Single‐cell transcriptomic atlas reveals distinct immunological responses between COVID‐19 vaccine and natural SARS‐CoV‐2 infection

  1. Yi Wang
  2. Xiaoxia Wang
  3. Laurence Don Wai Luu
  4. Jieqiong Li
  5. Xiaodai Cui
  6. Hailan Yao
  7. Shaojin Chen
  8. Jin Fu
  9. Licheng Wang
  10. Chongzhen Wang
  11. Rui Yuan
  12. Qingguo Cai
  13. Xiaolan Huang
  14. Junfei Huang
  15. Zhenjun Li
  16. Shijun Li
  17. Xiong Zhu
  18. Jun Tai

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Abstract

To control the ongoing coronavirus disease‐2019 (COVID‐19) pandemic, CoronaVac (Sinovac), an inactivated vaccine, has been granted emergency use authorization by many countries. However, the underlying mechanisms of the inactivated COVID‐19 vaccine‐induced immune response remain unclear, and little is known about its features compared to (Severe acute respiratory syndrome coronavirus 2) SARS‐CoV‐2 infection. Here, we implemented single‐cell RNA sequencing (scRNA‐seq) to profile longitudinally collected PBMCs (peripheral blood mononuclear cells) in six individuals immunized with CoronaVac and compared these to the profiles of COVID‐19 infected patients from a Single Cell Consortium. Both inactivated vaccines and SARS‐CoV‐2 infection altered the proportion of different immune cell types, caused B cell activation and differentiation, and induced the expression of genes associated with antibody production in the plasma. The inactivated vaccine and SARS‐COV‐2 infection also caused alterations in peripheral immune activity such as interferon response, inflammatory cytokine expression, innate immune cell apoptosis and migration, effector T cell exhaustion and cytotoxicity, however, the magnitude of change was greater in COVID‐19 patients, especially those with severe disease, than in immunized individuals. Further analyses revealed a distinct peripheral immune cell phenotype associated with CoronaVac immunization (HLA class II upregulation and IL21R upregulation in naïve B cells) versus SARS‐CoV‐2 infection (HLA class II downregulation and IL21R downregulation in naïve B cells from severe disease individuals). There were also differences in the expression of important genes associated with proinflammatory cytokines and thrombosis. In conclusion, this study provides a single‐cell atlas of the systemic immune response to CoronaVac immunization and revealed distinct immune responses between inactivated vaccines and SARS‐CoV‐2 infection.

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  1. Version published to 10.1002/jmv.28012
  2. ScreenIT

    SciScore for 10.1101/2021.08.30.21262863: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 41, 43, 45, 48 and 50. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

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  3. Version published to 10.1101/2021.08.30.21262863v1 on medRxiv