The spike-specific TCRβ repertoire shows distinct features in unvaccinated or vaccinated patients with SARS-CoV-2 infection

Vecchio, Eleonora; Rotundo, Salvatore; Veneziano, Claudia; Abatino, Antonio; Aversa, Ilenia; Gallo, Raffaella; Giordano, Caterina; Serapide, Francesca; Fusco, Paolo; Viglietto, Giuseppe; Cuda, Giovanni; Costanzo, Francesco; Russo, Alessandro; Trecarichi, Enrico Maria; Torti, Carlo; Palmieri, Camillo

doi:10.1186/s12967-024-04852-1

Table 3 Characteristics of the specificity clusters obtained by GLIPH analysis

From: The spike-specific TCRβ repertoire shows distinct features in unvaccinated or vaccinated patients with SARS-CoV-2 infection

Type^a	Tag^b	Size^c	Fisher score^d	Members^e	Epitope^f	S region (aa)^g
Local	SPDI_4_22	16	1.20E-27	CASSPDIACTF CASSPDIDQFF CASSPDIEAFF CASSPDIEDFF CASSPDIEQFF CASSPDIEQYF CASSPDIGAFF CASSPDIGLFF CASSPDILAFF CASSPDILDHNEQFF CASSPDILHTF CASSPDINYGYTF CASSPDIQAFF CASSPDITIYF CASSPDITQYF CASSPDIVAFF	YLQPRTFL YLQPRTFLL YYVGYLQPRTF	268—278
Global	%GYNE	8	6.00E-04	CSVDGYNEQFF CSVSGYNEQFF CATSGYNEQFF CASSGYNEQFF CGLAGYNEQFF CASKGYNEQFF CASGGYNEQFF CASRGYNEQFF	SSANNCTFEY VYSSANNCTF	158—169
Global	%RNTE	10	5.20E-06	CSVVRNTEAFF CASIRNTEAFF CSVARNTEAFF CASTRNTEAFF CSVERNTEAFF CASSRNTEAFF CSASRNTEAFF CSLQRNTEAFF CASKRNTEAFF CASGRNTEAFF	YFPLQSYGF HLMSFPQSA YHLMSFPQSA	488–496 1046—1055
Global	R%SYE	10	0.00015	CASRLSYEQYF CGTRVSYEQYF CASRFSYEQYF CASRYSYEQYF CASRHSYEQYF CSARSSYEQYF CSARGSYEQYF CASRDSYEQYF CASRQSYEQYF CASRSSYEQYF	LPPAYTNSF	24–32
Global	S%GET	17	2.70E-06	CSASTGETQYF CASSVGETQYF CAWSVGETQYF CASSAGETQYF CASSTGETQYF CSASLGETQYF CASSLGETQYF CASSIGETQYF CASSFGETQYF CASSMGETQYF CASSRGETQYF CASSQGETQYF CASSHGETQYF CASSEGETQYF CASSYGETQYF CASSDGETQYF CASSGGETQYF	AEIRASANL AEIRASANLA ASANLAATK VQPTESIVRF QPTESIVRF TESIVRFPNI FPNITNLCPF RFPNITNLCPF QYIKWPWYI YEQYIKWPW	1015–1027 319–337 1205–1215
Global	S%GLNTE	8	0.0014	CASSLGLNTEAFF CAWSIGLNTEAFF CASSVGLNTEAFF CASSSGLNTEAFF CASSQGLNTEAFF CASSTGLNTEAFF CATSDGLNTEAFF CASSHGLNTEAFF	KLPDDFTGCV AIPTNFTISV AYSNNSIAIPTNF IPTNFTISV NSIAIPTNF	423–432 705–721
Global	S%GNE	12	0.0015	CASSLGNEQFF CASSLGNEQYF CSASMGNEQFF CASSFGNEQFF CAISFGNEQFF CASSVGNEQFF CASSQGNEQYF CASSQGNEQFF CACSQGNEQFF CASSSGNEQFF CASSRGNEQFF CAISGGNEQFF	FFSNVTWFH FLPFFSNVT LPFFSNVTW PFFSNVTWF APHGVVFL APHGVVFLHV GVVFLHVTY VVFLHVTYV FGEVFNATRF FNATRFASVY GEVFNATRF NATRFASVY	54–65 1055–1067 337–350
Global	S%GNQP	10	0.00024	CASSGGNQPQHF CASSSGNQPQHF CASSFGNQPQHF CASSLGNQPQHF CASSYGNQPQHF CASSVGNQPQHF CASSEGNQPQHF CASSRGNQPQHF CSASTGNQPQHF CASSTGNQPQHF	ASQSIIAYTM RSVASQSII SQSIIAYTM VASQSIIAY	684–696
Global	S%GYE	9	0.011	CASSQGYEQYF CSASQGYEQYF CSASRGYEQYF CASSSGYEQYF CASSEGYEQYF CASSSGYEQFF CASSRGYEQYF CAWSGGYEQYF CASSGGYEQYF	DGVYFASTEK FPQSAPHGV GVYFASTEK FPQSAPHGVVF LPFNDGVYF LPFNDGVYFA VLPFNDGVY GAEHVNNSY IGAEHVNNSY	82–96 1051–1061 650–659
Global	S%SSYE	9	0.0031	CASSESSYEQYF CASSSSSYEQYF CASSQSSYEQYF CAVSKSSYEQYF CASSDSSYEQYF CASSRSSYEQYF CAISESSYEQYF CSASGSSYEQYF CASSGSSYEQYF	CFTNVYADSF FTNVYADSF FTNVYADSFV KLNDLCFTNV LNDLCFTNVY LEPLVDLPI SEPVLKGVKL	385–400 1260–1269
Global	S%STDT	10	0.024	CASSLSTDTQYF CASSVSTDTQYF CASSISTDTQYF CACSASTDTQYF CASSTSTDTQYF CSASGSTDTQYF CASSGSTDTQYF CASSASTDTQYF CSASSSTDTQYF CASSQSTDTQYF	ALDPLSETK CALDPLSETK	290–299
global	S%SYE	17	1.10E-05	CASSFSYEQYF CASSYSYEQYF CAWSLSYEQYF CASSLSYEQFF CASSLSYEQYF CASSISYEQYF CASSRSYEQYF CASSNSYEQYF CASSQSYEQYF CAISESYEQYF CASSESYEQYF CASSSSYEQYF CASSGSYEQYF CSASDSYEQYF CASSDSYEQYF CASSVSYEQYF CASSASYEQYF	TEILPVSMTK CMTSCCSCLK MTSCCSCLK	724–733 1236–1245
Global	S%TYE	10	0.00051	CASSVTYEQYF CASSATYEQYF CASSLTYEQYF CASSQTYEQYF CASSRTYEQYF CASSSTYEQYF CASSHTYEQYF CASSYTYEQYF CASSFTYEQYF CASSGTYEQYF	IYSKHTPINL	203–212
global	S%YE	8	6.40E-05	CASSSYEQYF CSASDYEQYF CASSAYEQYF CASSDYEQYF CASSGYEQYF CASSTYEQYF CASSVYEQYF CASSLYEQYF	APGQTGKIA GQTGKIADY KIADYNYKL QTGKIADYNY RQIAPGQTGK	407–424
Global	S%YNE	18	4.20E-09	CASSSYNEQFF CASSEYNEQFF CASSQYNEQFF CASSDYNEQFF CASSTYNEQFF CSVSGYNEQFF CATSGYNEQFF CASSGYNEQFF CSASSYNEQFF CASSKYNEQFF CASSAYNEQFF CASSRYNEQFF CASSHYNEQFF CASSLYNEQFF CSASLYNEQFF CASSIYNEQFF CASSVYNEQFF CASSYYNEQFF	STQDLFLPFF CTLKSFTVEK TQDLFLPFF SETKCTLKSF TLKSFTVEK	49–58 296–309
Global	SL%ET	13	0.00089	CSASLGETQYF CASSLGETQYF CASSLAETQYF CASSLSETQYF CASSLQETQYF CASSLRETQYF CASSLKETQYF CASSLEETQYF CASSLDETQYF CASSLMETQYF CASSLTETQYF CASSLVETQYF CASSLLETQYF	AEVQIDRLI AEVQIDRLIT VEAEVQIDRL VQIDRLITGR	986–999
Global	SL%GE	12	0.0011	CASSLGGEQYF CASSLAGEQYF CASSLGGEAFF CASSLAGEAFF CASSLSGEQFF CASSLGGEQFF CASSLRGEQYF CASSLEGEQFF CASSLVGEQFF CASSLLGEQYF CASSLVGEQYF CASSLIGEQYF	TEKSNIIRGW GRLQSLQTY LITGRLQSL RLQSLQTYV	95–104 996–1008
global	SL%GET	13	6.60E-06	CASSLTGETQYF CASSLAGETQYF CASSLVGETQYF CASSLSGETQYF CASSLNGETQYF CASSLFGETQYF CASSLYGETQYF CASSLLGETQYF CASSLWGETQYF CASSLIGETQYF CASSLEGETQYF CASSLRGETQYF CSASLQGETQYF	LLFNKVTLA	821–829
Global	SL%GNE	12	9.70E-06	CASSLAGNEQFF CASSLTGNEQFF CASSLVGNEQYF CASSLSGNEQFF CTSSLAGNEQYF CASSLVGNEQFF CASSLSGNEQYF CASSLGGNEQFF CAISLEGNEQFF CASSLEGNEQFF CASSLLGNEQFF CASSLLGNEQYF	KTSVDCTMYI	733–742
Global	SL%GNTE	12	0.00049	CASSLGGNTEAFF CASSLAGNTEAFF CASSLSGNTEAFF CASSLNGNTEAFF CASSLVGNTEAFF CASSLTGNTEAFF CASSLQGNTEAFF CASSLEGNTEAFF CASSLRGNTEAFF CASSLDGNTEAFF CASSLIGNTEAFF CASSLLGNTEAFF	LLLQYGSFC LLQYGSFCT CNDPFLGVY CNDPFLGVYY FCNDPFLGVY	135–144 752–760
Global	SL%GTE	9	0.00057	CASSLEGTEAFF CASSLSGTEAFF CASSLRGTEAFF CASSLSGTEQFF CASSLGGTEAFF CASSLTGTEAFF CASSLVGTEAFF CASSLLGTEAFF CASSLIGTEAFF	LLTDEMIAQY LTDEMIAQY LTDEMIAQYT VLPPLLTDEMIAQY	860–873
Global	SL%LNTE	11	7.90E-06	CASSLGLNTEAFF CASSLALNTEAFF CASSLNLNTEAFF CASSLSLNTEAFF CASSLVLNTEAFF CASSLTLNTEAFF CASSLKLNTEAFF CASSLQLNTEAFF CASSLELNTEAFF CASSLRLNTEAFF CASSLDLNTEAFF	GYQPYRVVVL PYRVVVLSF QPYRVVVL QPYRVVVLSF	504–513
Global	SL%QET	8	0.0039	CASSLNQETQYF CASSLGQETQYF CASSLSQETQYF CASSLDQETQYF CASSLQQETQYF CASSLTQETQYF CASSLAQETQYF CASSLVQETQYF	QTNSPRRAR SPRRARSVA TQTNSPRRAR SYQTQTNSPR	673–688
Global	SLG%E	15	3.10E-05	CASSLGNEQFF CASSLGGEQYF CASSLGNEQYF CASSLGSEQYF CASSLGDEQFF CASSLGTEAFF CASSLGGEAFF CASSLGHEQYF CASSLGGEQFF CASSLGREQFF CASSLGDEQYF CASSLGYEQYF CASSLGVEQFF CASSLGIEQYF CASSLGIEQFF	KVFRSSVLH VYYPDKVFR YPDKVFRSS YPDKVFRSSV AENSVAYSN AENSVAYSNN LGAENSVAY	36–49 699–710
Global	SLG%NTE	10	0.00035	CASSLGQNTEAFF CASSLGHNTEAFF CASSLGRNTEAFF CASSLGMNTEAFF CASSLGENTEAFF CASSLGSNTEAFF CASSLGLNTEAFF CASSLGVNTEAFF CASSLGGNTEAFF CASSLGANTEAFF	FTISVTTEIL KEIDRLNEV	718–727 1181–1189

^aType of cluster, where “global” similarity referes to CDR3 differing up to one amino acid, and “local” refers to shared enriched CDR3 amino acid motifs (> tenfold-enrichment, probability < 0.001) [12];
^bPatter of the cluster; global pattern contains '%', which indicates position allowing variants; local pattern starts with 'motif-Fisher_score estimates the bias of the pattern presenting in target data versus reference data using Fisher exact test;
^cNumber of distinct CDR3s included in the cluster;
^dFisher_score estimates the bias of the pattern presenting in target data versus reference data using Fisher exact test [12];
^eCDR3 amino acid sequences of clonotypes from the COVID-19 dataset; the clonotypes from VDJdb/MIRA dataset;
^fS-peptides associated with clonotypes of the VDJdb/MIRA dataset included in the cluster;
^gAmino acid position in the spike protein (uniprot ID P0DTC2)

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