Table 1. Summary of experimental studies on SARS-CoV-2 proteins/peptides in relation to T cell activation.
|
(A) Studies that only used peptide pools or intact
proteins |
||||
|---|---|---|---|---|
| Indications for | Indications for | |||
| SARS-CoV-2- | cross-virus | MHC | ||
| Reference | specific T cells a | T cell memory b | alleles c | The investigated peptides (and positive findings for
cross-virus shared 9-mer sequences) d, e |
| Anft et al., 2020 | CD4, CD8 | CD4, CD8 | n.d. | peptide pools derived from S |
| Bacher et al., 2020a | CD4 | CD4 | n.d. | peptides pools derived from S, M, N, E, NS6, NS7a, NS7b,
NS8, ORF3a, ORF9B, ORF10, and ORF14 |
| Braun et al., 2020 | CD4 | CD4 | n.d. | peptide pools derived from S |
| Dan et al., 2021 | CD4, CD8 | n.d. | n.d. | peptide pools derived from throughout the SARS-CoV-2
proteome |
| Grifoni et al., 2020 | CD4, CD8 | CD4, CD8 | n.d. | peptide pools derived from throughout the SARS-CoV-2
proteome |
| Meckiff et al., 2020 | CD4 | CD4 | n.d. | peptide pools derived from S and M |
| Ni et al., 2020 | Yes, not
specified |
Yes | n.d. | S, N, and NSP5 proteins |
| Rydyznski Moderbacher et al., 2020 | CD4, CD8 | CD4, CD8 | n.d. | peptide pools derived from throughout the SARS-CoV-2
proteome |
| Steiner et al., 2020 | CD4, CD8 | CD4, CD8 | n.d. | peptide pools derived from S and N |
| Thieme et al., 2020 | CD4, CD8 | CD4, CD8 | n.d. | peptide pools derived from S, M, and N |
| Weiskopf et al., 2020 | CD4, CD8 | CD4, CD8 | n.d. | peptide pools derived from throughout the SARS-CoV-2
proteome |
| (B) Studies that (also) investigated individual peptides | ||||
| Ferretti et al., 2020 | CD8 | CD8 | a, b | peptides derived from throughout the SARS-CoV-2
proteome; activation of CD8+ T cells by VYI and SPR peptides |
| Gangaev et al., 2020 | CD8 | CD8 | a, b | peptides throughout the SARS-CoV-2 proteome but the
preprint does not provide all details |
| Habel et al., 2020 | CD4, CD8 | maybe | a, b | peptides derived from S, M, N, NSP3, NSP4, NSP6, and
NSP12 |
| Kared et al., 2020 | CD8 | No | a, b | peptides derived from throughout the SARS-CoV-2
proteome; activation of CD8+ T cells by VYI and SPR peptides |
| Keller et al., 2020 | CD4, CD8 | Yes, not
specified |
a | peptides derived from S, M, N, and E |
| Le Bert et al., 2020 | CD4, CD8 | CD4, CD8 | a | peptides derived from N, NSP7, and NSP13; activation of
CD4+ T cells by SPR encompassing peptide |
| Mateus et al., 2020 | CD4, CD8 | CD4, CD8 | n.d. | peptides derived from throughout the SARS-CoV-2
proteome; activation of CD4+ T cells by LKS, YLR (+ LRK, RKH), IER (+ ERF, RFV, FVS, VSL), and NVN (+ VNR, NRF, RFN, FNV) encompassing peptides |
| Nelde et al., 2021 | CD4, CD8 | CD4, CD8 | a | peptides derived from throughout the SARS-CoV-2
proteome; activation of PBMC (probably CD8+ T cells) by VYI peptide; activation of CD4+ T cells by peptide that partially overlaps SPR peptide |
| Peng et al., 2020 | CD4, CD8 | No | a, b | peptides derived from S, M, N, E, ORF3a, ORF6, ORF7a,
and ORF8; binding of CD8+ T cells by HLA-B*07:02/ SPR pentamers; activation of CD4+ and CD8+ T cells by peptide encompassing SPR peptide |
| Poluektov et al., 2020 | n.d. | n.d. | b | peptides derived from throughout the SARS-CoV-2 proteome |
| Prachar et al., 2020 | n.d. | n.d. | b | peptides derived from throughout the SARS-CoV-2
proteome; SLA peptide bound to HLA-A*02:01; KYT, AYA, and VYI peptide bound to HLA-A*24:02; HRF peptide bound to HLA-B*40:01; peptide encompassing RFY (+ FYR, YRL, RLA) bound to HLA-DR4 |
| Schulien et al., 2021 | CD8 | CD8 | a, b | peptides derived from throughout the SARS-CoV-2
proteome; activation of CD8+ T cells by SPR peptide; binding of CD8+ T cells by HLA-B*07:02/ SPR tetramers |
| Sekine et al., 2020 | CD4, CD8 | CD4, CD8 | (a?), b | peptides derived from S, M, N, E, ORF3a, and ORF6;
activation of CD8+ T cells by SPR peptide |
| Shomuradova et al., 2020 | CD4, CD8 | CD4, CD8 | a, b | peptides derived from S, M, and N |
| Snyder et al., 2020 | CD8 | n.d. | a | peptides derived from throughout the SARS-CoV-2
proteome; activation of CD8+ T cells by FVD, RIL, AIM, and IVD peptides and by a combined set of SPR peptide plus an SPR-overlapping peptide |
| Takagi & Matsui, 2020 | CD8 (in
HLA-A*02+ mice) |
n.d. | a, b | peptides derived from NSP1-to-10 |
| Tarke et al., 2020 | CD4, CD8 | CD4, CD8 | a, b | peptides derived from throughout the SARS-CoV-2
proteome; activation of CD4 + T cells by peptides that encompass or partially overlap LKS, YPK (+ PKC), RFY (+ FYR, RLA, LAN), FNI (+ NIC, ICQ), IER (+ ERF, RFV, FVS, VSL, SLA), SPR (+ PRW, RWY, WYF, YFY), or RAK (+AKH); activation of CD8 + T cells by QTV encompassing 10-mer, YAI (+AIS) encompassing 10-mer, DLT encompassing 12-mer, and by 10-13 mers that encompassed DYV, YVY, VYL, YLP, LPY, and/or PYP |
| Woldemeskel et al., 2020 | CD4
(presumably) |
CD4
(presumably) |
(a?) | peptides derived from S, M, and N |
(a) In most of the listed studies experimental evidence was obtained for the existence of SARS-CoV-2-specific CD4 + and/or CD8 + T cells in COVID-19 convalescent donors
(b) In many of the listed studies experimental evidence was obtained suggesting that CCCoV infections induced, or could induce, anti-SARS-CoV-2 T cell memory. Naturally, no samples were used of healthy donors without CCCoV infection history, and for this table, as done in the majority of the listed studies, all positive reactions in healthy donors that indicated SARS-CoV-2-specific T cell activation were interpreted as indications for possible cross-virus T cell memory. In the Habel et al. (2020) study, for T cells from healthy donors activations of similar extent were found for SARS-CoV-2 peptides and peptides from other pathogens for which the donors did not have an infection history.
(c) Some of the listed studies determined the association (a) of T cell responses with MHC alleles or found binding (b) of peptides to MHC alleles
(d) This column lists the proteins or peptides that were investigated. In most cases, though not all, there had been a preselection of peptides based on software predictions for MHC binding. In addition, positive findings for identical 9-mers shared between SARS-CoV-2 and at least one of the CCCoVs are summarized, with VYI and SPR peptides highlighted in bold.
(e) The 3-letter names for peptides here only refer to the 9-mers "Not specified" indicates that it was not determined whether reacting cells were CD4+ or CD8+ T cells.
A question mark is added if we are uncertain about what the authors did.
n.d. = not determined