T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals
2022
Naranbhai, Vivek | Nathan, Anusha | Kaseke, Clarety | Berrios, Cristhian | Khatri, Ashok | Choi, Shawn | Getz, Matthew A. | Tano-Menka, Rhoda | Ofoman, Onosereme | Gayton, Alton | Senjobe, Fernando | Zhao, Zezhou | St Denis, Kerri J. | Lam, Evan C. | Carrington, Mary | Garcia-Beltran, Wilfredo F. | Balazs, Alejandro B. | Walker, Bruce D. | Iafrate, A John | Gaiha, Gaurav D.
The SARS-CoV-2 Omicron variant (B.1.1.529) contains mutations that mediate escape from antibody responses, although the extent to which these substitutions in spike and non-spike proteins affect T cell recognition is unknown. In this study, we show that T cell responses in individuals with prior infection, vaccination, both prior infection and vaccination, and boosted vaccination are largely preserved to Omicron spike and non-spike proteins. However, we also identify a subset of individuals (∼21%) with a >50% reduction in T cell reactivity to the Omicron spike. Evaluation of functional CD4⁺ and CD8⁺ memory T cell responses confirmed these findings and revealed that reduced recognition to Omicron spike is primarily observed within the CD8⁺ T cell compartment potentially due to escape from HLA binding. Booster vaccination enhanced T cell responses to Omicron spike. In contrast to neutralizing immunity, these findings suggest preservation of T cell responses to the Omicron variant, although with reduced reactivity in some individuals.
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