Table 1:
I-Ab-restricted CD4+ T cell Epitopes in SARS-CoV-2 BA.1 Spike and Nucleocapsid
| Epitope | Residues (BA.1) |
Residues (Wuhan) |
Sequence (MHC-binding core in bold) |
ELISpot Response |
Tetramer Response to: | |
|---|---|---|---|---|---|---|
| Peptide Immunization |
Protein Immunization |
|||||
| Spike | ||||||
| S-26 | 26-37 | 26-37 | PAYTNSFTRGVY | +++ | +++ | +++ |
| S-254* | 254-265 | 257-268 | GWTAGAAAYYVG | + | − | ND |
| S-298 | 298-309 | 301-312 | CTLKSFTVEKGI | ++ | ++ | ++ |
| S-529* | 529-540 | 532-543 | NLVKNKCVNFNF | +++ | − | ND |
| S-571 | 571-582 | 574-585 | DAVRDPQTLEIL | +++ | + | ++ |
| S-592 | 592-603 | 595-606 | VSVITPGTNTSN | + | ND | ND |
| S-655 | 655-666 | 658-669 | NSYECDIPIGAG | +++ | ND | ND |
| S-690 | 690-700 | 693-703 | IAYTMSLGAEN | + | + | + |
| S-883 * † | 883-893 | 886-896 | WTFGAGAALQI | + | + | ND |
| S-899 | 899-910 | 902-913 | MAYRFNGIGVTQ | + | − | ND |
| S-914 | 914-925 | 917-928 | YENQKLIANQFN | ++ | + | − |
| S-1008 | 1008-1019 | 1011-1022 | QLIRAAEIRASA | + | + | + |
| S-1104 | 1104-1115 | 1107-1118 | RNFYEPQIITTD | ++ | +++ | +++ |
| S-1116 | 1116-1127 | 1119-1130 | NTFVSGNCDVVI | ++ | +/− | +/− |
| Absent in BA.1 but present in Wuhan: | ||||||
| S-63 * | NA | 63-74 | TWFHAIHVSGTN | ND | +++ | +++ |
| Nucleocapsid | ||||||
| N-107 * | 107-118 | 110-121 | FYYLGTGPEAGL | +++ | ++ | ++ |
| N-125 * | 125-136 | 128-139 | DGIIWVATEGAL | +++ | ++ | + |
| N-143 | 143-154 | 146-157 | IGTRNPANNAAI | + | +++ | +++ |
Fully validated epitopes in bold
*
Multiple tetramers generated to test epitope
†
S-883 epitope absent in HexaPro Spike construct