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High-Dimensional Flow Cytometry in COVID-19 Research 

Targets of T cell responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals


The rapid spread of COVID-19 infections all over the world and the need to develop a vaccine has necessitated the understanding of the adaptive immune response to the SARS-CoV-2 virus. There is an urgent requirement to evaluate the response of human T cells to the SARS-CoV-2 virus through the quantification of virus-specific CD4+ and CD8+ T cells. In this article published in Cell, Grifoni used high dimensional flow cytometry to carry out immunophenotyping of PBMC samples taken from patients who had recovered from COVID-19 and unexposed donors. They performed T cell receptor (TCR) dependent activation-induced marker (AIM) assays to identify and quantify SARS-CoV-2-specific CD4+ T cells in recovered COVID-19 patients. To measure SARS-CoV-2-specific CD8+ T cells in the recovered patients, the authors utilized two complementary methodologies, AIM assays and intracellular cytokine staining (ICS). The authors evaluated whether stronger SARS-CoV-2-specific CD4+ T cell responses were associated with higher antibody titers in COVID-19 cases by examining spike protein-specific CD4+ cells. Finally, to evaluate what antigens were targeted by CD4+ and CD8+ T cells, the authors synthesised an overlapping pool of peptides spanning the entire sequence of SARS-CoV-2 and studied epitope reactivity.


The authors report, using multiple experimental, approaches, that SARS-CoV-2-specific CD4+ T cell and antibody responses are observed in 100% of the COVID-19 cases, and CD8+ responses are observed in approx. 70% of them. Interestingly, the authors also detect SARS-CoV-2 reactive CD4+ cells in 40-60% of the unexposed individuals, which they attribute to cross-reactive T cell recognition between circulating ‘common cold’ coronaviruses and SARS-CoV-2. The authors propose that mapping T cell specificities reveals valuable targets for incorporation in candidate vaccine development and distinct specificity patterns between COVID-19 cases and unexposed healthy controls.


The article can be accessed in the Cell journal website.



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