Table 2.
Top SARS-CoV-2 epitopes present in two or more individuals
| Protein | Amino acids | Sequence | Number of COVID-19 samples/19 | Number of unexposed samples/7 | Mutation (variant) |
|---|---|---|---|---|---|
| Spike (S) | |||||
| S | 1,121–1,159a | FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNH | 16 | 0 | |
| S | 1,141–1,179a | LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI | 16 | 0 | |
| S | 801–839a | NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGD | 15 | 0 | |
| S | 541–579 | FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP | 13 | 0 | A570D (B.1.1.7) |
| S | 621–659 | PVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNS | 4 | 0 | H655Y (P.1) |
| S | 661–699 | ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSL | 4 | 0 | P681H (B.1.1.7) |
| S | 761–799 | TQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGG | 4 | 0 | T761I (B.1.1.7) |
| S | 281–319 | ENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFR | 3 | 0 | |
| S | 521–559 | PATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKF | 3 | 0 | |
| S | 561–599 | PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVIT | 3 | 0 | A570D (B.1.1.7) |
| S | 641–679 | NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTN | 3 | 0 | H655Y (P.1) |
| S | 781–819 | VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIE | 3 | 0 | |
| S | 1,161–1,199 | SPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLID | 3 | 0 | |
| S | 1,235–1,273 | CCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT | 3 | 0 | |
| S | 21–59b | RTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFF | 1 | 1 | P26S (P.1) |
| S | 261–299 | GAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSET | 2 | 0 | |
| S | 301–339 | CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFG | 2 | 0 | |
| Nucleocapsid (N) | |||||
| N | 141–179 | TPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGG | 8 | 0 | |
| N | 161–199 | LPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTP | 8 | 0 | |
| N | 201–239 | SSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQ | 7 | 0 | S235F (B.1.1.7) T205I (B.1.351) |
| N | 381–419 | ALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA | 7 | 0 | |
| N | 1–39b | MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQ | 4 | 1 | D3L (B.1.1.7) |
| N | 21–59 | SDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQH | 3 | 0 | |
| N | 221–259 | LLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPR | 3 | 0 | S235F (B.1.1.7) |
| N | 341–379 | DKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADET | 3 | 0 | |
| N | 241–279a | QQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGP | 2 | 0 | |
| ORF1ab | |||||
| ORF1ab | 1,801–1,839b | ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHI | 4 | 2 | |
| ORF1ab | 1,961–1,999 | PDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATN | 4 | 0 | |
| ORF1ab | 741–779 | FLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLV | 2 | 0 | |
| ORF1ab | 5,961–5,999 | EGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI | 2 | 0 | |
| ORF1ab | 4,481–4,519b | LLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADL | 1 | 1 | |
a
Predicted cross-reactive peptides with high homology to other HCoVs (Figure 6).
b
Cross-reactive peptides present in SARS-CoV-2-unexposed samples.