Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, Beta, Delta, and Omicron variants

  1. Arinjay Banerjee
  2. Jocelyne Lew
  3. Andrea Kroeker
  4. Kaushal Baid
  5. Patryk Aftanas
  6. Kuganya Nirmalarajah
  7. Finlay Maguire
  8. Robert Kozak
  9. Ryan McDonald
  10. Amanda Lang
  11. Volker Gerdts
  12. Sharon E. Straus
  13. Lois Gilbert
  14. Angel Xinliu Li
  15. Mohammad Mozafarihashjin
  16. Sharon Walmsley
  17. Anne-Claude Gingras
  18. Jeffrey L. Wrana
  19. Tony Mazzulli
  20. Karen Colwill
  21. Allison J. McGeer
  22. Samira Mubareka
  23. Darryl Falzarano

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Abstract

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  1. Version published to 10.1016/j.medj.2022.04.002
  2. ScreenIT

    SciScore for 10.1101/2022.01.13.475409: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Use of clinical specimen for virus isolation and use of human serum samples for micro-neutralization assays were approved by the University of Saskatchewan’s Biomedical Research Ethics Board (REB# 2591)
    Consent: Cohort participants provided informed consent for sharing of serum, and studies were approved by the Sunnybrook Research Institute (REB# 149-1994) and/or the Mount Sinai Hospital (REB# 02-0118-U, 20-0339-E, and 21-0069-E) Research Ethics Board 13.
    Sex as a biological variablenot detected.
    RandomizationContexual sequences were incorporated into the phylogenetic analysis by using Nexstrain’s ingested GISAID metadata and pandas to randomly sample a representative subset of sequences (jointly deposited in NCBI and GISAID) that belonged to lineages observed in Canada (see also Supplemental Tables S1 and S2 for metadata).
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    For samples from each cohort, samples were selected to have a representative range of anti-spike trimer and anti-RBD antibodies as measured by enzyme-linked immunosorbent assay 14.
    anti-RBD
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    EXPERIMENTAL MODEL: Cells and viruses: Vero’76 cells (CRL-1587, ATCC) were used to isolate and/or propagate all virus isolates using a previously published protocol 8.
    Vero’76
    suggested: None
    Software and Algorithms
    SentencesResources
    Full sequences of the viral isolates have been deposited to NCBI BioProject PRJNA794206.
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)
    Paired-end (2×150 bp) sequencing was performed on a MiniSeq with a 300–cycle reagent kit (Illumina, USA) with a negative control library with no input SARS-CoV-2 RNA extract.
    MiniSeq
    suggested: None
    Raw reads underwent adapter/quality trimming (trim-galore v0.6.5) 15, host filtering and read mapping to reference [bwa v0.7.17 16, samtools v.1.7 17,18] trimming of primers (iVar v1.3 19) and variant/consensus calling (freebayes v1.3.2 20) using the SIGNAL workflow (https://github.com/jaleezyy/covid-19-signal) v1.4.4dev (#60dd466) with the ARTICv4 amplicon scheme (from https://github.com/artic-network/artic-ncov2019) and the MN908947.3 SARS-CoV-2 reference genome and annotations.
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Additional quality control and variant effect annotation (SnpEff v5.0-0 21) was performed using the ncov-tools v1.8.0 (https://github.com/jts/ncov-tools/).
    SnpEff
    suggested: (SnpEff, RRID:SCR_005191)
    Variants were summarised using PyVCF v0.6.8 [citation: https://github.com/jamescasbon/PyVCF] and pandas v1.2.4 24.
    PyVCF
    suggested: None

    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

    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 10.1101/2022.01.13.475409v1 on bioRxiv