Effects And Mechanism Of Inactivated SARS-CoV-2 Vaccination On T Cells Differentiation And Antigenic Epitopes

BackgroundSevere acute respiratory syndrome coronavirus 2(SARS-CoV-2)has infected millions of people around the world.Vaccination is a pillar in the strategy to control the transmission of SARS-CoV-2.Immune responses to vaccination require elucidation.Our study aims to investigate the effects and potential mechanism of inactivated SARS-CoV-2 vaccine inoculation on T cells differentiation and antigenic epitopes.MethodsIn the first part,three healthy adults who received three doses of inactivated SARS-CoV-2 vaccine inoculation were enrolled.Single-cell sequencing was performed after peripheral blood mononuclear cells were extracted from these three participants at four time points during the inactivated SARS-CoV-2 vaccination process.After library preparation,raw read data analysis;quality control;dimension reduction and clustering;single-cell T cell receptor(TCR)sequencing;TCR V(D)J sequencing;cell differentiation trajectory inference;differentially expressed genes and pathway enrichment were analyzed to explore the characteristics and mechanisms of postvaccination immunodynamics.In the second part of the study,the immune responses to vaccination with three doses of inactivated SARS-CoV-2 vaccine were followed in a cohort of 37 healthy adults(18-59 years old).Blood samples were collected at multiple time points.After performing peptide array,machine learning modeling,and sequence alignment analyses,vaccine-induced antibody-binding region(VIABR)was explored and the epitopes of vaccine action were analyzed.(Registration number:ChiCTR2200058571)Results1.Inactivated SARS-CoV-2 vaccination promoted T cell proliferation,TCR clone amplification.and TCR diversity.The proliferation and differentiation of CD8+ mucosal-associated invariant T(MAIT)cells were significantly upregulated,as was KLRD1 gene expression.2.Sequence alignment analyses revealed that a third vaccine dose generated a new highly represented VIABR near the A570D mutation,and the whole process of inoculation enhanced the VIABR near the N501Y mutation.In addition,the antigen conformational epitopes varied between short-and long-term samples.The amino acids with the highest scores in the short-term samples(within 4 weeks after each inoculation)distributed primarily in the receptor binding domain and N-terminal domain regions of spike(S)protein while in the long-term samples(12 weeks after the 2nd dose),new conformational epitopes were localized in the crevices within the head of the S protein trimer.Conclusion1.Upregulation of CD8+ MAIT cell differentiation and KLRD1 expression after inactivated SARS-CoV-2 vaccination was demonstrated by single-cell sequencing.We conclude that the inactivated SARS-CoV-2 vaccine elicits adaptive T cell immunity to enhance early immunity and rapid response to the targeted virus.2.Protective antigenic epitopes were revealed by immunosignatures after three doses of inactivated SARS-CoV-2 vaccine inoculation.A third dose results in a new top-10 VIABR near the A570D mutation site of S protein,and the whole process of inoculation enhanced the VIABR near the N501Y mutation,thus potentially providing immunity protection from SARS-CoV-2 strains and variants.