SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape

  1. Sandile Cele
  2. Farina Karim
  3. Gila Lustig
  4. James Emmanuel San
  5. Tandile Hermanus
  6. Houriiyah Tegally
  7. Jumari Snyman
  8. Thandeka Moyo-Gwete
  9. Eduan Wilkinson
  10. Mallory Bernstein
  11. Khadija Khan
  12. Shi-Hsia Hwa
  13. Sasha W. Tilles
  14. Lavanya Singh
  15. Jennifer Giandhari
  16. Ntombifuthi Mthabela
  17. Matilda Mazibuko
  18. Yashica Ganga
  19. Bernadett I. Gosnell
  20. Salim S. Abdool Karim
  21. Willem Hanekom
  22. Wesley C. Van Voorhis
  23. Thumbi Ndung’u
  24. Richard J. Lessells
  25. Penny L. Moore
  26. Mahomed-Yunus S. Moosa
  27. Tulio de Oliveira
  28. Alex Sigal

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Abstract

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  1. Version published to 10.1016/j.chom.2022.01.005
  2. Version published to 10.1101/2021.09.14.21263564v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.09.14.21263564: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethical statement: Nasopharyngeal and oropharyngeal swab samples and plasma samples were obtained from hospitalized adults with PCR-confirmed SARS-CoV-2 infection who were enrolled in a prospective cohort study approved by the Biomedical Research Ethics Committee at the University of KwaZulu–Natal (reference BREC/00001275/2020).
    Sex as a biological variablenot detected.
    RandomizationWe analysed sequences from the seven different time points (D0, D6, D20, D34, D71, D106 and D190) as well as a random sample of genotypes from South Africa (n=480) against the global reference dataset (n = 3,170) using a custom pipeline based on a local version of NextStrain (https://github.com/nextstrain/ncov).
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationAuthentication: Cell lines have not been authenticated.
    Contamination: The cell lines have been tested for mycoplasma contamination and are mycoplasma negative.

    Table 2: Resources

    Antibodies
    SentencesResources
    A02051 anti-spike monoclonal antibody was added.
    anti-spike
    suggested: None
    Secondary goat anti-rabbit horseradish peroxidase (Abcam ab205718) antibody was added at 1 μg/mL and incubated for 2 h at room temperature with shaking.
    anti-rabbit
    suggested: (Abcam Cat# ab205718, RRID:AB_2819160)
    Subsequently, goat anti-human IgG (1:5000)-horseradish peroxidase conjugated secondary antibodies (Jackson ImmunoResearch) were added a 100 µL/well and incubated at RT for 1h.
    anti-human IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    H1299 cells were passaged every second day.
    H1299
    suggested: NCI-DTP Cat# NCI-H1299, RRID:CVCL_0060)
    We used ACE2-expressing H1299-E3 cells for the initial isolation (P1 stock) followed by passaging in Vero E6 cells (P2 and P3 stocks, where P3 stock was used in experiments).
    H1299-E3
    suggested: None
    Then 1 mL was added to Vero E6 cells that had been seeded at 2 × 105 cells per mL 18–20 h earlier in a T25 flask (approximately 1:8 donor-to-target cell dilution ratio) for cell-to-cell infection.
    Vero E6
    suggested: None
    Pseudovirus neutralization assay: SARS-CoV-2 pseudotyped lentiviruses were prepared by co-transfecting the HEK 293T cell line with either the SARS-CoV-2 Beta spike (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V, 242-244 del) or the Delta spike (T19R, R158G L452R, T478K, D614G, P681R, D950N
    HEK 293T
    suggested: None
    Software and Algorithms
    SentencesResources
    Mutations were confirmed visually with BAM files using Geneious software (Biomatters).
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    The pipeline contains several Python scripts that manage the analysis workflow.
    Python
    suggested: (IPython, RRID:SCR_001658)
    It performs alignment of genotypes in MAFFT, phylogenetic tree inference in IQ-Tree20, tree dating and ancestral state construction and annotation.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    For microscopy images, automated image analysis was performed using a custom script in MATLAB v.
    MATLAB
    suggested: (MATLAB, RRID:SCR_001622)

    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

    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.

  4. Version published to 10.1101/2021.09.14.21263564v1 on medRxiv