Unbiased Screens Show CD8+ T Cells of COVID-19 Patients Recognize Shared Epitopes in SARS-CoV-2 that Largely Reside outside the Spike Protein

Abstract

Developing effective strategies to prevent or treat COVID-19 requires understanding the natural immune response to SARS-CoV-2. We used an unbiased, genome-wide screening technology to determine the precise peptide sequences in SARS-CoV-2 that are recognized by the memory CD8 + T cells of COVID-19 patients. In total, we identified 3–8 epitopes for each of the six most prevalent human leukocyte antigen (HLA) types. These epitopes were broadly shared across patients and located in regions of the virus that are not subject to mutational variation. Notably, only 3 of the 29 shared epitopes were located in the spike protein, whereas most epitopes were located in ORF1ab or the nucleocapsid protein. We also found that CD8 + T cells generally do not cross-react with epitopes in the four seasonal coronaviruses that cause the common cold. Overall, these findings can inform development of next-generation vaccines that better recapitulate natural CD8 + T cell immunity to SARS-CoV-2.

Th1 Dominant Nucleocapsid and Spike Antigen-Specific CD4+ and CD8+ Memory T Cell Recall Induced by hAd5 S-Fusion + N-ETSD Infection of Autologous Dendritic Cells from Patients Previously Infected with SARS-CoV-2

“…59 While it cannot be excluded that S (and other viral proteins) can induce T-cell responses, the evidence in the literature support a key role for N. Not only have T cell responses to N been found in the majority of patients recovered from COVID-19, 2 these responses to N in patients exposed to very similar virus SARS-CoV are remarkably durable. 2 Compelling evidence of the importance of N in natural T cell immunity can be found in the recent report of Ferretti et al 60 who found, using an unbiased genome-wide screen for the precise peptide sequences recognized by memory CD8+ T cells of COVID-19 patients, that only 3 of the 29 shared epitopes were from the spike protein, whereas the highest density of epitopes was located in the nucleocapsid protein. Thus, in the hAd5 S-Fusion + N-ETSD vaccine, N is expected to not only elicit a humoral response, but also a T-cell response that better recapitulates disease-limiting natural immunity.…”

Deciphering the ins and outs of SARS-CoV-2-specific T cells

“…Meanwhile, responses to commonly recognized epitopes from ORF5 and ORF10 in exposed individuals were not recognized by unexposed individuals. These divergent responses between exposed and unexposed individuals could partially explain the varying levels of cross-reactive responses reported in the other studies 4,10 , since the peptide pools used for earlier studies focused on structural proteins, such as ORF2 (spike), ORF4 (envelope), ORF5 (membrane) and ORF9 (nucleoprotein), rather than non-structural proteins, such as ORF1. Cross-reactive peptides were analyzed for sequence and physico-chemical similarities to the four CCCs (OC43, 229E, NL63 and HKU1), revealing that 70% of these cross-reactive peptides share some degree of similarity with peptides from other coronaviruses.…”

A new concept on anti-SARS-CoV-2 vaccines: strong CD8+ T-cell immune response in both spleen and lung induced in mice by endogenously engineered extracellular vesicles

“…Circulating SARS-CoV-2-specific CD8 + and CD4 + T cells were found in 70% and 100% of patients, respectively (18). Another study identified the most part of SARS-CoV-2-specific epitopes recognized by memory CD8 + T cells from COVID-19 patients in both N and ORF1ab proteins (19).…”

“…Conversely, memory T cells against SARS-CoV persist 11 years post-infection and have the potential to induce cross-reactive immunity (13)(14)(15)(16)(17). An increasing number of studies shows that also SARS-CoV-2 convalescent patients develop robust T-cell responses (18)(19)(20)(21)(22). Besides S protein, SARS-CoV-2 membrane (M) protein also elicits strong CD8 + T cell responses, and a significant reactivity was also reported for both nucleocapsid (N) (18) and ORF1ab (19) proteins.…”

“…An increasing number of studies shows that also SARS-CoV-2 convalescent patients develop robust T-cell responses (18)(19)(20)(21)(22). Besides S protein, SARS-CoV-2 membrane (M) protein also elicits strong CD8 + T cell responses, and a significant reactivity was also reported for both nucleocapsid (N) (18) and ORF1ab (19) proteins. Taken together, these evidences suggest that a long-lasting, broad vaccine formulation against SARS-CoV-2 could and should induce strong memory T cell responses against multiple viral antigens.…”