Reference: Laura Bricio-Moreno; Juliana Barreto de Albuquerque; Jake M Neary; Thao Nguyen; Lucy F Kuhn; YeePui Yeung; Kathryn M Hastie; Sara Landeras-Bueno; Eduardo Olmedillas; Chitra Hariharan; Anusha Nathan; Matthew A Getz; Alton C Gayton; Ashok Khatri; Gaurav D Gaiha; Erica Ollmann Saphire; Andrew D Luster; James J Moon. "Identification of mouse CD4<sup>+</sup> T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers." Frontiers in immunology (2024).

Epitope: SQCVNLTTRTQLPPA
Chemical type: Peptide from protein
Sequence: SQCVNLTTRTQLPPA
Position: 13-27
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: KVFRSSVLHSTQDLF
Chemical type: Peptide from protein
Sequence: KVFRSSVLHSTQDLF
Position: 41-55
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: NDGVYFASIEKSNII
Chemical type: Peptide from protein
Sequence: NDGVYFASIEKSNII
Position: 85-99
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GWIFGTTLDSKTQSL
Chemical type: Peptide from protein
Sequence: GWIFGTTLDSKTQSL
Position: 101-115
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: KCTLKSFTVEKGIYQ
Chemical type: Peptide from protein
Sequence: KCTLKSFTVEKGIYQ
Position: 297-311
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Positive-High
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: NCVADYSVLYNLAPF
Chemical type: Peptide from protein
Sequence: NCVADYSVLYNLAPF
Position: 357-371
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: DYSVLYNLAPFFTFK
Chemical type: Peptide from protein
Sequence: DYSVLYNLAPFFTFK
Position: 361-375
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: YGVSPTKLNDLCFTN
Chemical type: Peptide from protein
Sequence: YGVSPTKLNDLCFTN
Position: 377-391
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: FVIRGDEVRQIAPGQ
Chemical type: Peptide from protein
Sequence: FVIRGDEVRQIAPGQ
Position: 397-411
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: RQIAPGQTGNIADYN
Chemical type: Peptide from protein
Sequence: RQIAPGQTGNIADYN
Position: 405-419
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: FRKSNLKPFERDIST
Chemical type: Peptide from protein
Sequence: FRKSNLKPFERDIST
Position: 453-467
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: IYQAGNKPCNGVAGF
Chemical type: Peptide from protein
Sequence: IYQAGNKPCNGVAGF
Position: 469-483
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GNKPCNGVAGFNCYF
Chemical type: Peptide from protein
Sequence: GNKPCNGVAGFNCYF
Position: 473-487
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: FGGVSVITPGTNTSN
Chemical type: Peptide from protein
Sequence: FGGVSVITPGTNTSN
Position: 589-603
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Positive-Low
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: ARSVASQSIIAYTMS
Chemical type: Peptide from protein
Sequence: ARSVASQSIIAYTMS
Position: 681-695
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: ISVTTEILPVSMTKT
Chemical type: Peptide from protein
Sequence: ISVTTEILPVSMTKT
Position: 717-731
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: TKTSVDCTMYICGDS
Chemical type: Peptide from protein
Sequence: TKTSVDCTMYICGDS
Position: 729-743
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: MYICGDSTECSNLLL
Chemical type: Peptide from protein
Sequence: MYICGDSTECSNLLL
Position: 737-751
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: YGSFCTQLKRALTGI
Chemical type: Peptide from protein
Sequence: YGSFCTQLKRALTGI
Position: 753-767
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: PPIKYFGGFNFSQIL
Chemical type: Peptide from protein
Sequence: PPIKYFGGFNFSQIL
Position: 789-803
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: LADAGFIKQYGDCLG
Chemical type: Peptide from protein
Sequence: LADAGFIKQYGDCLG
Position: 825-839
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GFIKQYGDCLGDIAA
Chemical type: Peptide from protein
Sequence: GFIKQYGDCLGDIAA
Position: 829-843
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: KGLTVLPPLLTDEMI
Chemical type: Peptide from protein
Sequence: KGLTVLPPLLTDEMI
Position: 853-867
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: QYTSALLAGTITSGW
Chemical type: Peptide from protein
Sequence: QYTSALLAGTITSGW
Position: 869-883
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GTITSGWTFGAGAAL
Chemical type: Peptide from protein
Sequence: GTITSGWTFGAGAAL
Position: 877-891
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GIGVTQNVLYENQKL
Chemical type: Peptide from protein
Sequence: GIGVTQNVLYENQKL
Position: 905-919
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: DSLSSTASALGKLQD
Chemical type: Peptide from protein
Sequence: DSLSSTASALGKLQD
Position: 933-947
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: AQALNTLVKQLSSKF
Chemical type: Peptide from protein
Sequence: AQALNTLVKQLSSKF
Position: 953-967
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: AISSVLNDIFSRLDK
Chemical type: Peptide from protein
Sequence: AISSVLNDIFSRLDK
Position: 969-983
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: VLNDIFSRLDKVEAE
Chemical type: Peptide from protein
Sequence: VLNDIFSRLDKVEAE
Position: 973-987
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: IFSRLDKVEAEVQID
Chemical type: Peptide from protein
Sequence: IFSRLDKVEAEVQID
Position: 977-991
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GKGYHLMSFPQSAPH
Chemical type: Peptide from protein
Sequence: GKGYHLMSFPQSAPH
Position: 1041-1055
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: APHGVVFLHVTYVPA
Chemical type: Peptide from protein
Sequence: APHGVVFLHVTYVPA
Position: 1053-1067
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: TTAPAICHDGKAHFP
Chemical type: Peptide from protein
Sequence: TTAPAICHDGKAHFP
Position: 1073-1087
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: EGVFVSNGTHWFVTQ
Chemical type: Peptide from protein
Sequence: EGVFVSNGTHWFVTQ
Position: 1089-1103
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: VDLGDISGINASVVN
Chemical type: Peptide from protein
Sequence: VDLGDISGINASVVN
Position: 1161-1175
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: EVAKNLNESLIDLQE
Chemical type: Peptide from protein
Sequence: EVAKNLNESLIDLQE
Position: 1185-1199
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: CMTSCCSCLKGCCSC
Chemical type: Peptide from protein
Sequence: CMTSCCSCLKGCCSC
Position: 1233-1247
Source molecule (GenBank): UJU86738.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: LRITFGGPSDSTGSN
Chemical type: Peptide from protein
Sequence: LRITFGGPSDSTGSN
Position: 13-27
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: TNSSPDDQIGYYRRA
Chemical type: Peptide from protein
Sequence: TNSSPDDQIGYYRRA
Position: 73-87
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: KMKDLSPRWYFYYLG
Chemical type: Peptide from protein
Sequence: KMKDLSPRWYFYYLG
Position: 97-111
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: SRGGSQASSRSSSRS
Chemical type: Peptide from protein
Sequence: SRGGSQASSRSSSRS
Position: 173-187
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: DAALALLLLDRLNQL
Chemical type: Peptide from protein
Sequence: DAALALLLLDRLNQL
Position: 213-227
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: SKMSGKGQQQQGQTV
Chemical type: Peptide from protein
Sequence: SKMSGKGQQQQGQTV
Position: 229-243
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: KKSAAEASKKPRQKR
Chemical type: Peptide from protein
Sequence: KKSAAEASKKPRQKR
Position: 245-259
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: QKRTATKAYNVTQAF
Chemical type: Peptide from protein
Sequence: QKRTATKAYNVTQAF
Position: 257-271
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: QALPQRQKKQQTVTL
Chemical type: Peptide from protein
Sequence: QALPQRQKKQQTVTL
Position: 377-391
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: SKQLQQSMSSADSTQ
Chemical type: Peptide from protein
Sequence: SKQLQQSMSSADSTQ
Position: 401-415
Source molecule (GenBank): UWJ90169.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: VRDLPQGFSALEPLV
Chemical type: Peptide from protein
Sequence: VRDLPQGFSALEPLV
Position: 213-227
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GQTGKIADYNYKLPD
Chemical type: Peptide from protein
Sequence: GQTGKIADYNYKLPD
Position: 413-427
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: STEIYQAGSTPCNGV
Chemical type: Peptide from protein
Sequence: STEIYQAGSTPCNGV
Position: 469-483
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: YQAGSTPCNGVEGFN
Chemical type: Peptide from protein
Sequence: YQAGSTPCNGVEGFN
Position: 473-487
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GFNCYFPLQSYGFQP
Chemical type: Peptide from protein
Sequence: GFNCYFPLQSYGFQP
Position: 485-499
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: YFPLQSYGFQPTNGV
Chemical type: Peptide from protein
Sequence: YFPLQSYGFQPTNGV
Position: 489-503
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: FQPTNGVGYQPYRVV
Chemical type: Peptide from protein
Sequence: FQPTNGVGYQPYRVV
Position: 497-511
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: KCVNFNFNGLTGTGV
Chemical type: Peptide from protein
Sequence: KCVNFNFNGLTGTGV
Position: 537-551
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: GLTGTGVLTESNKKF
Chemical type: Peptide from protein
Sequence: GLTGTGVLTESNKKF
Position: 545-559
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: LLQYGSFCTQLNRAL
Chemical type: Peptide from protein
Sequence: LLQYGSFCTQLNRAL
Position: 753-767
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: SDSTGSNQNGERSGA
Chemical type: Peptide from protein
Sequence: SDSTGSNQNGERSGA
Position: 21-35
Source molecule (GenBank): QHD43423.2
Assay category: TCell
Result: Negative
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: S-63
Chemical type: Peptide from protein
Sequence: TWFHAIHVSGTN
Position: 63-74
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Positive-High
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: S-63
Chemical type: Peptide from protein
Sequence: TWFHAIHVSGTN
Position: 63-74
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Positive
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo

Epitope: S-63
Chemical type: Peptide from protein
Sequence: TWFHAIHVSGTN
Position: 63-74
Source molecule (GenBank): QHD43416.1
Assay category: TCell
Result: Positive-High
Host:  6-16 weeks
Cell type: T cell CD4+
Tissue: lymphoid
Culture conditions: Direct Ex Vivo