Table 2.

Identified class 2 epitopes in membrane, nucleocapsid, and spike proteins and predicted HLA restrictions

Peptide sequenceAmino acid locationSubjectHLA-DRB1HLA-DRB3HLA-DRB4HLA-DRB5HLA-DQA1HLA-DQB1HLA-DPA1HLA-DPB1
Membrane           
 LRGHLRIAGHHLGRC 144-159 07:01, 11:04 02:02 01:03  02:01, 05:01 03:01, 03:03 01:03, 02:01 03:01, 03:03 
   10 07:01, 11:01 02:02 01:01  02:01, 05:01 02:02, 03:01 01:03, 03:01 04:01, 11:01 
   13 11:04, 15:02 02:02 01:01, 01:03 01:02 01:03, 05:01 03:01, 06:01 01:03, 02:01 02:01, 14:01 
   18 11:04, 15:01 02:02   01:02, 05:01 03:01, 06:02 01:03, 02:01 04:01, 14:01 
 LRIAGHHLGRCDIKD 148-163 07:01, 11:04 02:02 01:03  02:01, 05:01 03:01, 03:03 01:03, 02:01 03:01, 03:03 
   13 11:04, 15:02 02:02 01:01, 01:03 01:02 01:03, 05:01 03:01, 06:01 01:03, 02:01 02:01, 14:01 
 SRTLSYYKLGASQRV 173-188 10 07:01, 11:01 02:02 01:01  02:01, 05:01 02:02, 03:01 01:03, 03:01 04:01, 11:01 
   13 11:04, 15:02 02:02 01:01, 01:03 01:02 01:03, 05:01 03:01, 06:01 01:03, 02:01 02:01, 14:01 
   17 12:01, 15:01 02:02 01:01 01:01 01:02, 05:01 03:01, 05:01 01:03, 01:03 02:01, 04:01 
   18 11:04, 15:01 02:02   01:02, 05:01 03:01, 06:02 01:03, 02:01 04:01, 14:01 
   21 03:02, 16:02 01:62 01:01, 01:03 02:02 01:02, 04:01 04:02, 05:02 02:02, 02:02 01:01, 01:01 
   23 01:01, 03:01 01:01 01:01, 01:03  01:01, 05:01 02:01, 05:01 01:03, 01:03 02:01, 02:01 
 SYYKLGASQRVAGDS 177-192 10 07:01, 11:01 02:02 01:01  02:01, 05:01 02:02, 03:01 01:03, 03:01 04:01, 11:01 
   17 12:01, 15:01 02:02 01:01 01:01 01:02, 05:01 03:01, 05:01 01:03, 01:03 02:01, 04:01 
   21 03:02, 16:02 01:62 01:01, 01:03 02:02 01:02, 04:01 04:02, 05:02 02:02, 02:02 01:01, 01:01 
   23 01:01, 03:01 01:01 01:01, 01:03  01:01, 05:01 02:01, 05:01 01:03, 01:03 02:01, 02:01 
 LGASQRVAGDSGFAA 181-195 23 01:01, 03:01 01:01 01:01, 01:03  01:01, 05:01 02:01, 05:01 01:03, 01:03 02:01, 02:01 
Nucleocapsid           
 KPRQKRTATKAYNVT 257-271 24 04:01, 07:01 01:01 01:03  03:01, 05;05 03:01, 03:02 02:01, 02:01 14:01, 14:01 
 AFFGMSRIGMEVTPS 313-327 18 11:04, 15:01 02:02   01:02, 05:01 03:01, 06:02 01:03, 02:01 04:01, 14:01 
Spike           
 PFFSNVTWFHAIHVS 57-71 03:01, 13:01 01:01 01:03  01:03, 05:01 02:01, 06:03 01:03, 01:03 04:01, 04:01 
 NVTWFHAIHVSGTNG 61-75 03:01, 13:01 01:01 01:03  01:03, 05:01 02:01, 06:03 01:03, 01:03 04:01, 04:01 
 SKHTPINLVRDLPQG 205-219 37 03:01, 04:01 01:01 01:03  03:01, 05:01 02:01, 03:02 01:03, 01:03 02:01, 03:01 
 PINLVRDLPQGFSAL 209-223 21 03:02, 16:02 01:62 01:01, 01:03  01:02, 04:01 04:02, 05:02 02:02, 02:02 01:01, 01:01 
   37 03:01, 04:01 01:01 01:03  03:01, 05:01 02:01, 03:02 01:03, 01:03 02:01, 03:01 
 YNYLYRLFRKSNLKP 449-463 37 03:01, 04:01 01:01 01:03  03:01, 05:01 02:01, 03:02 01:03, 01:03 02:01, 03:01 
Peptide sequenceAmino acid locationSubjectHLA-DRB1HLA-DRB3HLA-DRB4HLA-DRB5HLA-DQA1HLA-DQB1HLA-DPA1HLA-DPB1
Membrane           
 LRGHLRIAGHHLGRC 144-159 07:01, 11:04 02:02 01:03  02:01, 05:01 03:01, 03:03 01:03, 02:01 03:01, 03:03 
   10 07:01, 11:01 02:02 01:01  02:01, 05:01 02:02, 03:01 01:03, 03:01 04:01, 11:01 
   13 11:04, 15:02 02:02 01:01, 01:03 01:02 01:03, 05:01 03:01, 06:01 01:03, 02:01 02:01, 14:01 
   18 11:04, 15:01 02:02   01:02, 05:01 03:01, 06:02 01:03, 02:01 04:01, 14:01 
 LRIAGHHLGRCDIKD 148-163 07:01, 11:04 02:02 01:03  02:01, 05:01 03:01, 03:03 01:03, 02:01 03:01, 03:03 
   13 11:04, 15:02 02:02 01:01, 01:03 01:02 01:03, 05:01 03:01, 06:01 01:03, 02:01 02:01, 14:01 
 SRTLSYYKLGASQRV 173-188 10 07:01, 11:01 02:02 01:01  02:01, 05:01 02:02, 03:01 01:03, 03:01 04:01, 11:01 
   13 11:04, 15:02 02:02 01:01, 01:03 01:02 01:03, 05:01 03:01, 06:01 01:03, 02:01 02:01, 14:01 
   17 12:01, 15:01 02:02 01:01 01:01 01:02, 05:01 03:01, 05:01 01:03, 01:03 02:01, 04:01 
   18 11:04, 15:01 02:02   01:02, 05:01 03:01, 06:02 01:03, 02:01 04:01, 14:01 
   21 03:02, 16:02 01:62 01:01, 01:03 02:02 01:02, 04:01 04:02, 05:02 02:02, 02:02 01:01, 01:01 
   23 01:01, 03:01 01:01 01:01, 01:03  01:01, 05:01 02:01, 05:01 01:03, 01:03 02:01, 02:01 
 SYYKLGASQRVAGDS 177-192 10 07:01, 11:01 02:02 01:01  02:01, 05:01 02:02, 03:01 01:03, 03:01 04:01, 11:01 
   17 12:01, 15:01 02:02 01:01 01:01 01:02, 05:01 03:01, 05:01 01:03, 01:03 02:01, 04:01 
   21 03:02, 16:02 01:62 01:01, 01:03 02:02 01:02, 04:01 04:02, 05:02 02:02, 02:02 01:01, 01:01 
   23 01:01, 03:01 01:01 01:01, 01:03  01:01, 05:01 02:01, 05:01 01:03, 01:03 02:01, 02:01 
 LGASQRVAGDSGFAA 181-195 23 01:01, 03:01 01:01 01:01, 01:03  01:01, 05:01 02:01, 05:01 01:03, 01:03 02:01, 02:01 
Nucleocapsid           
 KPRQKRTATKAYNVT 257-271 24 04:01, 07:01 01:01 01:03  03:01, 05;05 03:01, 03:02 02:01, 02:01 14:01, 14:01 
 AFFGMSRIGMEVTPS 313-327 18 11:04, 15:01 02:02   01:02, 05:01 03:01, 06:02 01:03, 02:01 04:01, 14:01 
Spike           
 PFFSNVTWFHAIHVS 57-71 03:01, 13:01 01:01 01:03  01:03, 05:01 02:01, 06:03 01:03, 01:03 04:01, 04:01 
 NVTWFHAIHVSGTNG 61-75 03:01, 13:01 01:01 01:03  01:03, 05:01 02:01, 06:03 01:03, 01:03 04:01, 04:01 
 SKHTPINLVRDLPQG 205-219 37 03:01, 04:01 01:01 01:03  03:01, 05:01 02:01, 03:02 01:03, 01:03 02:01, 03:01 
 PINLVRDLPQGFSAL 209-223 21 03:02, 16:02 01:62 01:01, 01:03  01:02, 04:01 04:02, 05:02 02:02, 02:02 01:01, 01:01 
   37 03:01, 04:01 01:01 01:03  03:01, 05:01 02:01, 03:02 01:03, 01:03 02:01, 03:01 
 YNYLYRLFRKSNLKP 449-463 37 03:01, 04:01 01:01 01:03  03:01, 05:01 02:01, 03:02 01:03, 01:03 02:01, 03:01 

Boldface type indicates a strong binder (< 2); italic type indicates a weak binder (2-10).

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