CD8+ T cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients

Mallajosyula, Vamsee; Ganjavi, Conner; Chakraborty, Saborni; McSween, Alana M; Pavlovitch-Bedzyk, Ana Jimena; Wilhelmy, Julie; Nau, Allison; Manohar, Monali; Nadeau, Kari C; Davis, Mark M

A central feature of the SARS-CoV-2 pandemic is that some individuals become severely ill or die, whereas others have only a mild disease course or are asymptomatic. Here we report development of an improved multimeric αß T cell staining reagent platform, with each maxi-ferritin "spheromer" displaying 12 peptide-MHC complexes. Spheromers stain specific T cells more efficiently than peptide-MHC tetramers and capture a broader portion of the sequence repertoire for a given peptide-MHC. Analyzing the response in unexposed individuals, we find that T cells recognizing peptides conserved amongst coronaviruses are more abundant and tend to have a "memory" phenotype, compared to those unique to SARS-CoV-2. Significantly, CD8+ T cells with these conserved specificities are much more abundant in COVID-19 patients with mild disease versus those with a more severe illness, suggesting a protective role.