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

Understanding adaptive immunity to SARS-CoV-2 is important for vaccine development, interpreting coronavirus disease 2019 (COVID-19) pathogenesis, and calibration of pandemic control measures. Using HLA class I and II predicted peptide megapools, circulating SARS-CoV-2-specific CD8(+) and CD4(+) T cells were identified in similar to 70% and 100% of COVID-19 convalescent patients, respectively. CD4(+) T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the antiSARS-CoV-2 IgG and IgA titers. The M, spike, and N proteins each accounted for 11%-27% of the total CD4(+) response, with additional responses commonly targeting nsp3, nsp4, ORF3a, and ORF8, among others. For CD8(+) T cells, spike and M were recognized, with at least eight SARS-CoV-2 ORFs targeted. Importantly, we detected SARS-CoV-2-reactive CD4(+) T cells in similar to 40%-60% of unexposed individuals, suggesting cross-reactive T cell recognition between circulating common cold coronaviruses and SARS-CoV-2.