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. 2022 Jun 14;96(13):e00509-22. doi: 10.1128/jvi.00509-22

TABLE 2.

List of identified T cell epitopesa

Protein Peptide Positions Amino acid sequence No. of participants positive/tested (%) Ex vivo PBMC,
SFC/106 (range)		 T cell
response		 HLA restriction Reference(s)b
ORF1ab (n = 2) ORF1ab-10 1637–1646 TTDPSFLGRY 3/9 (33) 65–262.5 CD8 HLA-A*01:01 26, 27, 34, 40
ORF1ab-11 1636–1646 HTTDPSFLGRY 3/9 (33) 23–210 CD8 HLA-A*01:01 26, 27, 34, 40
Nucleocapsid phosphoprotein (n = 14) N5c 17–31 FGGPSDSTGSNQNGE 1/9 (11) 33 NAd NA
N15c 57–71 TQHGKEDLKFPRGQG 1/9 (11) 53 NA NA
N26/27
(9-mer)		 105–113 SPRWYFYYL 1/9 (11) 47.5 CD4 + CD8 12, 13, 26, 28, 30, 35, 40–42
N26 101–115 MKDLSPRWYFYYLGT 2/9 (22) 25–60 CD4 + CD8 12, 13, 28, 40, 41
N27 105–119 SPRWYFYYLGTGPEA 2/9 (22) 26.3–75 CD4 + CD8 12, 13, 28, 40, 41
N32 125–139 ANKDGIIWVATEGAL 1/9 (11) 30.5–75 CD4 + CD8 28, 34
N33 129–143 GIIWVATEGALNTPK 2/9 (22) 25–65 CD4 12, 34
N67 265–279 TKAYNVTQAFGRRGP 1/9 (11) 43 CD4 28
N76 301–315 WPQIAQFAPSASAFF 2/9 (22) 39.5–47.5 CD4 12, 34, 36, 37
N79 313–327 AFFGMSRIGMEVTPS 1/9 (11) 96–591.5 CD4/CD8 13, 29, 34, 37, 39
N81 321–335 GMEVTPSGTWLTYTG 2/9 (22) 25–68 CD4 + CD8 12, 13, 28, 29, 36, 37, 44
N82 325–339 TPSGTWLTYTGAIKL 1/9 (11) 39.5 CD4 + CD8 13, 29, 32, 34, 37, 44
N87 345–359 NFKDQVILLNKHIDA 1/9 (11) 89.5 CD4 + CD8 13, 28, 37, 44
N88 349–363 QVILLNKHIDAYKTF 3/9 (33) 20–637 CD4 + CD8 13, 28, 37, 44
Membrane glycoprotein (n = 16) M128-6
(9-mer)c 		42–50 RNRFLYIIK 1/9 (11) 60–150 CD8 HLA-A*30:01 25, 34
M128c 37–51 FAYANRNRFLYIIKL 3/9 (33) 42.5–60 CD8 HLA-A*30:01 NA
M129c 41–55 NRNRFLYIIKLIFLW 3/9 (33) 25–95 CD4/CD8 25
M130c 45–59 FLYIIKLIFLWLLWP 1/9 (11) 36 NA NA
M133c 57–71 LWPVTLACFVLAAVY 1/9 (11) 30 NA NA
M135 65–79 FVLAAVYRINWITGG 1/9 (11) 36.5 CD4 28
M141c 89–103 GLMWLSYFIASFRLF 2/9 (22) 162.5–545.5 CD4 NA
M148c 117–131 NILLNVPLHGTILTR 1/9 (11) 69.5 NA NA
M153 137–151 ELVIGAVILRGHLRI 1/9 (11) 44 CD4 13, 28
M154 141–155 GAVILRGHLRIAGHH 2/9 (22) 36–275 CD4 13, 28, 29
M155/156
(9-mer)		 148–156 HLRIAGHHL 1/9 (11) 72 CD4 + CD8 13, 28, 29, 33, 45
M155 145–159 LRGHLRIAGHHLGRC 3/9 (33) 105–4,630 CD4 + CD8 HLA-DR 13, 28, 29, 33, 45
M156 149–163 LRIAGHHLGRCDIKD 3/9 (33) 20–3,214 CD4 + CD8 HLA-DR 13, 28, 29, 33, 45
M160 165–179 PKEITVATSRTLSYY 1/9 (11) 95 CD4 13, 28, 33
M162 173–187 SRTLSYYKLGASQRV 4/9 (44) 20–137.5 CD4 13, 28, 29, 33, 34, 38
M163 177–191 SYYKLGASQRVAGDS 4/9 (44) 39.5–187.5 CD4 + CD8 13, 28, 29, 33, 34, 38
Spike Glycoprotein (n = 8) S173 334–348 NLCPFGEVFNATRFA 1/9 (11) 23 CD4 32, 33
S175 342–356 FNATRFASVYAWNRK 1/9 (11) 36.5–161 CD4/CD8 31 – 33
S176
(9-mer)		 349–357 SVYAWNRKR 1/9 (11) 65 CD4 32, 33, 39
S176 346–360 RFASVYAWNRKRISN 2/9 (22) 153–1,262 CD4 + CD8 32, 33, 39
S177 350–364 VYAWNRKRISNCVAD 1/9 (11) 182 CD4 32, 33, 39, 44
S178 354–368 NRKRISNCVADYSVL 1/9 (11) 29–55 CD4/CD8 13, 33, 43, 44
S179 358–372 ISNCVADYSVLYNSA 1/9 (11) 23 CD8 44
S202 450–464 NYLYRLFRKSNLKPF 1/9 (11) 62.5 CD4 + CD8 13, 29, 31–33
a

Underlined and bolded epitopes within peptide sequences indicate minimal epitopes confirmed in this study. CD4 or CD8 T cell responses that are bolded and underlined indicate confirmed responses in our study and others, italicized responses indicate confirmed responses in our study and only predicted in silico in others, and responses that are not bolded or italicized indicate predicted or confirmed responses in other studies only.

b

Reference(s) describing prior described epitopes that elicited IFN-γ responses.

c

Novel identified epitope confirmed with T cell IFN-γ ELISpot assays.

d

NA, not applicable.