Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host

  1. Sissy Therese Sonnleitner
  2. Martina Prelog
  3. Stefanie Sonnleitner
  4. Eva Hinterbichler
  5. Hannah Halbfurter
  6. Dominik B. C. Kopecky
  7. Giovanni Almanzar
  8. Stephan Koblmüller
  9. Christian Sturmbauer
  10. Leonard Feist
  11. Ralf Horres
  12. Wilfried Posch
  13. Gernot Walder

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Abstract

Different scenarios explaining the emergence of novel variants of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported, including their evolution in scarcely monitored populations, in animals as alternative hosts, or in immunocompromised individuals. Here we report SARS-CoV-2 immune escape mutations over a period of seven months in an immunocompromised patient with prolonged viral shedding. Signs of infection, viral shedding and mutation events are periodically analyzed using RT-PCR and next-generation sequencing based on naso-pharyngeal swabs, with the results complemented by immunological diagnostics to determine humoral and T cell immune responses. Throughout the infection course, 17 non-synonymous intra-host mutations are noted, with 15 (88.2%) having been previously described as prominent immune escape mutations (S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y) in VOCs. The high frequency of these non-synonymous mutations is consistent with multiple events of convergent evolution. Thus, our results suggest that specific mutations in the SARS-CoV-2 genome may represent positions with a fitness advantage, and may serve as targets in future vaccine and therapeutics development for COVID-19.

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  1. Version published to 10.1038/s41467-022-30163-4
  2. ScreenIT

    SciScore for 10.1101/2022.03.04.22271540: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: The patient gave full written consent for the case to be attended and published.
    Sex as a biological variablenot detected.
    RandomizationThe clade is embedded in a random composition of complete Austrian strains and variants of concern found in Europe and described and uploaded to GISAID platform in the same study period from January to May 2021 (Figure 6).
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    The analysis via immunoblot disclosed Spike 1 (S1) and the dedicated receptor-binding-domain (RBD) as the main epitopes of the IgG antibodies in the patient’s sera, whereas no IgG antibodies could be detected against the region Spike 2 (S2) or the nucleocapsid.
    IgG
    suggested: None
    Microarray immunoblots: The ViraChip® assay detects temporal antibody profiles of different immunoglobulin classes against S1, S2, and nucleocapsid (N) as well as against N of the four nonSARS human coronaviruses in a commercial, miniaturized 96 wells protein microarray.
    S1
    suggested: None
    S2
    suggested: None
    Serum IgG antibodies against SARS-CoV-2 were determined by Serion agile SARS-CoV-2 ELISA with a sensitivity of 96.2% and a specificity of 100% according to manufacturer’s instructions (Virion/Serion, Wuerzburg, Germany)
    SARS-CoV-2
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Isolation: Isolation trials were performed from swab samples taken on day 73, 93, 99, 104, 109, 117, 127, 133 and 182 on VeroB4-cells and were successful on day 73, 93, 109 and 127.
    VeroB4-cells
    suggested: None
    Isolation was performed on VeroB4 cells as described elsewhere (22).
    VeroB4
    suggested: CCLV Cat# CCLV-RIE 1146, RRID:CVCL_1912)
    Software and Algorithms
    SentencesResources
    Ion Torrent Suite software (v 5.12.2) of the Ion S5 sequencer was used to map the generated reads to a SARS-CoV-2 reference genome (Wuhan-Hu-1; GenBank accession numbers NC_045512 and MN908947.3), using TMAP software included in the Torrent Suite.
    TMAP
    suggested: (TMAP, RRID:SCR_000687)
    Variant Caller (v.5.12.04) for mutation calls both with “Generic □S5/S5XL (510/520/530) □Somatic □Low Stringency” and “Generic□S5/S5XL (510/520/530) □Germ Line□Low Stringency” default parameters and COVID19AnnotateSnpEff (v.1.0.), a plugin specifically developed for SARS=CoV=2 that can predict the effect of a base substitution.
    COVID19AnnotateSnpEff
    suggested: None
    FASTA files containing the raw reads were inspected for quality criteria (mapped, targeted, filtered reads, mean depth and uniformity) using Thermofisher Software.
    Thermofisher Software
    suggested: None
    All reads not mapping to human were trimmed for adapters und quality by using Cutadapt 3.2(30).
    Cutadapt
    suggested: (cutadapt, RRID:SCR_011841)
    Graphics were created using pandas 1.2 for Python 3.
    Python
    suggested: (IPython, RRID:SCR_001658)

    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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  3. Version published to 10.1101/2022.03.04.22271540 on medRxiv