Prediction of SARS-CoV-2 exposure through T cell activation profiles

In the ongoing effort to study the SARS-CoV-2 virus and COVID-19 disease, assessment of the T cell immune response has guided vaccine and therapeutic development. T cell immunity, as measured by T cell activation, is commonly assessed by the activation induced marker (AIM) assay. However, no concerted effort has been made to compare AIM pairs and identify those that best detect T cell activation. The emergence of SARS-CoV-2 provided unique access to both known naïve and COVID-19 convalescent donor samples for the comparison of 35 unique T cell AIM pairs using a 15-marker flow cytometry panel. Detailed comparative analysis identified top performing AIM pairs and informed the development of a machine learning algorithm that predictively classified samples as COVID-19 convalescent or naïve. This approach may be additionally applicable to the assessment and prediction of T cell antigen reactivity in cancer and autoimmune disease.