Tracking the clonal dynamics of SARS-CoV-2-specific T cells in children and adults with mild/asymptomatic COVID-19

  1. Weng Hua Khoo
  2. Katherine Jackson
  3. Chansavath Phetsouphanh
  4. John J. Zaunders
  5. José Alquicira-Hernandez
  6. Seyhan Yazar
  7. Stephanie Ruiz-Diaz
  8. Mandeep Singh
  9. Rama Dhenni
  10. Wunna Kyaw
  11. Fiona Tea
  12. Vera Merheb
  13. Fiona X.Z. Lee
  14. Rebecca Burrell
  15. Annaleise Howard-Jones
  16. Archana Koirala
  17. Li Zhou
  18. Aysen Yuksel
  19. Daniel R. Catchpoole
  20. Catherine L. Lai
  21. Tennille L. Vitagliano
  22. Romain Rouet
  23. Daniel Christ
  24. Benjamin Tang
  25. Nicholas P. West
  26. Shane George
  27. John Gerrard
  28. Peter I. Croucher
  29. Anthony D. Kelleher
  30. Christopher G. Goodnow
  31. Jonathan D. Sprent
  32. Joseph E. Powell
  33. Fabienne Brilot
  34. Ralph Nanan
  35. Peter S. Hsu
  36. Elissa K. Deenick
  37. Philip N. Britton
  38. Tri Giang Phan

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Abstract

No abstract available

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  1. Version published to 10.1016/j.clim.2022.109209
  2. ScreenIT

    SciScore for 10.1101/2022.01.30.478400: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: SCHN) Human Research Ethics Committee (2020/ETH00837).
    Consent: A waiver of informed consent, with the opportunity to opt-out was used for this study.
    Sex as a biological variableBoth patients were elderly males with severe COVID-19 who were intubated and ventilated ICU (WHO Clinical Progress Scale of 7 out of 10).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    HEK293 cells were transfected to express early-clade SARS-CoV-2 Spike antigens.
    HEK293
    suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
    Recombinant DNA
    SentencesResources
    Codon-optimised, wild-type SARS-CoV-2 strain Wuhan Spike protein ORF with 18 amino acids deleted from the cytoplasmic tail was cloned within the MCS of a lentiviral expression vector, pLVX-IRES-ZsGreen1, using EcoRI and XbaI restriction sites, resulting in pSpike-IRES-ZsGreen vector.
    pLVX-IRES-ZsGreen1
    suggested: None
    pSpike-IRES-ZsGreen
    suggested: None
    Recombinant RBD and S protein: Expression plasmids encoding His-tagged SARS-CoV-2 RBD (residues 319 to 541 of SARS-CoV-2 S protein) or S protein (with a C-terminal trimerization domain) were cloned into pCEP4 vector and transfected into Expi293F (ThermoFisher Scientific) and the proteins expressed for 7 days at 37°C (Rouet et al., 2021).
    pCEP4
    suggested: RRID:Addgene_16479)
    Software and Algorithms
    SentencesResources
    Data were analysed using FlowJo 10.4.1 (TreeStar, USA), Excel (Microsoft, USA) and GraphPad Prism (GraphPad Software, USA)
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Cytokine concentrations were imported into R (version 4.1.2), log transformed, and visualized with ggplot2 (version 3.3.5).
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    Differential gene expression analysis: Raw counts from defined cell populations were normalised using scran / scater (Lun et al., 2016; McCarthy et al., 2017) and differential gene expression analysis was performed using Limma voom (Law et al., 2014) with regression of Batch and Gender covariates.
    Limma
    suggested: (LIMMA, RRID:SCR_010943)
    Reads from each pool were then mapped to the GRCh38 genome using STAR (Dobin et al., 2013).
    STAR
    suggested: (STAR, RRID:SCR_004463)
    Clonal lineages were defined by IgBLAST called V, J and CDR3 amino acid sequences for both TRA and TRB, if available, or by a single chain if paired chains were not available.
    IgBLAST
    suggested: (IgBLAST, RRID:SCR_002873)
    Repertoire metrics were summarised in RStudio (v1.4.1106, RStudio Team (2021).
    RStudio
    suggested: (RStudio, RRID:SCR_000432)
    Clonotype distribution across cell types and time points was explored using Upset plots (Lex et al., 2014) as implemented by the ComplexHeatmap package (Gu et al., 2016).
    ComplexHeatmap
    suggested: (ComplexHeatmap, RRID:SCR_017270)
    Statistics: Statistical analysis was performed using Prism software (GraphPad) or in R.
    Prism
    suggested: (PRISM, RRID:SCR_005375)

    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: We detected the following sentences addressing limitations in the study:
    Limitations of the study and future directions: There are several limitations to our study. The sample size of our cohort is relatively small and this reduces the confidence in our conclusions. However, this is mitigated by the longitudinal study design and the fact that we have focused on the systemic immune response in patients with the same asymptomatic/mild disease severity from the same households. We longitudinally followed patients from the acute stage to convalescence, and complemented our cohort with an additional two patients with severe COVID-19. We also analyzed 433,301 single cells directly ex vivo, making it one of the larger single cell datasets to be made available. Another limitation of our study is the short study period and it will be interesting to see the impact of immunity on intercurrent hCoV and SARS-CoV- 2 reinfection rates with long term follow-up. Accordingly, large-scale prospective studies involving longitudinal study of homogeneous patient groups with the same disease severity will be needed to determine the relative merits and risks of infection- vs vaccine-induced immunity against SARS- CoV-2. Due to technical reasons and the volume of blood sample available from children, we were only able to test memory CD4+ T cell responses to RBD and S protein. In addition, the identification of SARS-CoV-2-specific T cells in our study was dependent on the annotation of their TCR in ImmuneCODE and VDJdb databases, which are almost certainly incomplete. Anot...

    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 10.1101/2022.01.30.478400v1 on bioRxiv