Clonal structure and epitope specificity of Ad5-nCoV vaccine-induced T cell response to SARS-CoV-2

Abstract

Abstract As a part of phase 3 clinical trial of a single-dose adenoviral COVID-19 vaccine, we evaluated the dynamics and clonal structure of T cell response to the SARS-CoV-2 Spike protein. T cell response measured in 50 donors by IFNg ELISpot after Spike stimulation peaked on the 14th day (d14) after vaccination. Flow cytometry demonstrated that the response was skewed to CD4+ cells. To isolate Spike-specific T cells we performed short-term T cell expansion of d14 samples (n=17 donors) with the recombinant Spike, restimulated and FACS sorted IFNg+ cells. T cell receptor (TCR) beta chain sequencing identified from 36 to 629 Spike-specific clones (median 186) per individual. CD4+ response was more clonal than CD8+ (median 116 and 17 respectively) but CD8+ occupied a larger share of the total TCR repertoire (median 0.25% for CD4+ and 0.52% for CD8+) as a result of the larger average clone size at d14 (3.4×10−5 for CD8+ vs. 6.6×10−6 for CD4+). Both the number and total share of Spike-specific clones in the TCR repertoire decreased at day 28 and further at day 180. At 6 months a median of 1 (0 to 18) of the initial Spike-specific clones were detectable in the peripheral blood. This number increased to 39 (9 to 105) as a result of T cell expansion. For 14 donors we also performed rapid expansion of T cells sampled at d14 with 11 Spike-epitopes (9 MHC I and 2 MHC II) followed by sorting of activated cells and TCR sequencing. We identified on average 41 unique epitope-specific clones (2 to 141). They were mostly undetectable in the peripheral blood at 6 months (0 to 8 clones), but their numbers increased to the median of 7 clones (0 to 35) after cultivation with Spike. Overall this demonstrates the induction of polyclonal and stable T cell response by a single injection of adenoviral vaccine. The work was supported by the Russian Science Foundation grant 20-15-00395.