Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma

  1. Network for Genomic Surveillance in South Africa
  2. COMMIT-KZN Team
  3. Sandile Cele
  4. Inbal Gazy
  5. Laurelle Jackson
  6. Shi-Hsia Hwa
  7. Houriiyah Tegally
  8. Gila Lustig
  9. Jennifer Giandhari
  10. Sureshnee Pillay
  11. Eduan Wilkinson
  12. Yeshnee Naidoo
  13. Farina Karim
  14. Yashica Ganga
  15. Khadija Khan
  16. Mallory Bernstein
  17. Alejandro B. Balazs
  18. Bernadett I. Gosnell
  19. Willem Hanekom
  20. Mahomed-Yunus S. Moosa
  21. Richard J. Lessells
  22. Tulio de Oliveira
  23. Alex Sigal

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1038/s41586-021-03471-w
  2. ScreenIT

    SciScore for 10.1101/2021.01.26.21250224: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethical statement: Nasopharyngeal/oropharyngeal swab samples and plasma samples were obtained from six hospitalized adults with PCR-confirmed SARS-CoV-2 infection enrolled in a prospective cohort study approved by the Biomedical Research Ethics Committee (BREC) at the University of KwaZulu-Natal (reference BREC/00001275/2020).
    IACUC: Viral Outgrowth: All live virus work was performed in Biosafety level 3 containment using AHRI Institutional Biosafety Committee approved protocols for SARS-CoV-2.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    For staining of foci, a rabbit anti-Spike monoclonal antibody (mAb BS-R2B12, GenScript A02058) was used at 0.5µg/mL as the primary detection antibody.
    anti-Spike
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Cells: Vero E6 cells (ATCC CRL-1586, obtained from Cellonex) were propagated in complete DMEM with 10% fetal bovine serum (Hylone) containing 1% each of HEPES, sodium pyruvate, L-glutamine, and non-essential amino acids (Sigma-Aldrich).
    Vero E6
    suggested: None
    H1299 cells were propagated in complete RPMI with 10% fetal bovine serum containing 1% each of HEPES, sodium pyruvate, L-glutamine, and non-essential amino acids and and passaged every second day.
    H1299
    suggested: None
    H1299-E3 cell line for first passage SARS-CoV-2 outgrowth: The H1299-H2AZ clone with nuclear labelled YFP [30] was constructed to overexpress ACE2 as follows: VSVG-pseudotyped lentivirus containing the human ACE2 was generated by co-transfecting 293T cells with the pHAGE2-EF1alnt-ACE2-WT plasmid along with the lentiviral helper plasmids HDM-VSVG, HDM-Hgpm2, HDM-tat1b and pRC-CMV-Rev1b using TransIT-LT1 (Mirus) transfection reagent.
    H1299-E3
    suggested: None
    293T
    suggested: None
    ACE-2 transduced H1299-H2AZ cells were then subcloned at the single cell density in 96-well plates (Eppendorf) in conditioned media derived from confluent cells.
    H1299-H2AZ
    suggested: None
    H1299-ACE2-E3 cells were seeded at 1.5 ×105 cells/ml and incubated for 18-20 hours.
    H1299-ACE2-E3
    suggested: None
    Software and Algorithms
    SentencesResources
    Mutations were confirmed visually with bam files using Geneious software (Biomatters Ltd, Auckland, New Zealand).
    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 [29], phylogenetic tree inference in IQ-Tree20, tree dating and ancestral state construction and annotation (https://github.com/nextstrain/ncov).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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.

    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.

  3. Version published to 10.1101/2021.01.26.21250224v2 on medRxiv
  4. Version published to 10.1101/2021.01.26.21250224v1 on medRxiv