitness cost in the absence of remdesivir. Sustained clinical and virologic response was achieved after treatment with casirivimab-imdevimab. Although the fitness cost observed in vitro may limit the risk posed by E802D, this case illustrates the importance of monitoring for remdesivir resistance and the potential benefit of combinatorial therapies in immunocompromised patients with SARS-CoV-2 infection.

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  1. Version published to 10.1038/s41467-022-29104-y
  2. Version published to 10.1101/2021.11.08.21266069v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.11.08.21266069: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: This study was also approved by Yale Human Research Protection Program Institutional Review Boards (FWA00002571, protocol ID 2000027690, 2000029277).
    Consent: Informed consent was obtained from both the patient and healthcare workers
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationContamination: The cell line was obtained from the ATCC and has been tested negative for contamination with mycoplasma.

    Table 2: Resources

    Antibodies
    SentencesResources
    Flow cytometry: As described previously, antibody clones and vendors used for flow cytometry analysis were as follows: BB515 anti-hHLA-DR (G46-6) (1:400
    anti-hHLA-DR ( G46-6 )
    suggested: None
    Plates were washed three times with PBS-T (PBS with 0.1% Tween-20) and 50 μl of HRP anti-Human IgG Antibody (GenScript #A00166, 1:5,000) diluted in dilution solution added to each well.
    anti-Human IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Diluted NP samples were added on a monolayer of Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    15 μg of each mutant transcript was electroporated into BHK cells using the Electro Square Porator Device (BTX)
    BHK
    suggested: RRID:CVCL_HA32)
    Electroporated cells were seeded into a T75 flask containing 1:2 ratio of BHK-N:Vero-E6 cells.
    BHK-N:Vero-E6
    suggested: None
    Replication kinetics of icSARS-CoV-2 mutants: Isolates from initial stocks were expanded and used to infect Vero-E6 cells with 0.01 MOI of each E802D and E802A mutant virus to assess their replication kinetics.
    Vero-E6
    suggested: None
    Software and Algorithms
    SentencesResources
    This study was also approved by Yale Human Research Protection Program Institutional Review Boards (FWA00002571, protocol ID 2000027690, 2000029277).
    Yale Human Research Protection Program
    suggested: None
    Variants were examined longitudinally with a modified Python script adapted from LAVA (https://github.com/greninger-lab/lava).
    Python
    suggested: (IPython, RRID:SCR_001658)
    Data were analysed using FlowJo software version 10.6 software (Tree Star).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    Results from OddPub: Thank you for sharing your data.

    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: 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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  4. Version published to 10.1101/2021.11.08.21266069v1 on medRxiv