Table 1 Summary of single-cell TCR sequencing

Subject	Vaccination	Interval vaccination-BD	Tetramer	# Wells	# Cells	# Clonotypes with >1 isolate	# Isolates of each expanded clonotype					Subject	Interval onset-BD	Vaccination	Interval vaccination-BD	Tetramer	# Wells	# Cells	# Clonotypes with >1 isolate	# Isolates of each expanded clonotype
Set A
C1			L	96	61	2	4	2				P1	5.7 y			L	96	52	0
C1			H1	96	38	1			2			P1	5.7 y			H1	96	38	0
C2	x	5–6 y	L	96	17	1	2					P2	4.2 y	x	5 y	L	96	17	0
C2	x	5–6 y	H1	96	27	0	1					P2	4.2 y	x	5 y	H1	96	50	0
C3	x	5–6 y	L	96	69	4	17	11	7	2	1	P3	1.6 y			L	96	63	4	16	11	2	1	1	1	3
C3	x	5–6 y	H1	96	69	4	10	11	3	1	2	P3	1.6 y			H1	96	60	3	8	4	1	1	1	1		2
C4	x	5–6 y	L	96	52	3	10	6	1	2	1	P4	4.4 y	x	5–6 y	L	96	38	2	2	2
C4	x	5–6 y	H1	96	54	3	16	5	3	1	1	P4	4.4 y	x	5–6 y	H1	96	55	1	6
Set B
C5	*	56 d	L	96	49	1	3					P5	17.6 y	*	8 d	L	96	50	0
C5	*	56 d	H2	96	32	1		2				P5	17.6 y	*	8 d	H2	96	53	1	2
C6	*	7 d	L	86	26	2	2	2				P6	0.3 y			L	96	29	0
C6	*	7 d	H2	96	51	0						P6	0.3 y			H2	83	58	0
C7	x	5 y	L	95	59	0						P7	29.8 y			L	96	37	2	3	1	1	1	2
			H2	96	32	0										H2	81	42	5	3	2	2	1		2	2
			H25	96	50	1	2									H25	96	43	0	1	1
C8	x	5 y	L	96	54	0						P8	9.7 y			L	96	75	0	1	1	1	1
			H2	96	48	0										H2	96	68	1	2	1	1
			H25	96	46	0										H25	96	42	0				1
C9			L	96	43	0						P9	8.5 y			L	96	68	4	13	2	2	2
			H2	88	28	0										H2	96	47	2	3	2	1
																H25	96	48	0		1
C10			L	96	61	0						P10	11.7 y			L	96	60	0
			H2	87	34	0										H2	96	46	0
																H25	96	51	0
C11	*	141 d	L	96	66	2	2	1	1	2		P11	5.6 y	x	5.7 y	L	96	65	0
			H2	96	43	1	1	1	1		4					H2	96	54	0
			H25	96	43	0										H25	96	48	0
C12	x	4.75 y	L	96	47	0						P12	3.3 y			L	87	51	1	11	1	1
			H2	96	43	0										H2	96	39	2	4	2	1
			H25	96	28	0										H25	96	45	0	1
Total							146													143

Subject numbers indicate the order of pairs (C: control; P: patient) used in blinded experiments. “x” indicates vaccination using Pandemrix during the 2009 flu pandemic, y: year. “^*” indicates seasonal trivalent inactivated influenza vaccination (TIV) prior to blood draw (BD), d: day. “# Wells” counts single CD4⁺ T cells sorted by the indicated tetramer for sequencing analysis. “# Cells” counts sequenced cells with fully identified TCRαβ gene information and productive CDR3 sequences. “# Clonotypes with isolates >1” counts expanded TCRαβ clonotypes. Isolates of an expanded clonotypes share identical α/β CDR3 sequences. Identical clonotypes identified by different tetramers (expanded cross-binding clonotypes) are aligned, but the alignment across subjects does not reflect related TCRs. Highly expanded clonotypes (≥5 total isolates per subject) are indicated in bold. Tetramer specificities are as follow, L: HCRT_1–13, H1: HCRT_56–69, H2: HCRT_87–100, H25: HCRT_25–37. Elucidation of functionality and the triggers for highly expanded cross-binding clonotypes found in controls (e.g., C3 and C4) are beyond the scope of this study

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