Algorithm for assessing the level of T cell immune response against SARS-CoV-2 and the results of its application in unvaccinated and vaccinated people who have been infected with COVID-19

Antigen (AG)-specific T cell activity was compared in two groups of patients: those who underwent COVID-19 in 2021 during the circulation of the SARS-CoV-2 delta virus strain (43 individuals); and those who underwent COVID-19 in 2022 (Omicron strain, 23 individuals). The diagnosis was confirmed by PCR analysis of nasopharyngeal and oropharyngeal swabs. The 23 individuals following COVID-19 caused by SARS-CoV-2 (omicron) were part of a cohort of 41 volunteers who were examined multiple times during 2021–2023: during vaccination, after vaccination, before revaccination, and subsequently after illness (6–8 times in total). Due to this, it was possible to compare the indices of specific humoral and cellular immunity in the same patients 1–2 months before and after breakthrough infection. Detection of AG-specific T cells and assessment of their activity by AG-stimulated IFNγ production was carried out by our own previously developed method (Patent RU № 2780369 C1). For stimulation of memory T effectors in vitro, the same antigens were used to determine the concentration of antibodies against SARS-CoV-2 by ELISA method. A total of about 300 blood samples from healthy subjects and patients after COVID-19 were analyzed. Each sample was tested against 3 SARS-CoV-2 antigens and in 2 stimulation modes. A qualitative assessment algorithm for AG-specific T cell activity has been proposed that can be used to monitor the state of cellular immunity in a population in which SARS-CoV-2 virus continues to circulate and to create insights into what level of T cell activation is sufficient to prevent or reduce the severity of SARS-CoV-2 infection. Unvaccinated COVID-19 (SARS-CoV-2, Delta) survivors lacked AG-specific T cells to RBD SARS-CoV-2, but T cell specificity to full-length S glycoprotein at the same level, qualitatively assessed as low in 52% of the group, persisted for up to six months. In previously unvaccinated COVID-19 vaccinees, this duration of persistence of AG-specific T cells in circulating blood was achieved only after revaccination. Hybrid immunity, which we traced as a result of vaccination after COVID-19 (Delta strain) or as a breakthrough infection (SARS-CoV-2, Omicron), is characterized by the highest indices of memory T cell activity (43–46% of the group — normal activity of AG-specific cells, 30–43% — high activity) to all used antigens and the longest duration of preservation of indices at this level. Further investigation of the level of antiviral immunity after COVID-19 may be important for predicting the outcome of new waves of SARS-CoV-2 infection.