Chronic SARS-CoV-2 infection and viral evolution in a hypogammaglobulinaemic individual

  1. Maia Kavanagh Williamson
  2. Fergus Hamilton
  3. Stephanie Hutchings
  4. Hannah M. Pymont
  5. Mark Hackett
  6. David Arnold
  7. Nick A Maskell
  8. Alasdair MacGowan
  9. Mahableshwar Albur
  10. Megan Jenkins
  11. Izak Heys
  12. Francesca Knapper
  13. Mustafa Elsayed
  14. Rachel Milligan
  15. The COVID-19 Genomics UK (COG-UK) Consortium
  16. Peter Muir
  17. Barry Vipond
  18. David A Matthews
  19. Ed Moran
  20. Andrew D. Davidson

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Abstract

There is widespread interest in the capacity for SARS-CoV-2 evolution in the face of selective pressures from host immunity, either naturally acquired post-exposure or from vaccine acquired immunity. Allied to this is the potential for long perm persistent infections within immune compromised individuals to allow a broader range of viral evolution in the face of sub-optimal immune driven selective pressure. Here we report on an immunocompromised individual who is hypogammaglobulinaemic and was persistently infected with SARS-CoV-2 for over 290 days, the longest persistent infection recorded in the literature to date. During this time, nine samples of viral nucleic acid were obtained and analysed by next-generation sequencing. Initially only a single mutation (L179I) was detected in the spike protein relative to the prototypic SARS-CoV-2 Wuhan-Hu-1 isolate, with no further changes identified at day 58. However, by day 155 the spike protein had acquired a further four amino acid changes, namely S255F, S477N, H655Y and D1620A and a two amino acid deletion (ΔH69/ΔV70). Infectious virus was cultured from a nasopharyngeal sample taken on day 155 and next-generation sequencing confirmed that the mutations in the virus mirrored those identified by sequencing of the corresponding swab sample. The isolated virus was susceptible to remdesivir in vitro , however a 17-day course of remdesivir started on day 213 had no effect on the viral RT-PCR cycle threshold (C t ) value. On day 265 the patient was treated with the combination of casirivimab and imdevimab. The patient experienced progressive resolution of all symptoms over the next 8 weeks and by day 311 the virus was no longer detectable by RT-PCR. The ΔH69/ΔV70 deletion in the N-terminus of the spike protein which arose in our patient is also present in the B.1.1.7 variant of concern and has been associated with viral escape mutagenesis after treatment of another immunocompromised patient with convalescent plasma. Our data confirms the significance of this deletion in immunocompromised patients but illustrates it can arise independently of passive antibody transfer, suggesting the deletion may be an enabling mutation that compensates for distant changes in the spike protein that arise under selective pressure.

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  1. ScreenIT

    SciScore for 10.1101/2021.05.31.21257591: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Cell culture: African green monkey kidney (VeroE6, ATCC® CRL 1586™) cells constitutively expressing TMPRSS2 (VeroE6/TMPRSS2 (11) obtained from NIBSC, UK) and human Caco-2 cells expressing ACE2 (Caco-2-ACE2; a kind gift from Dr Yohei Yamauchi, University of Bristol) were cultured in Dulbecco’s Minimal Essential Media with GlutaMAX (DMEM, Gibco™, ThermoFisher) containing 10% foetal bovine serum (FBS, Gibco) and 0.1mM non-essential amino acids (NEAA, Sigma Aldrich).
    VeroE6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Caco-2
    suggested: None
    The sample was filtered through a 0.2 µm filter and added to VeroE6/TMPRSS2 cells cultured in Eagle’s Minimum Essential Media with GlutaMAX (MEM, Gibco™, ThermoFisher) containing 2% FBS, 0.1mM NEAA, penicillin (100 units/ml) and streptomycin (100 μg/ml).
    VeroE6/TMPRSS2
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Software and Algorithms
    SentencesResources
    Data were plotted using GraphPad Prism v8.4.3.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Sequencing at COG-UK sites was performed using a combination of Oxford Nanopore or Illumina platforms.
    Oxford Nanopore
    suggested: (Oxford Nanopore Technologies, RRID:SCR_003756)
    Library preparation and sequencing was performed for the majority of samples using the MinION platform (Oxford Nanopore, UK) with the nCoV-2019 sequencing protocol v3 (LoCost) (16).
    MinION
    suggested: (MinION, RRID:SCR_017985)

    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: 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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  2. Version published to 10.1101/2021.05.31.21257591v1 on medRxiv